Author: "Kamel Jabbari" / Topic: 0303 health sciences - Searchworks@Jio Institute Digital Library Search Results

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26 results on '"Kamel Jabbari"'

1. A common genomic code for chromatin architecture and recombination landscape

Author: Johannes Wirtz, Martina Rauscher, Kamel Jabbari, and Thomas Wiehe
Subjects: Heredity, Gene Expression, Biochemistry, Linkage Disequilibrium, Histones, Geographical Locations, chemistry.chemical_compound, Mice, 0302 clinical medicine, DNA Breaks, Double-Stranded, Homologous Recombination, 0303 health sciences, Multidisciplinary, Mammalian Genomics, DNA methylation, Chromosome Biology, Genomics, Chromatin, Recombinant Proteins, Europe, Nucleic acids, Meiosis, Physical Sciences, Medicine, Epigenetics, DNA modification, Isochores, Chromatin modification, Recombination, Research Article, Spo11, DNA recombination, Permutation, Science, Biology, 03 medical and health sciences, Genetics, Animals, Humans, 030304 developmental biology, Discrete Mathematics, fungi, Biology and Life Sciences, Proteins, Cell Biology, DNA, Chromosomes, Mammalian, chemistry, Animal Genomics, Combinatorics, Evolutionary biology, People and Places, biology.protein, H3K4me3, DMC1, Homologous recombination, 030217 neurology & neurosurgery, Mathematics
Abstract: Recent findings established a link between DNA sequence composition and interphase chromatin architecture and explained the evolutionary conservation of TADs (Topologically Associated Domains) and LADs (Lamina Associated Domains) in mammals. This prompted us to analyse conformation capture and recombination rate data to study the relationship between chromatin architecture and recombination landscape of human and mouse genomes. The results reveal that: (1) low recombination domains and blocks of elevated linkage disequilibrium tend to coincide with TADs and isochores, indicating co-evolving regulatory elements and genes in insulated neighbourhoods; (2) double strand break (DSB) and recombination frequencies increase in the short loops of GC-rich TADs, whereas recombination cold spots are typical of LADs and (3) the binding and loading of proteins, which are critical for DSB and meiotic recombination (SPO11, DMC1, H3K4me3 and PRMD9) are higher in GC-rich TADs. One explanation for these observations is that the occurrence of DSB and recombination in meiotic cells are associated with compositional and epigenetic features (genomic code) that influence DNA stiffness/flexibility and appear to be similar to those guiding the chromatin architecture in the interphase nucleus of pre-leptotene cells.
Published: 2018

2. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Author: Gaëtan Droc, Adriana Alberti, Philippe Francois, Rémy Habas, Patrick Wincker, Jaroslav Dolezel, Mouna Jeridi, Cyril Jourda, E. Hribova, Thomas Wicker, Kamel Jabbari, Julie Leclercq, Cees Waalwijk, Olivier Panaud, Benjamin Noel, Marlã̈ne Souquet, Manuel Ruiz, Didier Mbéguié-A-Mbéguié, Margot Correa, Nicolas Roux, Saravanaraj Ayyampalayam, Ronan Rivallan, Spencer Brown, Françoise Carreel, Maria Bernard, Andrzej Kilian, Jose Barbosa, Olivier Jaillon, Olivier Garsmeur, Jean-Marc Aury, Ange-Marie Risterucci, Julie Poulain, Karine Labadie, Xavier Argout, Steeve Joseph, Pat Heslop-Harrison, Jean-Christophe Glaszmann, Ana Maria Rocha de Almeida, Mathieu Rouard, Jean Weissenbach, Stéphanie Bocs, Juliette Lengellé, Nabila Yahiaoui, Eric Lyons, Anne Dievart, Corinne Da Silva, Marguerite Rodier-Goud, Dheema Burthia, Céline Cardi, Michael Freeling, Angélique D'Hont, Claire Poiron, Valentin Guignon, Matthieu Chabannes, Frédéric Bakry, Christophe Jenny, Franc-Christophe Baurens, Michael R. McKain, Miguel A. Dita, Francis Quetier, Diane Burgess, Jim Leebens-Mack, Gert H. J. Kema, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Optique Atmosphérique - UMR 8518 (LOA), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Plant Research International (PRI), Wageningen University and Research [Wageningen] (WUR), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Wageningen University and Research Centre [Wageningen] (WUR), University of Zurich, and D'Hont, Angélique
Subjects: MESH: Genome, Plant, 0106 biological sciences, Phylogénie, Lineage (evolution), Plant genetics, Évolution, 580 Plants (Botany), Haploidy, resource, in-situ hybridization, Musa acuminata, 01 natural sciences, F30 - Génétique et amélioration des plantes, MESH: Genotype, sequence count data, 10126 Department of Plant and Microbial Biology, Gene Duplication, Musa balbisiana, dna sequences, MESH: Genes, Plant, maximum likelihood, MESH: Phylogeny, Conserved Sequence, Phylogeny, MESH: Evolution, Molecular, 2. Zero hunger, 0303 health sciences, MESH: Conserved Sequence, Multidisciplinary, MESH: Gene Duplication, food and beverages, F70 - Taxonomie végétale et phytogéographie, MESH: Haploidy, MESH: DNA Transposable Elements, Génotype, Genome, Plant, dna-sequences, Séquence nucléotidique, diversification, Poales, Genotype, Molecular Sequence Data, Biology, Poaceae, Genes, Plant, differential expression, Evolution, Molecular, Zingiberales, Biointeractions and Plant Health, 03 medical and health sciences, MESH: Musa, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, gene, Domestication, 030304 developmental biology, 1000 Multidisciplinary, Génome, MESH: Molecular Sequence Data, Bioint Moleculair Phytopathology, rice, Musa, 15. Life on land, biology.organism_classification, Arecales, DNA Transposable Elements, identification, maximum-likelihood, in situ hybridization, 010606 plant biology & botany
Abstract: International audience; Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.
Published: 2012

3. Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum

Author: Uma Maheswari, Chris Bowler, Kamel Jabbari, and Anton Montsant
Subjects: 0106 biological sciences, Physiology, Thalassiosira pseudonana, Gene Expression, Chlamydomonas reinhardtii, Plant Science, Computational biology, 01 natural sciences, Evolution, Molecular, 03 medical and health sciences, Species Specificity, Botany, Genetics, Animals, Phaeodactylum tricornutum, Phylogeny, 030304 developmental biology, Diatoms, Expressed Sequence Tags, Comparative genomics, Base Composition, 0303 health sciences, Expressed sequence tag, Genome, biology, fungi, biology.organism_classification, Cyanidioschyzon merolae, Diatom, GenBank, Focus Issue on Chlamydomonas, 010606 plant biology & botany
Abstract: Diatoms are one of the most important constituents of phytoplankton communities in aquatic environments, but in spite of this, only recently have large-scale diatom-sequencing projects been undertaken. With the genome of the centric species Thalassiosira pseudonana available since mid-2004, accumulating sequence information for a pennate model species appears a natural subsequent aim. We have generated over 12,000 expressed sequence tags (ESTs) from the pennate diatom Phaeodactylum tricornutum, and upon assembly into a nonredundant set, 5,108 sequences were obtained. Significant similarity (E < 1E-04) to entries in the GenBank nonredundant protein database, the COG profile database, and the Pfam protein domains database were detected, respectively, in 45.0%, 21.5%, and 37.1% of the nonredundant collection of sequences. This information was employed to functionally annotate the P. tricornutum nonredundant set and to create an internet-accessible queryable diatom EST database. The nonredundant collection was then compared to the putative complete proteomes of the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the centric diatom T. pseudonana. A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism. Finally, codon usage and utilization of C and G relative to gene expression (as measured by EST redundance) were studied, and preferences for utilization of C and CpG doublets were noted among the P. tricornutum EST coding sequences.
Published: 2005

4. Compositional features of eukaryotic genomes for checking predicted genes

Author: Kamel Jabbari, Giorgio Bernardi, Oliver K. Clay, and Stéphane Cruveiller
Subjects: Gene prediction, Computational biology, Genome, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Arabidopsis, False positive paradox, Animals, Humans, Coding region, Molecular Biology, Gene, 030304 developmental biology, Genetics, 0303 health sciences, biology, Reproducibility of Results, DNA, biology.organism_classification, chemistry, 030220 oncology & carcinogenesis, Identification (biology), Information Systems
Abstract: Gene prediction relies on the identification of characteristic features of coding sequences that distinguish them from non-coding DNA. The recent large-scale sequencing of entire genomes from higher eukaryotes, in conjunction with currently used gene prediction algorithms, has provided an abundance of putative genes that can now be analysed for their compositional properties. Strong, systematic differences still exist, in several species, between the compositional properties of sets of ex novo predicted genes and genes that have been experimentally detected and/or verified. This is particularly evident in the estimated gene set (>45,000 genes) of the recently sequenced rice genome, where roughly half the predicted genes are compositionally unusual and have no known orthologues in the dicot Arabidopsis. In a few cases such differences might suggest a bias in experimental gene-finding protocols, but the quasi-random nature of the compositionally aberrant predicted genes is a strong indication that many, if not most, of them are false positives. It therefore appears that some important features of coding regions have not yet been taken into account in existing gene prediction programs. Statistical base compositional properties of curated gene data sets from vertebrates, which we briefly review here, should therefore provide a useful benchmark for fine-tuning probabilistic gene models and model parameters that are currently in use.
Published: 2003

5. An Isochore Framework Underlies Chromatin Architecture

Author: Kamel Jabbari and Giorgio Bernardi
Subjects: 0301 basic medicine, Interphase nucleus, Gene Expression, lcsh:Medicine, Genome, Conserved sequence, Mice, Database and Informatics Methods, 0302 clinical medicine, Cluster Analysis, lcsh:Science, Genetics, 0303 health sciences, Base Composition, Mammalian Genomics, Multidisciplinary, Chromosome Biology, Chromosome Mapping, Genomics, Genomic Databases, Chromatin, Physical Sciences, Epigenetics, Interphase, Isochores, Research Article, Permutation, Biology, Research and Analysis Methods, Synteny, Chromosomes, Human Genomics, DNA sequencing, Evolution, Molecular, 03 medical and health sciences, Animals, Humans, Molecular Biology Techniques, Molecular Biology, 030304 developmental biology, Comparative genomics, Discrete Mathematics, Gene Mapping, lcsh:R, Biology and Life Sciences, Computational Biology, Cell Biology, Comparative Genomics, Genome Analysis, Chromosomes, Mammalian, GC Rich Sequence, Biological Databases, 030104 developmental biology, Animal Genomics, Combinatorics, Evolutionary biology, lcsh:Q, 030217 neurology & neurosurgery, Mathematics
Abstract: A recent investigation showed the existence of correlations between the architectural features of mammalian interphase chromosomes and the compositional properties of isochores. This result prompted us to compare maps of the Topologically Associating Domains (TADs) and of the Lamina Associated Domains (LADs) with the corresponding isochore maps of mouse and human chromosomes. This approach revealed that: 1) TADs and LADs correspond to isochores, i.e., isochores are the genomic units that underlie chromatin domains; 2) the conservation of TADs and LADs in mammalian genomes is explained by the evolutionary conservation of isochores; 3) chromatin domains corresponding to GC-poor isochores (e.g., LADs) interact with other domains also corresponding to GC-poor isochores even if located far away on the chromosomes; in contrast, chromatin domains corresponding to GC-rich isochores (e.g., TADs) show more localized chromosomal interactions, many of which are inter-chromosomal. In conclusion, this investigation establishes a link between DNA sequences and chromatin architecture, explains the evolutionary conservation of TADs and LADs and provides new information on the spatial distribution of GC-poor/gene-poor and GC-rich/gene-rich chromosomal regions in the interphase nucleus.
Published: 2017

6. Early allopolyploid evolution in the post-Neolithic[i] Brassica napus[/i] oilseed genome

Author: Patrick Wincker, Pascal Bento, Sahana Manoli, Agnieszka A. Golicz, G. Deniot, Shengyi Liu, Christine Sidebottom, Chu Shin Koh, Ian Bancroft, Christian Daviaud, David C. Tack, Rod J. Snowdon, Jörg Tost, Guangyi Fan, Hui Guo, Smahane Chalabi, Boulos Chalhoub, Xinfa Wang, Harry Belcram, Aurélie Chauveau, Gilles Lassalle, Jean-Marc Aury, Tae-Ho Lee, Houda Chelaifa, Jinling Meng, Christopher D. Town, Haibao Tang, Zhongsong Liu, Julien Chiquet, Andrew G. Sharpe, Salman Alamery, Chunyun Guan, Mathieu Charles, Qiong Hu, Xiyin Wang, Xiaowu Wang, Jianxin Ma, Régine Delourme, Mei Guan, Eric Lyons, Chaobo Tong, Margot Correa, Adriana Alberti, Keith L. Adams, Patrick P. Edger, Marie-Christine Le Paslier, Yunhai Lu, Corinne Da Silva, Christophe Battail, Andrew H. Paterson, Isabelle Le Clainche, Benjamin Noel, Jérémy Just, Jacqueline Batley, Jinxiong Shen, Fengming Sun, Kamel Jabbari, Karine Labadie, Michel Renard, Maria Bernard, Birgit Samans, Aurélie Canaguier, Isobel A. P. Parkin, Yong Pyo Lim, Vinh Ha Dinh Thi, Victor Renault, Meixia Zhao, David Edwards, Graham J.W. King, Nicolas Schnel, Dominique Brunel, Cyril Falentin, Reece Tollenaere, Aurélie Bérard, Yongming Zhou, Dominique Arnaud, Imen Mestiri, Philippe E. Bayer, Chuchuan Fan, Wei Hua, J. Chris Pires, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Agriculture and Agri-Food (AAFC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University (FAFU), University of Georgia [USA], School of Life Sciences, Center of Genomics and Computational Biology, Hebei United University, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Research Center for Biosystems, Land Use and Nutrition, Department of Plant Breeding, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, National Research Council of Canada (NRC), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Centre National de Genotypage, Plant Genome Mapping Laboratory, Laboratoire épigénétique et environnement, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Cologne Center for Genomics, University of Cologne, Department of Agronomy, Purdue University [West Lafayette], Department of Plant and Microbial Biology, University of California (UC), Department of Botany [Vancouver] (UBC Botany), University of British Columbia (UBC), National Key Laboratory of Crop Genetic Improvement [China], Huazhong Agricultural University [Wuhan] (HZAU), Beijing Genome Institute, Fondation Jean Dausset - Centre d’Étude du Polymorphisme Humain, College of Agronomy, Hunan Agricultural University [Changsha], Department of Horticulture, Molecular Genetics and Genomics Laboratory, Chungnam National University (CNU), School of Plant Sciences, iPlant Collaborative, University of Arizona, Department of Biology, University of York [York, UK], Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Division of Biological Sciences, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Southern Cross Plant Science, Southern Cross University (SCU), School of Plant Biology, The University of Western Australia (UWA), Laboratory for Epigenetics and Environment, Agriculture and Agri-Food [Ottawa] (AAFC), Laboratoire de Mathématiques et Modélisation d'Evry, Justus-Liebig-Universität Gießen (JLU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of California, Huazhong Agricultural University, Euralis Semences, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), BIOGEMMA, Unité de Recherches Zootechniques (URZ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Limagrain, J. Craig Venter Institute, Fujian Agriculture and Forestry University, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Botany, University of Missouri [Columbia], Southern Cross University, Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1165 Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique ( INRA ) -Université d'Evry Val d'Essonne, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ministry of Agriculture-Chinese Academy of Agricultural Sciences ( CAAS ), Agriculture and Agri-Food [Ottawa] ( AAFC ), University of Georgia, Laboratoire de Mathématiques et Modélisation d'Evry ( LaMME ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -ENSIIE-Centre National de la Recherche Scientifique ( CNRS ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Justus Liebig University Giessen, Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, National Research Council of Canada ( NRC ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), University of British Columbia ( UBC ), National Key Laboratory of Crop Genetic Improvement, Chungnam National University, Institute of Vegetables and Flowers ( IVF ), Chinese Academy of Agricultural Sciences ( CAAS ), University of Missouri ( Saisissez le sigle en majuscules sans points ), The University of Western Australia ( UWA ), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, plant genome, [SDV]Life Sciences [q-bio], Brassica, rapeseed, Biology, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, chemistry.chemical_compound, Gene duplication, genetics, Epigenetics, Domestication, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, [ SDV ] Life Sciences [q-bio], molecular evolution, Brassica napus, chromosome duplication, food and beverages, plant seed, biology.organism_classification, chemistry, Glucosinolate, Seeds, cytology, Genome, Plant, 010606 plant biology & botany
Abstract: Oilseed rape (Brassica napus L.) was formed ∼7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content.We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement., Erratum published in Vol 345, no. 6202 September 2014 DOI: 10.1126/science.1260782
Published: 2014

7. Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure

Author: Fernando Alvarez-Valin, Giovanni Colonna, Maria Luisa Chiusano, Giorgio Bernardi, Giuseppe D'Onofrio, Kamel Jabbari, Chiusano, MARIA LUISA, D’Onofrio, G., ALVAREZ VALIN, F., Jabbari, K., Colonna, G., and Bernardi, G.
Subjects: Mammals, Genetics, Nonsynonymous substitution, Base Composition, 0303 health sciences, 030302 biochemistry & molecular biology, General Medicine, Composition (combinatorics), Biology, Genome, Protein Structure, Secondary, Base (group theory), 03 medical and health sciences, Protein structure, Mutation, Animals, Coding region, Codon, Synonymous substitution, Protein secondary structure, 030304 developmental biology
Abstract: We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (alpha-helix, beta-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be alpha-helix, beta-sheet, or coil. Likewise, the nonsynonymous rates also differ, although expectedly at a lower extent, in the three types of secondary structure, suggesting that different selective constraints associated with the different structures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different in coding sequence regions corresponding to different secondary structures of proteins.
Published: 1999

8. Different hydrophobicities of orthologous proteins from Xenopus and human

Author: Kamel Jabbari, Stéphane Cruveiller, Giuseppe D'Onofrio, and Giacomo Bernardi
Subjects: Guanine, Xenopus, Molecular Sequence Data, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Mole, Genetics, Animals, Humans, Amino Acid Sequence, Gene, 030304 developmental biology, 0303 health sciences, Transition (genetics), biology, Proteins, Water, General Medicine, biology.organism_classification, Order (biology), chemistry, 030220 oncology & carcinogenesis, Cattle, Cytosine, DNA
Abstract: A compositional transition was previously detected by comparing orthologous coding sequences from cold- and warm-blooded vertebrates (see Bernardi, G., Hughes, S., Mouchiroud, D., 1997. The major compositional transitions in the vertebrate genome. J. Mol. Evol. 44, S44–S51 for a review). The transition is characterized by higher GC levels (GC is the molar ratio of guanine+cytosine in DNA) and, especially, by higher GC3 levels (GC3 is the GC level of third codon positions) in coding sequences from warm-blooded vertebrates. This transition essentially affects GC-rich genes, although the nucleotide substitution rate is of the same order of magnitude in both GC-poor and GC-rich genes. In order to understand the evolutionary basis of the changes, we have compared the hydrophobicity of orthologous proteins from Xenopus and human. Although the differences are small in proteins encoded by coding sequences ranging from 0 to 65% in GC3, they are large in the proteins encoded by sequences characterized by GC3 values higher than 65%. The latter proteins are more hydrophobic in human than in Xenopus.
Published: 1999

9. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

Author: Tristan Barbeyron, Wilfrid Carré, Michael Katinka, Loraine Brillet, Klaus Valentin, Karine Labadie, Betina M. Porcel, Zofia Nehr, Francisco Cabello-Hurtado, Mirjam Czjzek, Benjamin Noel, Philippe Deschamps, Susana M. Coelho, John H. F. Bothwell, Pascal J. Lopez, Marek Eliáš, François Artiguenave, François-Yves Bouget, Thierry Tonon, Jean Weissenbach, Christophe Colleoni, Deirdre H. McLachlan, Ahmed A. Moustafa, Cécile Hervé, Olivier Panaud, Catherine Boyen, Jonas Collén, Antonios Zambounis, Frédéric Partensky, Cristian Chaparro, Ludovic Delage, Jose Fernandes Barbosa-Neto, Salvador Capella-Gutierrez, Bernard Kloareg, Nathalie Kowalczyk, Gaelle Samson, Gurvan Michel, Simon M. Dittami, Jean-Marc Aury, J. Mark Cock, Patrick Wincker, Agnès Groisillier, Pi Nyvall Collén, Bénédicte Charrier, Corinne Da Silva, Catherine Leblanc, Lionel Cladière, Alok Arun, Laurence Meslet-Cladiere, Claire M. M. Gachon, Sylvie Rousvoal, Kamel Jabbari, Stefan A. Rensing, Toni Gabaldón, Steven G. Ball, Aikaterini Symeonidi, Julie Poulain, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Department of Plant Physiology, Faculty of Sciences, Charles University [Prague] (CU), Belfast e-Science Centre [Belfast] (BESC), Queen's University [Belfast] (QUB), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Scottish Association for Marine Science (SAMS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biology and Biotechnology Graduate Program, American University in Cairo, American University in Cairo, University of Freiburg [Freiburg], Freiburg Initiative in Systems Biology, Centre for Research and Technology Hellas (CERTH), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Charles University [Prague], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona], Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Center for Research and Technology Hellas, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), and Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Transposable element, Genome evolution, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Bacterial genome size, Biology, Chondrus, MESH: Base Sequence, MESH: RNA, Plant, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, MESH: Genes, Plant, 14. Life underwater, Gene, Genome size, MESH: Evolution, Molecular, 030304 developmental biology, Plant Proteins, Genetics, 0303 health sciences, Multidisciplinary, MESH: Molecular Sequence Data, Base Sequence, MESH: Plant Proteins, Archaeplastida, Biological Sciences, biology.organism_classification, MicroRNAs, RNA, Plant, MESH: MicroRNAs, MESH: Chondrus, 010606 plant biology & botany
Abstract: Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.
Published: 2013

10. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Author: Jean-Marc Aury, Frithjof C. Küpper, Diego Miranda-Saavedra, John H. F. Bothwell, Claire Jubin, Chris Bowler, Bernhard Gschloessl, James W. Tregear, Andrés Ritter, Andrew E. Allen, Carolyn A. Napoli, Ludovic Delage, Bernard Kloareg, Takahiro Yamagishi, Pi Nyvall-Collén, Svenja Heesch, Julia Morales, Gaelle Samson, Kei Kimura, Ga Youn Cho, Grigoris D. Amoutzias, Yves Van de Peer, Simon M. Dittami, Kenny Billiau, Julie Poulain, François Artiguenave, Sylvie Doulbeau, Marek Eliáš, Bank Beszteri, Carl J. Carrano, Daniel Lang, Florian Maumus, Stefan A. Rensing, Jonathan H. Badger, Béatrice Segurens, Martina Strittmatter, Sylvie Rousvoal, Hervé Moreau, Patrice Lerouge, Colin Brownlee, Betsy Read, Akira F. Peters, J. Mark Cock, Corinne Da Silva, Declan C. Schroeder, Catherine Boyen, Pierre Rouzé, Eric Bonnet, Jonas Collén, Susana M. Coelho, Aude Le Bail, Kamel Jabbari, David R. Nelson, Thierry Tonon, Pascal J. Lopez, Véronique Anthouard, Hadi Quesneville, Manoj P. Samanta, Delphine Scornet, Klaus Valentin, Nicolas Delaroque, Bénédicte Charrier, Cindy Martens, Peter von Dassow, Martin Lohr, Garry Farnham, Chikako Nagasato, Claire M. M. Gachon, Gurvan Michel, Lieven Sterck, Philippe Potin, Erwan Corre, Catherine Leblanc, Taizo Motomura, Cyril Pommier, Patrick Wincker, Hiroshi Kawai, Publica, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, J Craig Venter Institute, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Marine Biological Association, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), San Diego State University (SDSU), Phophorylation de protéines et Pathologies Humaines (P3H), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Charles University [Prague], Scottish Association for Marine Science (SAMS), Kobe University, Institute of Algological Research [Muroran], Hokkaido University, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Johannes Gutenberg - Universität Mainz (JGU), École normale supérieure - Paris (ENS Paris), Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Haematology, University of Cambridge [UK] (CAM), Mer et santé (MS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Arizona, The University of Tennessee Health Science Center [Memphis] (UTHSC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), California State University [Los Angeles] (CAL STATE LA), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Systemix Institute, Savelli, Bruno, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), J. Craig Venter Institute, Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Charles University [Prague] (CU), Hokkaido University [Sapporo, Japan], Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris
Subjects: 0106 biological sciences, Lineage (evolution), Molecular Sequence Data, Phaeophyta, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Algae, [SDV.BDD] Life Sciences [q-bio]/Development Biology, Botany, BIOLOGIE CELLULAIRE, Animals, 14. Life underwater, [SDV.BDD]Life Sciences [q-bio]/Development Biology, flore marine, Phylogeny, Organism, ComputingMilieux_MISCELLANEOUS, phéophycées, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, Ectocarpus siliculosus, Algal Proteins, Eukaryota, Pigments, Biological, Ectocarpus, 15. Life on land, biology.organism_classification, Biological Evolution, Brown algae, Multicellular organism, Evolutionary biology, algues brunes, Biologie, Signal Transduction, 010606 plant biology & botany
Abstract: Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. © 2010 Macmillan Publishers Limited. All rights reserved.
Published: 2010

11. Digital expression profiling of novel diatom transcripts provides insight into their biological functions

Author: Jean Weissenbach, Michael Katinka, Jean-Paul Cadoret, Pascal J. Lopez, Raymond Kaas, Agnès Meichenin, Marc Heijde, Véronique Martin-Jézéquel, Jean-Louis Petit, Betina M. Porcel, Assaf Vardi, Kamel Jabbari, Micaela S. Parker, Uma Maheswari, Thomas Mock, E. Virginia Armbrust, Alessandra De Martino, Chris Bowler, Andrew E. Allen, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Physiologie et biotechnologie des Algues (PBA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Marine Biogeochemistry, Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), School of Oceanography [Seattle], University of Washington [Seattle], School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Department of Plant Sciences, Weizmann Institute of Science [Rehovot, Israël], Funding for the Diatom Digital Gene Expression Database was from the European Union-funded Diatomics project and the Agence Nationale de la Recherche (France). cDNA construction and DNA sequencing was funded by Genoscope (France)., BMC, Ed., Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Biotechnologies et Ressources Marines (BRM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, and Université de Nantes (UN)-Université de Nantes (UN)-Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST)
Subjects: 0106 biological sciences, Salinity, [SDV.GEN] Life Sciences [q-bio]/Genetics, MESH: Carbon Dioxide, 01 natural sciences, Genome, MESH: Nitrogen, Expressed Sequence Tags, Genetics, 0303 health sciences, Expressed sequence tag, MESH: Iron, biology, Temperature, Adaptation, Physiological, MESH: Gene Expression Regulation, MESH: Temperature, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Diatoms, Nitrogen, Iron, Molecular Sequence Data, Thalassiosira pseudonana, Computational biology, Environment, MESH: Expressed Sequence Tags, 03 medical and health sciences, MESH: Gene Expression Profiling, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA, Messenger, Phaeodactylum tricornutum, MESH: Environment, Gene, 030304 developmental biology, MESH: RNA, Messenger, Diatoms, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Molecular Sequence Data, Gene Expression Profiling, Silicates, Research, fungi, Carbon Dioxide, biology.organism_classification, MESH: Adaptation, Physiological, Gene expression profiling, Diatom, Gene Expression Regulation, MESH: Silicates, Function (biology), MESH: Salinity, 010606 plant biology & botany
Abstract: International audience; BACKGROUND: Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. RESULTS: We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. CONCLUSIONS: The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.
Published: 2010

12. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

Author: Corinne Mhiri, Marie-Angèle Grandbastien, Assaf Vardi, Chris Bowler, Andrew E. Allen, Kamel Jabbari, Hanhua Hu, and Florian Maumus
Subjects: 0106 biological sciences, Genome evolution, Retroelements, lcsh:QH426-470, lcsh:Biotechnology, Thalassiosira pseudonana, Retrotransposon, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, DNA, Algal, Species Specificity, Stress, Physiological, Phylogenetics, lcsh:TP248.13-248.65, Research article, Genetics, Phaeodactylum tricornutum, Phylogeny, 030304 developmental biology, Diatoms, Recombination, Genetic, Aldehydes, 0303 health sciences, Nitrates, Polymorphism, Genetic, biology, Gene Expression Profiling, Heterokont, fungi, food and beverages, Sequence Analysis, DNA, DNA Methylation, biology.organism_classification, lcsh:Genetics, Diatom, Haplotypes, Metagenome, Sequence Alignment, 010606 plant biology & botany, Biotechnology
Abstract: Background Transposable elements (TEs) are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have been shown to have important functions in genome dynamics and species evolution. Recent genomic data can now enlarge the identification and study of TEs to other branches of the eukaryotic tree of life. Diatoms, which belong to the heterokont group, are unicellular eukaryotic algae responsible for around 40% of marine primary productivity. The genomes of a centric diatom, Thalassiosira pseudonana, and a pennate diatom, Phaeodactylum tricornutum, that likely diverged around 90 Mya, have recently become available. Results In the present work, we establish that LTR retrotransposons (LTR-RTs) are the most abundant TEs inhabiting these genomes, with a much higher presence in the P. tricornutum genome. We show that the LTR-RTs found in diatoms form two new phylogenetic lineages that appear to be diatom specific and are also found in environmental samples taken from different oceans. Comparative expression analysis in P. tricornutum cells cultured under 16 different conditions demonstrate high levels of transcriptional activity of LTR retrotransposons in response to nitrate limitation and upon exposure to diatom-derived reactive aldehydes, which are known to induce stress responses and cell death. Regulatory aspects of P. tricornutum retrotransposon transcription also include the occurrence of nitrate limitation sensitive cis-regulatory components within LTR elements and cytosine methylation dynamics. Differential insertion patterns in different P. tricornutum accessions isolated from around the world infer the role of LTR-RTs in generating intraspecific genetic variability. Conclusion Based on these findings we propose that LTR-RTs may have been important for promoting genome rearrangements in diatoms.
Published: 2009

13. The $Phaeodactylum$ genome reveals the evolutionary history of diatom genomes

Author: Yves Van de Peer, Michael R. Sussman, Frédéric Verret, Miyoshi Haruta, Angela Falciatore, John A. Berges, Leszek Rychlewski, Anusuya Willis, Richard E. Jorgensen, Michael Katinka, Jane Grimwood, Betina M. Porcel, Magali Siaut, Klaus Valentin, Pascal J. Lopez, Marc Heijde, Véronique Martin-Jézéquel, Jean-Louis Petit, Wim Vyverman, Edda Rayko, Klaas Vandepoele, Miroslav Oborník, Anthony Chiovitti, Alan Kuo, E. Virginia Armbrust, Matthew Robison, Alessandra De Martino, Nils Kröger, Susan Lucas, Colin Brownlee, Alison Taylor, Igor V. Grigoriev, Jonathan H. Badger, Kamel Jabbari, Jérome Fournet, Jeremy Schmutz, Uma Maheswari, Sacha Coesel, Michele S. Stanley, J. Chris Detter, Chang Jae Choi, Thomas Mock, Assaf Vardi, Markus Lommer, Aaron Kaplan, Yolaine Joubert, Florian Maumus, Katerina Jiroutova, Anton Montsant, Colleen A. Durkin, Cindy Martens, Bank Beszteri, Micaela S. Parker, Asaf Salamov, Linda K. Medlin, Karen M. McGinnis, Ansgar Gruber, Marie J. J. Huysman, Manuela Mangogna, Lucyan S. Wyrwicz, Jean-Paul Cadoret, Peter von Dassow, Daniel S. Rokhsar, Marie-Pierre Oudot-Le Secq, Carolyn A. Napoli, Beverley R. Green, Erica Lindquist, Peter G. Kroth, Chris Bowler, Andrew E. Allen, Tatiana A. Rynearson, Nicole Poulsen, Bethany D. Jenkins, Harris Shapiro, Robert Otillar, Jean Weissenbach, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL), J. Craig Venter Institute, J. Craig Venter Institute [La Jolla, USA] (JCVI), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), DOE Joint Genome Institute [Walnut Creek], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut de biologie de l'Ecole Normale Supérieure (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Biologie moléculaire des organismes photosynthétiques (UMR8186), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Environnement, Bioénergie, Microalgues et Plantes (EBMP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Marine Biological Association, Physiologie et biotechnologie des Algues (PBA), Biotechnologies et Ressources Marines (BRM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn (SZN), Génomique des Microorganismes (LGM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Marine Biogeochemistry, Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Biology Institute, University of Arizona, School of Oceanography [Seattle], University of Washington [Seattle], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Station biologique de Roscoff [Roscoff] (SBR), European Project: 29849,DIATOMICS, Savelli, Bruno, Understanding Diatom Biology by Functional Genomics Approaches - DIATOMICS - 29849 - OLD, École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bioénergie et Microalgues (EBM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génomique des microorganismes, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)
Subjects: 0106 biological sciences, Thalassiosira pseudonana, Molecular Sequence Data, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, DNA, Algal, Phylogenetics, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, 14. Life underwater, Phaeodactylum tricornutum, Gene, 030304 developmental biology, Genetics, Diatoms, 0303 health sciences, Multidisciplinary, biology, Sequence Homology, Amino Acid, Heterokont, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, biology.organism_classification, Protein Structure, Tertiary, Diatom, Genes, Bacterial, Biologie, 010606 plant biology & botany, Signal Transduction
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (
Published: 2008

14. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Author: Evelyne Derelle, Jeremy Schmutz, Carolyn A. Napoli, Andrea L Manuell, Marc Heijde, Asaf Salamov, Robert Otillar, Séverine Jancek, Hervé Moreau, Stephane Rombauts, Karla C Gendler, Gwenael Piganeau, Charles F. Delwiche, Olivier Vallon, Qinghu Ren, Gregory Werner, Igor V. Grigoriev, Jane Grimwood, Ian T. Paulsen, Daniel S. Rokhsar, Martin Lohr, Gregory J. Pazour, Terry Gaasterland, Sabeeha S. Merchant, Pierre Rouzé, Steven Robbens, Kamel Jabbari, Christopher L. Dupont, Chris Bowler, Richard A. Jorgensen, Brian Palenik, Sheila Podell, Andrea Aerts, Kemin Zhou, Vera Tai, Inna Dubchak, Yves Van de Peer, Nicholas H. Putnam, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Genome evolution, Protein family, Gene Transfer, Horizontal, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, Environment, 01 natural sciences, Genome, Chromosomes, Ostreococcus tauri, Ostreococcus, 03 medical and health sciences, Chlorophyta, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Selenoproteins, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, Cell Nucleus, 0303 health sciences, Multidisciplinary, Metal metabolism, Vitamins, Biological Sciences, biology.organism_classification, Plankton, Adaptation, Physiological, Biological Evolution, Eukaryotic Cells, Metals, Horizontal gene transfer, 010606 plant biology & botany
Abstract: The smallest known eukaryotes, at ≈1-μm diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri . This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
Published: 2007

15. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

Author: Bernard De Baets, Yves Van de Peer, Benoît Piégu, Chris Bowler, Kamel Jabbari, Frédéric Partensky, Evelyne Derelle, Richard G. Cooke, Pierre Rouzé, Sophie Echeynié, André Picard, François-Yves Bouget, Conchita Ferraz, Gwenael Piganeau, Stephane Rombauts, Sven Degroeve, Alexandra Z. Worden, Hervé Moreau, Jacques G. Demaille, Jean-Philippe Ral, Michel Delseny, Steven G. Ball, Yvan Saeys, Olivier Panaud, Jan Wuyts, Steven Robbens, Modèles en biologie cellulaire et évolutive (MBCE), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Laboratoire Génome et développement des plantes (LGDP), and Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Genome evolution, MESH: Sequence Analysis, DNA, Nuclear gene, Lineage (genetic), Gene prediction, 01 natural sciences, Genome, MESH: Eukaryotic Cells, Ostreococcus tauri, Ostreococcus, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, MESH: Algae, Green, Gene density, Animals, MESH: Animals, MESH: Genome, Photosynthesis, MESH: Evolution, Molecular, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, MESH: Molecular Sequence Data, biology, Biological Sciences, biology.organism_classification, Phytoplankton, MESH: Chromosomes, 010606 plant biology & botany
Abstract: The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world’s smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C 4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.
Published: 2006

16. The evolution of introns in human duplicated genes

Author: Kamel Jabbari, Giorgio Bernardi, Edda Rayko, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, and Stazione Zoologica Anton Dohrn (SZN)
Subjects: Alus, Alu element, Biology, Genome, Evolution, Molecular, 03 medical and health sciences, Alu Elements, Genes, Duplicate, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Compartment (development), Animals, Humans, Codon, Gene, 030304 developmental biology, 0303 health sciences, Base Composition, Transition (genetics), Genome, Human, 030302 biochemistry & molecular biology, Intron, Chromosome, LINEs, General Medicine, Introns, Long Interspersed Nucleotide Elements, CpG site, Vertebrates, CpG Islands, Isochores
Abstract: In previous work [Jabbari, K., Rayko, E., Bernardi, G., 2003. The major shifts of human duplicated genes. Gene 317, 203–208], we investigated the fate of ancient duplicated genes after the compositional transitions that occurred between the genomes of cold- and warm-blooded vertebrates. We found that the majority of duplicated copies were transposed to the “ancestral genome core”, the gene-dense genome compartment that underwent a GC enrichment at the compositional transitions. Here, we studied the consequences of the events just outlined on the introns of duplicated genes. We found that, while intron number was highly conserved, total intron size (the sum of intron sizes within any given gene) was smaller in the GC-rich copies compared to the GC-poor copies, especially in dispersed copies (i.e., copies located on different chromosomes or chromosome arms). GC-rich copies also showed higher densities of CpG islands and Alus, whereas GC-poor copies were characterized by higher densities of LINEs. The features of the copies that underwent the compositional transition and became GC-richer are suggestive of, or related to, functional changes.
Published: 2005

17. The new genes of rice: a closer look

Author: Giorgio Bernardi, Oliver Clay, Jérôme Le Saux, Stéphane Cruveiller, and Kamel Jabbari
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, Oryza sativa, DNA, Complementary, biology, Transcription, Genetic, cDNA library, Arabidopsis, Oryza, Plant Science, biology.organism_classification, Genes, Plant, 01 natural sciences, 03 medical and health sciences, Complementary DNA, Genomic library, Gene, 030304 developmental biology, 010606 plant biology & botany, Gene Library, Plant Proteins
Abstract: Reports accompanying draft or finished sequences of rice chromosomes and full-length cDNA libraries indicate that between a third and half of the (largely predicted) protein-coding genes of rice might have no identifiable homologs in Arabidopsis and/or other species. The set of apparent ‘no-homolog' sequences are predicted to exhibit striking compositional and structural deviations from experimentally verified protein-coding sequences. Here we discuss evolutionary and other implications of the proposed gene set and argue that a more likely answer to the riddle is that a large proportion of the anomalous rice sequences are never translated into functional proteins in vivo , that is, they represent incorrect gene predictions.
Published: 2004

18. Compositional Gene Landscapes in Vertebrates

Author: Oliver K. Clay, Kamel Jabbari, Giorgio Bernardi, and Stéphane Cruveiller
Subjects: Biology, ENCODE, 03 medical and health sciences, chemistry.chemical_compound, Mice, Xenopus laevis, Species Specificity, Gene cluster, Genetics, Methods, Animals, Humans, Gene, Genetics (clinical), 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Gene Expression Profiling, 030302 biochemistry & molecular biology, Computational Biology, Proteins, Amino acid, Gene expression profiling, chemistry, Protein Biosynthesis, Chromosomal region, Crest, Chickens, DNA
Abstract: The existence of a well conserved linear relationship between GC levels of genes' second and third codon positions (GC2, GC3) prompted us to focus on the landscape, or joint distribution, spanned by these two variables. In human, well curated coding sequences now cover at least 15%–30% of the estimated total gene set. Our analysis of the landscape defined by this gene set revealed not only the well documented linear crest, but also the presence of several peaks and valleys along that crest, a property that was also indicated in two other warm-blooded vertebrates represented by large gene databases, that is, mouse and chicken. GC2 is the sum of eight amino acid frequencies, whereas GC3 is linearly related to the GC level of the chromosomal region containing the gene. The landscapes therefore portray relations between proteins and the DNA environments of the genes that encode them.
Published: 2004

19. Incorrectly predicted genes in rice?

Author: Stéphane Cruveiller, Kamel Jabbari, Oliver Clay, and Giorgio Bernardi
Subjects: 0106 biological sciences, Genes, Plant, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, Arabidopsis, Genetics, Homologous chromosome, Codon, Gene, 030304 developmental biology, Plant Proteins, chemistry.chemical_classification, 0303 health sciences, Base Composition, biology, food and beverages, Computational Biology, Reproducibility of Results, Oryza, General Medicine, biology.organism_classification, Amino acid, chemistry, 010606 plant biology & botany
Abstract: Between one third and one half of the proposed rice genes appear to have no homologs in other species, including Arabidopsis. Compositional considerations, and a comparison of curated rice sequences with ex novo predictions, suggest that many or most of the putative genes without homologs may be false positive predictions, i.e., sequences that are never translated into functional proteins in vivo.
Published: 2004

20. Comparative genomics of Anopheles gambiae and Drosophila melanogaster

Author: Giorgio Bernardi and Kamel Jabbari
Subjects: 0106 biological sciences, Anopheles gambiae, Genes, Insect, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Intergenic region, Gene density, Anopheles, Genetics, Animals, Codon, Gene, Genome size, 030304 developmental biology, Comparative genomics, 0303 health sciences, Base Composition, biology, fungi, General Medicine, DNA, Genomics, biology.organism_classification, Introns, Drosophila melanogaster
Abstract: A sequence analysis of the genomes of Anopheles gambiae and Drosophila melanogaster reveals that Anopheles DNA is more heterogeneous and GC-richer than Drosophila DNA. The gene concentration across the Anopheles genome is characterized by low levels in the GC-poor part of the genome and a 3-fold increase in the GC-richest part; this gene density gradient is approximately half that of Drosophila . GC levels of introns and flanking sequences are correlated with GC 3 values (GC levels of third codon positions) of the corresponding genes with slopes much lower than unity; in other words, most introns and intergenic sequences are less GC-rich than the corresponding GC 3 values. These findings, which describe a compositional shift within Diptera, is of interest because of their parallels in the well studied major shift in vertebrates.
Published: 2003

21. Body temperature and evolutionary genomics of vertebrates: a lesson from the genomes of Takifugu rubripes and Tetraodon nigroviridis

Author: Giorgio Bernardi and Kamel Jabbari
Subjects: Takifugu rubripes, Genomics, Tetraodon nigroviridis, Genome, Body Temperature, Evolution, Molecular, 03 medical and health sciences, Genetics, Animals, 14. Life underwater, 030304 developmental biology, Evolutionary genomics, 0303 health sciences, Base Composition, biology, Tetraodontiformes, 030302 biochemistry & molecular biology, General Medicine, DNA, biology.organism_classification, Adaptation, Physiological, Takifugu, Fishery, Cold Temperature, Evolutionary biology, Vertebrates, Puffer fishes, Isochores, Body Temperature Regulation
Abstract: In this paper, we provide evidence for the body temperature effect on the formation of GC-rich isochores, by analysing genomic sequences from two puffer fishes living at different temperatures. The higher body temperature of Tetraodon nigroviridis compared to Takifugu rubripes (DeltaT approximately 15 degrees C) appears to be the cause of a higher compositional heterogeneity of the former due to the formation of GC-rich regions. Such an effect does not only concern large DNA segments but also coding sequences.
Published: 2003

22. The major shifts of human duplicated genes

Author: Giorgio Bernardi, Kamel Jabbari, and Edda Rayko
Subjects: Biology, Genome, Body Temperature, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Genes, Duplicate, Gene density, Genetics, Compartment (development), Animals, Humans, Codon, Gene, 030304 developmental biology, 0303 health sciences, Base Composition, Transition (genetics), Models, Genetic, Genome, Human, Proteins, General Medicine, Adaptation, Physiological, Duplicated genes, Human genome, Hydrophobic and Hydrophilic Interactions, 030217 neurology & neurosurgery, Function (biology)
Abstract: Since many gene duplications in the human genome are ancient duplications going back to the origin of vertebrates, the question may be asked about the fate of such duplicated genes at the compositional genome transitions that occurred between cold- and warm-blooded vertebrates. Indeed, at that transition, about half of the (GC-poor) genes of cold-blooded vertebrates (the genes of the gene-dense “ancestral genome core”) underwent a GC enrichment to become the genes of the “genome core” of warm-blooded vertebrates. Since the compositional distribution of the human duplicated genes investigated (1111 pairs) mimics the general distribution of human genes (about 50% GC 3 -poor and 50% GC 3 -rich genes, the border being at 60% GC 3 ), we considered two possibilities, namely that the compositional transition affected either (i) about half of the copies on a random basis, or (ii) preferentially only one copy of the duplicated genes. The two possibilities could be distinguished if each copy is put into one of two subsets according to its GC 3 level. Indeed, in the first case, the two distributions would be similar, whereas in the second case, the two distributions would be different, one copy having maintained the ancestral GC-poor composition, and one copy having undergone the compositional change. Using this approach, we could show that, by far and large, one copy of the duplicated genes preferentially underwent the GC enrichment. This result implies that this copy, which had possibly acquired a different function and/or regulation, was preferentially translocated into the gene-dense compartment of the genome, the “ancestral genome core”, namely the “gene space” which underwent the compositional transition at the emergence of warm-blooded vertebrates.
Published: 2003

23. The correlation between GC3 and hydropathy in human genes

Author: Stéphane Cruveiller, Kamel Jabbari, Giorgio Bernardi, and Oliver Clay
Subjects: 0303 health sciences, Base Composition, Base Sequence, Models, Genetic, Proteins, General Medicine, DNA, Biology, Composition (combinatorics), Positive correlation, Bioinformatics, Correlation, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, 030220 oncology & carcinogenesis, Genetics, Humans, Human genome, Amino Acids, Codon, Hydrophobic and Hydrophilic Interactions, 030304 developmental biology
Abstract: A positive correlation holds between the GC level of third codon positions of human genes (GC3) and hydropathy of the encoded proteins. This correlation may appear counterintuitive, since it links a physical property of proteins to the base composition of ‘synonymous’ sites. We here establish the nontriviality of the correlation, which has recently been contested. In particular, the correlation cannot simply be a consequence of an analogous correlation for first and second codon positions, since no such correlation exists. More generally, for any explanation via two chained correlations, the intermediate property would need to be strongly correlated with hydrophobicity and/or GC3.
Published: 2003

24. The correlation of protein hydropathy with the base composition of coding sequences

Author: Giorgio Bernardi, Kamel Jabbari, Héctor Musto, and Giuseppe D'Onofrio
Subjects: chemistry.chemical_classification, Genetics, 0303 health sciences, Base Composition, Genome, Base (chemistry), Base Sequence, 030302 biochemistry & molecular biology, Proteins, General Medicine, Biology, Composition (combinatorics), Genetic code, Amino acid, Correlation, 03 medical and health sciences, chemistry, Biochemistry, Amino Acids, Codon, Gene, 030304 developmental biology, Cysteine
Abstract: The ‘‘universal correlation’’ (D’Onofrio, G., Bernardi, G., 1992. A universal compositional correlation amomg codon positions. Gene 110, 81‐88.) that holds between GC 3 and GC 1 or GC 2 (GC values are the average values of the coding sequences of each genome analyzed) at both the inter- and intra-genomic level, was re-analyzed on a vastly larger dataset. The results showed a slight, but significant, diVerence in the GC 3 vs. GC 1 correlations exhibited by prokaryotes and eukaryotes. This finding prompted an analysis of the correlation between GC 3 and the amino acid frequencies in the encoded proteins, which has shown that positive correlations exist between GC 3 values of coding sequences and the hydropathy of the corresponding proteins. These correlations are due to the fact that hydrophobic and amphypathic amino acids increase, whereas hydrophilic amino acids decrease with increasing GC 3 values. Hydropathy values of prokaryotic proteins are systematically higher than those of eukaryotes, but the slopes of the regression lines are identical. The lower hydrophobicity of eukaryotic proteins is due to diVerences in the amino acid composition. In particular, the twofold higher cysteine (and disulfide bond ) level of eukaryotic proteins compared to prokaryotic proteins most probably compensates for their lower hydrophobicity. This supports the viewpoint that hydrophobicity plays a structural and functional role as far as protein stability is concerned. © 1999 Elsevier Science B.V. All rights reserved.
Published: 1999

25. Simple proteomic checks for detecting noncoding RNA

Author: Kamel Jabbari, Stéphane Cruveiller, Giorgio Bernardi, and Oliver Clay
Subjects: Proteomics, Genetics, Base Composition, 0303 health sciences, RNA, Untranslated, 030302 biochemistry & molecular biology, RNA, Computational biology, Biology, Genetic code, Non-coding RNA, Biochemistry, 03 medical and health sciences, Electrophoresis, Gel, Two-Dimensional, Isoelectric Point, Gene, Molecular Biology, Sequence (medicine), 030304 developmental biology
Abstract: Proper validation can accelerate sequence-based discovery of proteins and protein-coding genes. Databases currently contain a backlog of experimentally unverified gene models and tentative assignments of observed transcripts to coding or noncoding RNA. We present and apply a general principle, founded on base composition and the genetic code and validated here by bulk 2-D gels, that can improve the reliability of such classifications and of the algorithms or pipelines that lead to them.
Published: 2007

26. Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17

Author: Kamel Jabbari, Giorgio Bernardi, Jan Pačes, Adam Pavlicek, and Oliver Clay
Subjects: Biophysics, Biology, Major histocompatibility complex, Biochemistry, Chromosomes, Major Histocompatibility Complex, 03 medical and health sciences, Mice, 0302 clinical medicine, Chromosome (genetic algorithm), Structural Biology, Chromosome regions, Sequence Homology, Nucleic Acid, Genetics, Animals, Humans, Molecular Biology, Conserved Sequence, 030304 developmental biology, 0303 health sciences, Base Composition, Cell Biology, GC Rich Sequence, Chromosome 17 (human), Long Interspersed Nucleotide Elements, 030220 oncology & carcinogenesis, biology.protein, Chromosomes, Human, Pair 6
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26 results on '"Kamel Jabbari"'

1. A common genomic code for chromatin architecture and recombination landscape

2. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

3. Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum

4. Compositional features of eukaryotic genomes for checking predicted genes

5. An Isochore Framework Underlies Chromatin Architecture

6. Early allopolyploid evolution in the post-Neolithic[i] Brassica napus[/i] oilseed genome

7. Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure

8. Different hydrophobicities of orthologous proteins from Xenopus and human

9. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

10. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

11. Digital expression profiling of novel diatom transcripts provides insight into their biological functions

12. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

13. The $Phaeodactylum$ genome reveals the evolutionary history of diatom genomes

14. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

15. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

16. The evolution of introns in human duplicated genes

17. The new genes of rice: a closer look

18. Compositional Gene Landscapes in Vertebrates

19. Incorrectly predicted genes in rice?

20. Comparative genomics of Anopheles gambiae and Drosophila melanogaster

21. Body temperature and evolutionary genomics of vertebrates: a lesson from the genomes of Takifugu rubripes and Tetraodon nigroviridis

22. The major shifts of human duplicated genes

23. The correlation between GC3 and hydropathy in human genes

24. The correlation of protein hydropathy with the base composition of coding sequences

25. Simple proteomic checks for detecting noncoding RNA

26. Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17

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26 results on '"Kamel Jabbari"'

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