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8 results on '"Jacques Dainat"'

1. Methods to identify and study the evolution of pseudogenes using a phylogenetic approach

Author

Jacques Dainat, Pierre Pontarotti, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Laura Poliseno, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0303 health sciences, Phylogenetic tree, Pseudogene, food and beverages, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, phylogeny, 01 natural sciences, Genome, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 03 medical and health sciences, speciation, Evolutionary biology, Phylogenetics, Genetic algorithm, orthology, Gene, paralogy, Pseudogenes, 030304 developmental biology, 010606 plant biology & botany
Abstract

International audience; The discovery that pseudogenes are involved in important biological processes has excited enthusiasm and increased the research interest on them. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow for studying pseudogene history are described.

Published
2021
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2. Pervasive hybridizations in the history of wheat relatives

Author

Jacques David, Celine Scornavacca, Vincent Ranwez, Sylvain Glémin, Morgane Ardisson, Sylvain Santoni, Concetta Burgarella, Jacques Dainat, Gautier Sarah, Veronique Viader, Glémin, Sylvain, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Uppsala University, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), This work was supported by the French National Research Agency (ANR-11-BSV7-013-03), ANR-13-BSV7-0011,FunFit,Une approche basée sur les traits d'histoire de vie des champignons phytopathogènes pour faire le lien entre fitness individuelle et stratégies écologiques.(2013), 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), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institut National de la Recherche Agronomique (INRA)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ANR-11-BSV7-0013,TRANS,Les transitions de systèmes de reproduction chez les angiosperms et leurs conséquences génomiques(2011), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and 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)

Subjects
Gene Flow, 0106 biological sciences, DNA, Complementary, Lineage (evolution), Biology, Genes, Plant, 010603 evolutionary biology, 01 natural sciences, Genome, Gene flow, Evolution, Molecular, Polyploidy, Transcriptome, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Polyploid, blé, Phylogenetics, histoire, Genetics, RNA, Messenger, Genetik, Clade, Gene, Phylogeny, Triticum, Research Articles, 030304 developmental biology, 0303 health sciences, Polymorphism, Genetic, Multidisciplinary, Vegetal Biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], food and beverages, SciAdv r-articles, Agriculture, Diploidy, Evolutionary biology, DNA Transposable Elements, Hybridization, Genetic, Ploidy, hybridation, Genome, Plant, Biologie végétale, 010606 plant biology & botany, Research Article
Abstract

A comprehensive phylogenomic analysis reveals that the genomes of cultivated wheats result from multiple rounds of hybridization., Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought—Aegilops mutica, an overlooked wild species—instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.

Published
2019
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3. Single-molecule genome assembly of the BasketWillow, Salix viminalis, reveals earliest stages of sex chromosome expansion

Author

Lucile Soler, Pedro Almeida, Allison M. Churcher, Ann Christine Rönnberg-Wästljung, Judith E. Mank, Björn Nystedt, Pascal Pucholt, Jacques Dainat, Sofia Berlin, Tom Martin, Jessica Nordlund, and Estelle Proux-Wera

Subjects
0106 biological sciences, 0303 health sciences, Genome evolution, Phylogenetic tree, Haplotype, Chromosome, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Evolutionary biology, Homologous chromosome, Gene, Heterogametic sex, 030304 developmental biology
Abstract

Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes and this leads to a range of non-adaptive modifications causing the gradual degeneration and gene loss on the sex-limited chromosome. However, because studies on sex chromosomes have primarily focused on old and highly differentiated sex chromosomes, the causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. Here, we use long- and short-read single molecule sequencing approaches to assemble and annotate a draft genome of the basket willow,Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W divergence, largely the result of the accumulation of single nucleotide polymorphisms in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although a few genes present on the Z have already been lost from the W. Furthermore, we use multiple lines of evidence to test for inversions, which have long been assumed to halt recombination between the sex chromosomes. Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation.

Published
2019
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4. Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540

Author

Huifeng Jiang, Jure Piškur, Zhenglong Gu, Mats Sandgren, Jens Nielsen, Marc P. Hoeppner, Jacques Dainat, Ievgeniia A. Tiukova, Volkmar Passoth, and Henrik Lantz

Subjects
Microbiology (medical), Computational biology, Bioinformatik och systembiologi, Biology, yeast, Genome, Microbiology, 03 medical and health sciences, Virology, lcsh:QH301-705.5, genome, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Phylogenetic tree, Contig, Bioinformatics and Systems Biology, 030306 microbiology, Genome project, Yeast, Brettanomyces naardenensis, Mikrobiologi, lcsh:Biology (General), brettanomyces naardenensis, High attenuation
Abstract

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.

Published
2019

5. Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis

Author

Volkmar Passoth, Ievgeniia A. Tiukova, Jacques Dainat, Mats E. Pettersson, Max Käller, Remi Andre Olsen, Marc P. Hoeppner, Jonas Söderberg, Jens Nielsen, and Henrik Lantz

Subjects
Gene Dosage, Yeast and Fungal Models, Genome, Contig Mapping, Genome Size, Copy-number variation, Phylogeny, Genetics, 0303 health sciences, Multidisciplinary, Organic Compounds, Eukaryota, Genomics, Genome project, Mitochondria, Chemistry, Experimental Organism Systems, Physical Sciences, Saccharomyces Cerevisiae, Medicine, Chromosomes, Fungal, Ploidy, Research Article, Nuclear gene, Science, Brettanomyces, Biology, Research and Analysis Methods, Gene dosage, Evolution, Molecular, Saccharomyces, 03 medical and health sciences, Model Organisms, Genetik, Genome size, Gene, 030304 developmental biology, Ethanol, Whole Genome Sequencing, 030306 microbiology, Organic Chemistry, Organisms, Fungi, Chemical Compounds, Gene Amplification, Biology and Life Sciences, Computational Biology, Genetic Variation, Molecular Sequence Annotation, Comparative Genomics, Genome Analysis, Genomic Libraries, Genome Annotation, Yeast, Alcohols, Animal Studies
Abstract

Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.

Published
2019

6. Impact of recurrent gene duplication on adaptation of plant genomes

Author

Iris Fischer, Jean-François Dufayard, Sylvain Glémin, Jacques Dainat, Vincent Ranwez, Nathalie Chantret, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), French Agence Nationale de la Recherche [ANR-11-BSV7-013-03], French Agence Nationale de la Recherche Investissements d'avenir/Bioinformatique [ANR-10-BINF-01-02], Institut National de la Recherche Agronomique (INRA)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), ANR-11-BSV7-0013,TRANS,Les transitions de systèmes de reproduction chez les angiosperms et leurs conséquences génomiques(2011), ANR-10-BINF-0001,ANCESTROME,Approche de phylogénie intégrative pour la reconstruction de génomes ancestraux(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Time Factors, Gene duplication, Ultraparalogs (UP), 2R hypothesis, Évolution, Plant Science, adaptation, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Negative selection, Databases, Genetic, Cluster Analysis, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Sélection individuelle, Genetics, 0303 health sciences, Superorthologs (SO), F70 - Taxonomie végétale et phytogéographie, Adaptation, Physiological, Positive selection, Multigene Family, Gene retention, Empreinte ADN, Genome, Plant, Research Article, Genome evolution, Séquence nucléotidique, F60 - Physiologie et biochimie végétale, Biology, Magnoliophyta, 03 medical and health sciences, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Adaptation, Codon, Gene, Selection (genetic algorithm), réplication, 030304 developmental biology, Comparative genomics, Génome, Polymorphism, Genetic, Molecular Sequence Annotation, Lineage specific expansion (LSE), Amélioration des plantes, Gène, Mutation, 010606 plant biology & botany
Abstract

Publis014-agap-018; Background: Recurrent gene duplication and retention played an important role in angiosperm genome evolution. It has been hypothesized that these processes contribute significantly to plant adaptation but so far this hypothesis has not been tested at the genome scale.[br/]Results: We studied available sequenced angiosperm genomes to assess the frequency of positive selection footprints in lineage specific expanded (LSE) gene families compared to single-copy genes using a dN/dS-based test in a phylogenetic framework. We found 5.38% of alignments in LSE genes with codons under positive selection. In contrast, we found no evidence for codons under positive selection in the single-copy reference set. An analysis at the branch level shows that purifying selection acted more strongly on single-copy genes than on LSE gene clusters. Moreover we detect significantly more branches indicating evolution under positive selection and/or relaxed constraint in LSE genes than in single-copy genes.[br/]Conclusions: In this – to our knowledge –first genome-scale study we provide strong empirical support for the hypothesis that LSE genes fuel adaptation in angiosperms. Our conservative approach for detecting selection footprints as well as our results can be of interest for further studies on (plant) gene family evolution.

Published
2014
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7. The chordate proteome history database

Author

Olivier Poch, Pierre Pontarotti, Anthony Levasseur, Philippe Gouret, Jacques Dainat, Julien Paganini, Julie D. Thompson, Levasseur, Anthony, Laboratoire d'Analyse, Topologie, Probabilités (LATP), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), and ANR EvolHHuPro: ANR-07-BLAN-0054-01

Subjects
phylogénétique, alignement de séquences, Genome evolution, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Architecture domain, taille famille, Lineage (evolution), lcsh:Evolution, Genomics, Biology, gène paralogue, genome evolution, computer.software_genre, analyse phylogénétique, gain génétique, 03 medical and health sciences, duplication de gènes, Phylogenetics, Biologie animale, Genetics, lcsh:QH359-425, chordata, base de données protéomique, gène orthologue, protéome, Ecology, Evolution, Behavior and Systematics, protein architecture, 030304 developmental biology, Original Research, Animal biology, 0303 health sciences, Phylogenetic tree, Database, family size, functional inference, ortholog groups, phylogenetic reconstruction, séquence génomique, 030302 biochemistry & molecular biology, Phylogenetic network, réarrangement génétique, Computer Science Applications, protéine, Proteome, évolution du génome, arbre phylogénétique, computer
Abstract

International audience; The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture.

Published
2012
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8. Integration of evolutionary biology concepts for functional annotation and automation of complex research in evolution: the multi-agent software system DAGOBAH

Author

Anthony Levasseur, Elodie Darbo, Dorra Louati, Jacques Dainat, Julien Paganini, Pierre Pontarotti, Philippe Gouret, EBM, Laboratoire d'Analyse, Topologie, Probabilités (LATP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS)-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Modélisation Mathématique et Numérique dans les Sciences de l'Ingénieur (LAMSIN), Ecole Nationale d'Ingénieurs de Tarbes (ENIT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Phylogénomique, Université de Provence - Aix-Marseille 1-EA 3781, Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Modélisation Mathématique et Numérique dans les Sciences de l'Ingénieur [Tunis] (LR-LAMSIN-ENIT), Ecole Nationale d'Ingénieurs de Tunis (ENIT), Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), and Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0303 health sciences, 030306 microbiology, business.industry, Computer science, Inference, Phylogenetic comparative methods, Automation, Genome, Prolog, 03 medical and health sciences, Annotation, ComputingMethodologies_PATTERNRECOGNITION, Description logic, Software agent, Evolutionary biology, business, computer, 030304 developmental biology, computer.programming_language
Abstract

Various strategies have been proposed for predicting protein function. They are derived from the classical homology-based approaches and emerging alternative approaches taking into account gene history in the framework of phylogenetic comparative methods. The growing numbers of available genome sequences and data require bioinformatics tools, in which methodological approaches are set according to the biological issues to be addressed. Much effort has already been devoted to integrating evolutionary biology into bioinformatics tools; e.g., homology-based functional annotation has been successfully integrated in a pipeline-assisted method. In addition, new concepts based on correlation of evolutionary events are emerging. For example, two independent events (e.g., systematic loss of specific genes) that happen repetitively can therefore be functionally linked. However, correlated gene profiles, also called “contextual annotation,” makes use of different bioinformatics resources based on multi-agent development. In this chapter, we describe evolutionary concepts and bioinformatics approaches proposed for future functional inference.

Published
2011
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