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11 results on '"Bombarely, Aureliano"'

1. EasyGDB: a low-maintenance and highly customizable system to develop genomics portals.

Author

Fernandez-Pozo N and Bombarely A

Subjects
Software, Computational Biology, Molecular Sequence Annotation, Genomics, Genome
Abstract

Summary: EasyGDB is an easy-to-implement low-maintenance tool developed to create genomic data management web platforms. It can be used for any species, group of species, or multiple genome or annotation versions. EasyGDB provides a framework to develop a web portal that includes the general information about species, projects and members, and bioinformatics tools such as file downloads, BLAST, genome browser, annotation search, gene expression visualization, annotation and sequence download, and gene ids and orthologs lookup. The code of EasyGDB facilitates data maintenance and update for non-experienced bioinformaticians, using BLAST databases to store and retrieve sequence data in gene annotation pages and bioinformatics tools, and JSON files to customize metadata. EasyGDB is a highly customizable tool. Any section and tool can be enabled or disabled like a switch through a single configuration file. This tool aims to simplify the development of genomics portals in non-model species, providing a modern web style with embedded interactive bioinformatics tools to cover all the common needs derived from genomics projects., Availability and Implementation: The code and manual to use EasyGDB can be found at https://github.com/noefp/easy_gdb., (© The Author(s) 2022. Published by Oxford University Press.)

Published
2022
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2. The era of reference genomes in conservation genomics.

Author

Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, and Bálint M

Subjects
Biodiversity, Genome, Genomics
Abstract

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Competing Interests: Declaration of interests The authors declare no conflicts of interest., (Copyright © 2021. Published by Elsevier Ltd.)

Published
2022
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3. Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

Author

Frazier, Taylor P, Palmer, Nathan A, Xie, Fuliang, Tobias, Christian M, Donze-Reiner, Teresa J, Bombarely, Aureliano, Childs, Kevin L, Shu, Shengqiang, Jenkins, Jerry W, Schmutz, Jeremy, Zhang, Baohong, Sarath, Gautam, and Zhao, Bingyu

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Alleles, Amino Acid Sequence, Computational Biology, Databases, Nucleic Acid, Disease Resistance, Gene Expression Profiling, Genes, Plant, Genetic Association Studies, Genetic Predisposition to Disease, Genome, Plant, Genomics, Panicum, Phylogeny, Polymorphism, Single Nucleotide, Position-Specific Scoring Matrices, Protein Interaction Domains and Motifs, Reproducibility of Results, Biofuel, Disease resistance, Gene expression, NB-LRR, Panicum virgatum, RNA-seq, SNP, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundSwitchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass.ResultsIn this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from 'Alamo', a rust-resistant switchgrass cultivar, and 'Dacotah', a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar 'Summer' plants indicated that the expression of some of these RGHs was developmentally regulated.ConclusionsOur results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop.

Published
2016

4. Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya (Annona cherimola).

Author

Talavera, Alicia, Fernandez‐Pozo, Noe, Matas, Antonio J., Hormaza, Jose I., and Bombarely, Aureliano

Abstract

Copyright of Plants, People, Planet is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2023
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6. De novo assembly of the zucchini genome reveals a whole‐genome duplication associated with the origin of the Cucurbita genus.

Author

Montero‐Pau, Javier, Blanca, José, Bombarely, Aureliano, Ziarsolo, Peio, Esteras, Cristina, Martí‐Gómez, Carlos, Ferriol, María, Gómez, Pedro, Jamilena, Manuel, Mueller, Lukas, Picó, Belén, and Cañizares, Joaquín

Subjects
CUCURBITA, PLANT phylogeny, PLANT genomes, GENETIC transcription in plants, PLANT gene mapping
Abstract

Summary: The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high‐quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole‐genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus. [ABSTRACT FROM AUTHOR]

Published
2018
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7. Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

Author

Frazier, Taylor P, Palmer, Nathan A, Xie, Fuliang, Tobias, Christian M, Donze-Reiner, Teresa J, Bombarely, Aureliano, Childs, Kevin L, Shu, Shengqiang, Jenkins, Jerry W, Schmutz, Jeremy, Zhang, Baohong, Sarath, Gautam, and Zhao, Bingyu

Subjects
Bioinformatics, SNP, Genes, Plant, Panicum, Medical and Health Sciences, Polymorphism, Single Nucleotide, Databases, Biofuel, NB-LRR, Information and Computing Sciences, Genetics, Position-Specific Scoring Matrices, Genetic Predisposition to Disease, Protein Interaction Domains and Motifs, Amino Acid Sequence, Polymorphism, Alleles, Genetic Association Studies, Phylogeny, Disease Resistance, Disease resistance, Genome, Nucleic Acid, Gene Expression Profiling, fungi, Computational Biology, Reproducibility of Results, food and beverages, Single Nucleotide, Plant, Genomics, Biological Sciences, Panicum virgatum, Genes, Gene expression, RNA-seq, Databases, Nucleic Acid, Genome, Plant, Research Article, Panicum virgatum (switchgrass), Biotechnology
Abstract

Background Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. Results In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from ‘Alamo’, a rust-resistant switchgrass cultivar, and ‘Dacotah’, a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar ‘Summer’ plants indicated that the expression of some of these RGHs was developmentally regulated. Conclusions Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3201-5) contains supplementary material, which is available to authorized users.

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8. The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian Cricket Laupala.

Author

Blankers, Thomas, Oh, Kevin P., Bombarely, Aureliano, and Shaw, Kerry L.

Subjects
*ALLELES, *GENETIC polymorphisms, *INSECTS, *GENETIC mutation, *POPULATION geography, *RECOMBINANT DNA, *GENOMICS, *CHROMOSOME structure
Abstract

Phenotypic evolution and speciation depend on recombination in many ways. Within populations, recombination can promote adaptation by bringing together favorable mutations and decoupling beneficial and deleterious alleles. As populations diverge, crossing over can give rise to maladapted recombinants and impede or reverse diversification. Suppressed recombination due to genomic rearrangements, modifier alleles, and intrinsic chromosomal properties may offer a shield against maladaptive gene flow eroding coadapted gene complexes. Both theoretical and empirical results support this relationship. However, little is known about this relationship in the context of behavioral isolation, where coevolving signals and preferences are the major hybridization barrier. Here we examine the genomic architecture of recently diverged, sexually isolated Hawaiian swordtail crickets (Laupala). We assemble a de novo genome and generate three dense linkage maps from interspecies crosses. In line with expectations based on the species' recent divergence and successful interbreeding in the laboratory, the linkage maps are highly collinear and show no evidence for large-scale chromosomal rearrangements. Next, the maps were used to anchor the assembly to pseudomolecules and estimate recombination rates across the genome to test the hypothesis that loci involved in behavioral isolation (song and preference divergence) are in regions of low interspecific recombination. Contrary to our expectations, the genomic region where a male song and female preference QTL colocalize is not associated with particularly low recombination rates. This study provides important novel genomic resources for an emerging evolutionary genetics model system and suggests that trait--preference coevolution is not necessarily facilitated by locally suppressed recombination. [ABSTRACT FROM AUTHOR]

Published
2018
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9. The era of reference genomes in conservation genomics

Author

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José A. Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklós Bálint, Fedor Čiampor, Jacob Hoglund, Per Palsbøll, María José Ruiz-López, Goujie Zhang, Erich Jarvis, Sargis A. Aghayan, Tyler S. Alioto, Isabel Almudi, Nadir Alvarez, Paulo C. Alves, Isabel R. Amorim, Agostinho Antunes, Paula Arribas, Petr Baldrian, Paul R. Berg, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit L. Boštjančić, Bastien Boussau, Catherine M. Breton, Elena Buzan, Paula F. Campos, Carlos Carreras, L. FIlipe Castro, Luis J. Chueca, Elena Conti, Robert Cook-Deegan, Daniel Croll, Mónica V. Cunha, Frédéric Delsuc, Alice B. Dennis, Dimitar Dimitrov, Rui Faria, Adrien Favre, Olivier D. Fedrigo, Rosa Fernández, Gentile Francesco Ficetola, Jean-François Flot, Toni Gabaldón, Dolores R. Galea Agius, Guido R. Gallo, Alice M. Giani, M. Thomas P. Gilbert, Tine Grebenc, Katerina Guschanski, Romain Guyot, Bernhard Hausdorf, Oliver Hawlitschek, Peter D. Heintzman, Berthold Heinze, Michael Hiller, Martin Husemann, Alessio Iannucci, Iker Irisarri, Kjetill S. Jakobsen, Sissel Jentoft, Peter Klinga, Agnieszka Kloch, Claudius F. Kratochwil, Henrik Kusche, Kara K.S. Layton, Jennifer A. Leonard, Emmanuelle Lerat, Gianni Liti, Tereza Manousaki, Tomas Marques-Bonet, Pável Matos-Maraví, Michael Matschiner, Florian Maumus, Ann M. Mc Cartney, Shai Meiri, José Melo-Ferreira, Ximo Mengual, Michael T. Monaghan, Matteo Montagna, Robert W. Mysłajek, Marco T. Neiber, Violaine Nicolas, Marta Novo, Petar Ozretić, Ferran Palero, Lucian Pârvulescu, Marta Pascual, Octávio S. Paulo, Martina Pavlek, Cinta Pegueroles, Loïc Pellissier, Graziano Pesole, Craig R. Primmer, Ana Riesgo, Lukas Rüber, Diego Rubolini, Daniele Salvi, Ole Seehausen, Matthias Seidel, Simona Secomandi, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja C. Vernes, Cristiano Vernesi, David R. Vieites, Robert M. Waterhouse, Christopher W. Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit, Repositório da Universidade de Lisboa, Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlo, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Höglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Svardal, Hanne, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Mazzoni, Camila J., Jarvis, Erich D., Bálint, Mikló, Čiampor, Fedor, Hoglund, Jacob, Palsbøll, Per, José Ruiz-López, María, Zhang, Goujie, Jarvis, Erich, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., R Amorim, Isabel, Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, R Berg, Paul, Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, L Boštjančić, Ljudevit, Boussau, Bastien, M Breton, Catherine, Buzan, Elena, F Campos, Paula, Carreras, Carlo, FIlipe Castro, L., Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, V Cunha, Mónica, Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Francesco Ficetola, Gentile, Flot, Jean-Françoi, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Thomas P Gilbert, M., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, D Heintzman, Peter, Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, S Jakobsen, Kjetill, Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, F Kratochwil, Claudiu, Kusche, Henrik, KS Layton, Kara, A Leonard, Jennifer, Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Toma, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Robertwmysłajek, T Neiber, Marco, Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loc, Pesole, Graziano, R Primmer, Craig, Riesgo, Ana, Rüber, Luka, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthia, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyro, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, C Vernes, Sonja, Vernesi, Cristiano, R Vieites, David, M Waterhouse, Robert, W Wheat, Christopher, Wörheide, Gert, Wurm, Yannick, Zammit., and Gabrielle, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), 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 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), Barcelona Supercomputing Center, European Reference Genome Atlas (ERGA) Consortium, University of St Andrews. School of Biology, University of St Andrews. St Andrews Bioinformatics Unit, Palsbøll lab, Marine Biology, University of Zurich, and Bálint, Miklós

Subjects
QH301 Biology, 580 Plants (Botany), Genetics -- Research, Evolutionsbiologi, biodiversity conservation, conservation genetics, ERGA, European Reference Genome Atlas, Conservation genetics, Biodiversity conservation, Animal genome mapping, udc:630*1, Genome, GE, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDE.BE.BIOD]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.biod, Biodiversity [MeSH], Genomics [MeSH], Ecology, Evolution, Behavior and Systematics, Genome [MeSH], 3rd-DAS, Genomics, Biodiversity, referenčni genomi, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDE.BE.BEC]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.bec, Chemistry, 10121 Department of Systematic and Evolutionary Botany, genomika, GE Environmental Sciences, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], biodiverziteta, Settore BIO/18 - GENETICA, education, QH426 Genetics, QH301, VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470, [SDE.BE.EVO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.evo, Genetics, genomi, 10211 Zurich-Basel Plant Science Center, Genomes, Genetik, Biology, QH426, Evolutionary Biology, Ambientale, Ecología, Genética, 1105 Ecology, Evolution, Behavior and Systematics, Wildlife conservation, 570 Life sciences, biology, Human medicine, Animal genetics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genètica
Abstract

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Published
2022

10. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Author

Lukas A. Mueller, T. P. Robbins, Gonzalo H. Villarino, Trude Schwarzacher, Julia Weiss, Eva Nouri, Natalia Dudareva, Jan Zethof, Kevin M. Davies, Michiel Vandenbussche, Xiaodan Lv, Marcel Bucher, Philipp Franken, Nunzio D’Agostino, Massimo Delledonne, Mélanie K. Rich, Neil S. Mattson, Eric Lyons, Patrice Morel, Mattijs Bliek, Jennifer D. Hintzsche, Ronald Koes, Mitrick A. Johns, Laurie Grandont, Susan L. Urbanus, M. Eric Schranz, Qinzhou Qi, Michael C. Schatz, Enrico Martinoia, Laure Bapaume, Robert C. Schuurink, Aureliano Bombarely, Didier Reinhardt, Rémy Bruggmann, Katja R. Richert-Pöggeler, Mario Pezzotti, Maaike R. Boersma, Michel Moser, J. S. Heslop-Harrison, Uwe Druege, Diwa Malla, Kitty Vijverberg, Lorenzo Borghi, Ryan M. Warner, Haibao Tang, Avichai Moshe Amrad, Kees Spelt, Thomas L. Sims, Valentina Passeri, Francesca Quattrocchio, Manzhu Bao, Joëlle K. Muhlemann, Marcos Egea-Cortines, Cornelius S. Barry, Zhen Yue, Noe Fernandez-Pozo, Cris Kuhlemeier, Plant Physiology (SILS, FNWI), Plant Development & (Epi)Genetics (SILS, FNWI), Department of Horticulture, University of Wisconsin-Madison, Institute of Plant Sciences, University of Bern, Huazhong Agricultural University, Department of Biology, Northern Arizona University [Flagstaff], University of Amsterdam [Amsterdam] (UvA), Universität Zürich [Zürich] = University of Zurich (UZH), Universität Bern- University of Bern [Bern], Partenaires INRAE, University of Cologne, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Plant & Food Research, Leibniz Institute of Vegetable and Ornamental Crops, Leibniz Association, Purdue University, Universidad Politécnica de Cartagena, Dipartimento di Biotecnologie, University of Verona (UNIVR), Boyce Thompson Institute [Ithaca], Wageningen University and Research Centre (WUR), Department of Genetics [Leicester], University of Leicester, Department of Biological Sciences, The Open University [Milton Keynes] (OU), Northern University, Beijing Genomics Institute [Shenzhen] (BGI), School of Plant Sciences, iPlant Collaborative, University of Arizona, Cornell University [New York], Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants, University of Nottingham, UK (UON), Cold Spring Harbor Laboratory (CSHL), School of Plant Sciences, Radboud university [Nijmegen], Institute of Plant Science, NWO-ALW grant 022.001.018 820.02.015, Marie Curie Independent Fellowship, Swiss NSF grant 31003A_159493 31003A_135778, NCCR Plant Survival, NWO-TOP grant 854.11.006, Borsa di Studio Lanzi per Genetica Agraria, Accademia dei Lincei, CNRS ATIP-AVENIR award, Deutsche Forschungsgemeinschaft grant DR411/2-1, Bombarely, Aureliano, Moser, Michel, Amrad, Avichai, Bao, Manzhu, Bapaume, Laure, Barry, Cornelius S., Bliek, Mattij, Boersma, Maaike R., Borghi, Lorenzo, Bruggmann, Rémy, Bucher, Marcel, D'Agostino, Nunzio, Davies, Kevin, Druege, Uwe, Dudareva, Natalia, Egea-Cortines, Marco, Delledonne, Massimo, Fernandez-Pozo, Noe, Franken, Philipp, Grandont, Laurie, Heslop-Harrison, J. S., Hintzsche, Jennifer, Johns, Mitrick, Koes, Ronald, Lv, Xiaodan, Lyons, Eric, Malla, Diwa, Martinoia, Enrico, Mattson, Neil S., Morel, Patrice, Mueller, Lukas A., Muhlemann, Joëlle, Nouri, Eva, Passeri, Valentina, Pezzotti, Mario, Qi, Qinzhou, Reinhardt, Didier, Rich, Melanie, Richert-Pöggeler, Katja R., Robbins, Tim P., Schatz, Michael C., Schranz, M. Eric, Schuurink, Robert C., Schwarzacher, Trude, Spelt, Kee, Tang, Haibao, Urbanus, Susan L., Vandenbussche, Michiel, Vijverberg, Kitty, Villarino, Gonzalo H., Warner, Ryan M., Weiss, Julia, Yue, Zhen, Zethof, Jan, Quattrocchio, Francesca, Sims, Thomas L., Kuhlemeier, Cris, Huazhong Agricultural University [Wuhan] (HZAU), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA), Purdue University [West Lafayette], Università degli studi di Verona = University of Verona (UNIVR), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and Radboud University [Nijmegen]

Subjects
0106 biological sciences, 0301 basic medicine, Animal Ecology and Physiology, Plant Science, 580 Plants (Botany), Plant Genetics, 01 natural sciences, Petunia, Genome, Petunia axillaris, NUMBER, Plant evolution, SYNTHASE, Genetics, biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Biosystematiek, Life Sciences & Biomedicine, Solanaceae, Genome, Plant, Evolution, Genetics, Plant evolution, Plant sciences, EXPRESSION, DATABASE, Evolution, SEQUENCE, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Genetic model, Life Science, Gene, SUPPRESSION, Whole genome sequencing, Science & Technology, Plant Sciences, 15. Life on land, biology.organism_classification, GENE, 030104 developmental biology, POLLINATOR ATTRACTION, TRANSPOSABLE ELEMENTS, Biosystematics, Hybridization, Genetic, EPS, Plant sciences, GENERATION, 010606 plant biology & botany
Abstract

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.

Published
2016

11. Genomic analysis of the native European Solanum species, S. dulcamara

Author

Celestina Mariani, Nunzio D’Agostino, Ivo Rieu, Nicky Driedonks, Jan-Peter Nap, Erik Wijnker, Joachim W. Bargsten, T. M. Golas, Jan Zethof, Henri van de Geest, Aureliano Bombarely, Thikra Dawood, D'Agostino, Nunzio, Golas, Tomek, van de Geest, Henri, Bombarely, Aureliano, Dawood, Thikra, Zethof, Jan, Driedonks, Nicky, Wijnker, Erik, Bargsten, Joachim, Nap, Jan-Peter, Mariani, Celestina, and Rieu, Ivo

Subjects
0106 biological sciences, Solanum dulcamara, De novo transcriptome assembly, Molecular Plant Physiology, de novo transcriptome assembly, tomato, 01 natural sciences, Genome, polymorphism, Genetic map, Genetic Marker, Cluster Analysis, genes, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), 2. Zero hunger, Genetics, 0303 health sciences, biology, food and beverages, Genomics, Bittersweet, Microsatellite Repeat, potato, Laboratory of Genetics, Biotechnology, Research Article, Genetic Markers, Genome evolution, phytophthora-infestans, solanaceae, Solanum, Laboratorium voor Erfelijkheidsleer, Polymorphism, Single Nucleotide, Chromosomes, Plant, Evolution, Molecular, 03 medical and health sciences, Gene mapping, Species Specificity, Comparative genomic, evolution, 030304 developmental biology, Comparative genomics, Cluster Analysi, Models, Genetic, Gene Expression Profiling, Molecular Sequence Annotation, sequence, biology.organism_classification, Genetic marker, Evolutionary biology, Genomic, identification, EPS, 010606 plant biology & botany, Microsatellite Repeats
Abstract

Background Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been recognized as one of the alternative hosts for pathogens and pests responsible for many important diseases in potato, such as Phytophthora. At the same time, it may represent an alternative source of resistance genes against these diseases. Despite its unique ecology and potential as a genetic resource, genomic research tools are lacking for S. dulcamara. We have taken advantage of next-generation sequencing to speed up research on and use of this non-model species. Results In this work, we present the first large-scale characterization of the S. dulcamara transcriptome. Through comparison of RNAseq reads from two different accessions, we were able to predict transcript-based SNP and SSR markers. Using the SNP markers in combination with genomic AFLP and CAPS markers, the first genome-wide genetic linkage map of bittersweet was generated. Based on gene orthology, the markers were anchored to the genome of related Solanum species (tomato, potato and eggplant), revealing both conserved and novel chromosomal rearrangements. This allowed a better estimation of the evolutionary moment of rearrangements in a number of cases and showed that chromosomal breakpoints are regularly re-used. Conclusion Knowledge and tools developed as part of this study pave the way for future genomic research and exploitation of this wild Solanum species. The transcriptome assembly represents a resource for functional analysis of genes underlying interesting biological and agronomical traits and, in the absence of the full genome, provides a reference for RNAseq gene expression profiling aimed at understanding the unique biology of S. dulcamara. Cross-species orthology-based marker selection is shown to be a powerful tool to quickly generate a comparative genetic map, which may speed up gene mapping and contribute to the understanding of genome evolution within the Solanaceae family.

Published
2013

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