1. Insights into the Musa genome: Syntenic relationships to rice and between Musa species
- Author
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Olivier Garsmeur, Felipe Rodrigues da Silva, Georgios J. Pappas, Foo Cheung, Ang lique D'Hont, Christopher D. Town, Ryan Althoff, Manoel Souza, C. M. R. Santos, Tammy Arbogast, Catherine M. Ronning, Ana Y. Ciampi, Guillaume Blanc, Jim Leebens-Mack, Alberto Duarte Vilarinhos, Brian J. Haas, Pietro Piffanelli, Jean-Christophe Glaszmann, Magali Lescot, Manuel Ruiz, Robert N.G. Miller, Hiroyuki Kanamori, Takashi Matsumoto, Takuji Sasaki, Erin Hine, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Magali Lescot, CIRAD/IBSM, Pietro Piffanelli, CIRAD/PADANO, Ana Yamaguishi Ciampi, Embrapa Recursos Genéticos e Biotecnologia, Manuel Ruiz, CIRAD, Guillaume Blanc, IGS, Jim Leebens-Mack, University of Georgia, Felipe Rodrigues da Silva, Embrapa Recursos Genéticos e Biotecnologia, Candice Mello Romero Santos bolsista Embrapa Recursos Genéticos e Biotecnologia, Angélique D'Hont, CIRAD, Olivier Garsmeur, CIRAD, Alberto Duarte Vilarinhos, CNPMF, Hiroyuki Kanamori, RGP, Takashi Matsumoto, RGP, Catherine M. Ronning, J. Craig Venter Institute, Foo Cheung, J. Craig Venter Institute, Brian J. Haas, J. Craig Venter Institute, Ryan Althoff, J. Craig Venter Institute, Tammy Arbogast, J. Craig Venter Institute, Erin Hine, J. Craig Venter Institute, Georgios Joannis Pappas Junior, Embrapa Recursos Genéticos e Biotecnologia, Takuji Sasaki, RGP, Manoel Teixeira Souza Junior, Embrapa Recursos Genéticos e Biotecnologia, Robert N. G. Miller, UCB, Jean-Christophe Glaszmann, CIRAD, and Christopher D. Town, J. Craig Venter Institute.
- Subjects
0106 biological sciences ,Chromosomes, Artificial, Bacterial ,Phylogénie ,Arabidopsis ,comparative sequence-analysis ,01 natural sciences ,Genome ,F30 - Génétique et amélioration des plantes ,Banana ,Gene Duplication ,Musa balbisiana ,ComputingMilieux_MISCELLANEOUS ,Expressed Sequence Tags ,2. Zero hunger ,Genetics ,Base Composition ,0303 health sciences ,gibberellin 20-oxidase ,food and beverages ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,genetic-recombination map ,duplicate genes ,Genome, Plant ,Polymorphism, Restriction Fragment Length ,Research Article ,Biotechnology ,Genome evolution ,DNA, Complementary ,Séquence nucléotidique ,lcsh:QH426-470 ,lcsh:Biotechnology ,Zingiberales ,Genomics ,arabidopsis-thaliana ,Biology ,Genes, Plant ,Synteny ,Evolution, Molecular ,03 medical and health sciences ,Species Specificity ,Zingiberaceae ,lcsh:TP248.13-248.65 ,Musa acuminata ,acuminata colla ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Musa species ,splice-site prediction ,Sorghum ,Repetitive Sequences, Nucleic Acid ,030304 developmental biology ,Comparative genomics ,Whole genome sequencing ,molecular evidence ,flowering plants ,Génome ,Biointeracties and Plant Health ,Musa ,Oryza ,15. Life on land ,biology.organism_classification ,lcsh:Genetics ,DNA Transposable Elements ,PRI Biointeractions en Plantgezondheid ,nuclear-dna content ,010606 plant biology & botany - Abstract
Background Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.
- Published
- 2008
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