Insights into the Musa genome : Syntenic relationships to rice and between Musa species
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.
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Subjects: | F30 - Génétique et amélioration des plantes, Musa, Oryza, séquence nucléotidique, génome, phylogénie, http://aims.fao.org/aos/agrovoc/c_4993, http://aims.fao.org/aos/agrovoc/c_5435, http://aims.fao.org/aos/agrovoc/c_27583, http://aims.fao.org/aos/agrovoc/c_3224, http://aims.fao.org/aos/agrovoc/c_13325, |
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dig-cirad-fr-5436552024-01-28T15:44:21Z http://agritrop.cirad.fr/543655/ http://agritrop.cirad.fr/543655/ Insights into the Musa genome : Syntenic relationships to rice and between Musa species. Lescot Magali, Piffanelli Pietro, Ciampi Ana, Ruiz Manuel, Blanc Guillaume, Leebens-Mack Jim, Da Silva Felipe, Santos Candice M.R., D'Hont Angélique, Garsmeur Olivier, Vilarinhos Alberto Duarte, Kanamori Hiroyuki, Matsumoto Takashi, Ronning Catherine, Cheung Foo, Haas Brian, Althoff Ryan, Arbogast Tammy, Hine Erin, Pappas Junior Georgios, Sasaki Takuji, Souza Manoel, Miller Roberto Neil Gerard, Glaszmann Jean-Christophe, Town Christopher. 2008. BMC Genomics, 9 (58), 20 p.https://doi.org/10.1186/1471-2164-9-58 <https://doi.org/10.1186/1471-2164-9-58> Insights into the Musa genome : Syntenic relationships to rice and between Musa species Lescot, Magali Piffanelli, Pietro Ciampi, Ana Ruiz, Manuel Blanc, Guillaume Leebens-Mack, Jim Da Silva, Felipe Santos, Candice M.R. D'Hont, Angélique Garsmeur, Olivier Vilarinhos, Alberto Duarte Kanamori, Hiroyuki Matsumoto, Takashi Ronning, Catherine Cheung, Foo Haas, Brian Althoff, Ryan Arbogast, Tammy Hine, Erin Pappas Junior, Georgios Sasaki, Takuji Souza, Manoel Miller, Roberto Neil Gerard Glaszmann, Jean-Christophe Town, Christopher eng 2008 BMC Genomics F30 - Génétique et amélioration des plantes Musa Oryza séquence nucléotidique génome phylogénie http://aims.fao.org/aos/agrovoc/c_4993 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/543655/1/document_543655.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/1471-2164-9-58 10.1186/1471-2164-9-58 info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-9-58 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/1471-2164-9-58 |
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F30 - Génétique et amélioration des plantes Musa Oryza séquence nucléotidique génome phylogénie http://aims.fao.org/aos/agrovoc/c_4993 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 F30 - Génétique et amélioration des plantes Musa Oryza séquence nucléotidique génome phylogénie http://aims.fao.org/aos/agrovoc/c_4993 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 |
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F30 - Génétique et amélioration des plantes Musa Oryza séquence nucléotidique génome phylogénie http://aims.fao.org/aos/agrovoc/c_4993 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 F30 - Génétique et amélioration des plantes Musa Oryza séquence nucléotidique génome phylogénie http://aims.fao.org/aos/agrovoc/c_4993 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 Lescot, Magali Piffanelli, Pietro Ciampi, Ana Ruiz, Manuel Blanc, Guillaume Leebens-Mack, Jim Da Silva, Felipe Santos, Candice M.R. D'Hont, Angélique Garsmeur, Olivier Vilarinhos, Alberto Duarte Kanamori, Hiroyuki Matsumoto, Takashi Ronning, Catherine Cheung, Foo Haas, Brian Althoff, Ryan Arbogast, Tammy Hine, Erin Pappas Junior, Georgios Sasaki, Takuji Souza, Manoel Miller, Roberto Neil Gerard Glaszmann, Jean-Christophe Town, Christopher Insights into the Musa genome : Syntenic relationships to rice and between Musa species |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes Musa Oryza séquence nucléotidique génome phylogénie http://aims.fao.org/aos/agrovoc/c_4993 http://aims.fao.org/aos/agrovoc/c_5435 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 |
author |
Lescot, Magali Piffanelli, Pietro Ciampi, Ana Ruiz, Manuel Blanc, Guillaume Leebens-Mack, Jim Da Silva, Felipe Santos, Candice M.R. D'Hont, Angélique Garsmeur, Olivier Vilarinhos, Alberto Duarte Kanamori, Hiroyuki Matsumoto, Takashi Ronning, Catherine Cheung, Foo Haas, Brian Althoff, Ryan Arbogast, Tammy Hine, Erin Pappas Junior, Georgios Sasaki, Takuji Souza, Manoel Miller, Roberto Neil Gerard Glaszmann, Jean-Christophe Town, Christopher |
author_facet |
Lescot, Magali Piffanelli, Pietro Ciampi, Ana Ruiz, Manuel Blanc, Guillaume Leebens-Mack, Jim Da Silva, Felipe Santos, Candice M.R. D'Hont, Angélique Garsmeur, Olivier Vilarinhos, Alberto Duarte Kanamori, Hiroyuki Matsumoto, Takashi Ronning, Catherine Cheung, Foo Haas, Brian Althoff, Ryan Arbogast, Tammy Hine, Erin Pappas Junior, Georgios Sasaki, Takuji Souza, Manoel Miller, Roberto Neil Gerard Glaszmann, Jean-Christophe Town, Christopher |
author_sort |
Lescot, Magali |
title |
Insights into the Musa genome : Syntenic relationships to rice and between Musa species |
title_short |
Insights into the Musa genome : Syntenic relationships to rice and between Musa species |
title_full |
Insights into the Musa genome : Syntenic relationships to rice and between Musa species |
title_fullStr |
Insights into the Musa genome : Syntenic relationships to rice and between Musa species |
title_full_unstemmed |
Insights into the Musa genome : Syntenic relationships to rice and between Musa species |
title_sort |
insights into the musa genome : syntenic relationships to rice and between musa species |
url |
http://agritrop.cirad.fr/543655/ http://agritrop.cirad.fr/543655/1/document_543655.pdf |
work_keys_str_mv |
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