Open Access Highly Accessed Research article

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

Magali Lescot19*, Pietro Piffanelli110, Ana Y Ciampi3, Manuel Ruiz1, Guillaume Blanc5, Jim Leebens-Mack6, Felipe R da Silva3, Candice MR Santos3, Angélique D'Hont1, Olivier Garsmeur1, Alberto D Vilarinhos17, Hiroyuki Kanamori8, Takashi Matsumoto8, Catherine M Ronning2, Foo Cheung2, Brian J Haas2, Ryan Althoff2, Tammy Arbogast2, Erin Hine2, Georgios J Pappas4, Takuji Sasaki8, Manoel T Souza3, Robert NG Miller4, Jean-Christophe Glaszmann1 and Christopher D Town2

Author affiliations

1 French Agricultural Research Center for International Development (CIRAD), UMR 1096, Avenue Agropolis, TA40/03, FR-34398, Montpellier, Cedex 5, France

2 The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville MD 20850, USA

3 Embrapa Genetic Resources and Biotechnology (CENARGEN), P B I., Final Av. W/5 Norte, Asa Norte 70770-900, Caixa-Postal: 02372, Brasília, Brazil

4 Genomic Sciences and Biotechnology program, Catholic University of Brasília (UCB), SGAN 916, Modulo B, Asa Norte 70790-160, Brasília DF, Brazil

5 Structural and Genomic Information Laboratory (IGS), C.N.R.S. UPR 2589, Institute of Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 avenue de Luminy, FR-13288 Marseille Cedex 9, France

6 Department of Plant Biology, University of Georgia, Athens, GA 30602, USA

7 Brazilian Agricultural Research Corporation (EMBRAPA), National Research Center of Cassava and Fruit Crops (CNPMF), P.O Box 007, Zip Code 44380.000, Cruz das Almas BA, Brazil

8 Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences (NIAS)/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8602, Japan

9 Structural and Genomic Information Laboratory (IGS), C.N.R.S. UPR 2589, Institute of Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 avenue de Luminy, FR-13288 Marseille Cedex 9, France

10 Parco Tecnologico Padano, Via Einstein, Lodi 26900, Italy

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Citation and License

BMC Genomics 2008, 9:58  doi:10.1186/1471-2164-9-58

Published: 30 January 2008

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.