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

<p>Abstract</p> <p>Background</p> <p><it>Musa </it>species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning <it>Musa </it>genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of <it>Musa </it>genomic sequence have been conducted. This study compares genomic sequence in two <it>Musa </it>species with orthologous regions in the rice genome.</p> <p>Results</p> <p>We produced 1.4 Mb of <it>Musa </it>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 <it>Musa</it>-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the <it>Musa </it>lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from <it>M. acuminata </it>and <it>M. balbisiana </it>revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya.</p> <p>Conclusion</p> <p>These results point to the utility of comparative analyses between distantly-related monocot species such as rice and <it>Musa </it>for improving our understanding of monocot genome evolution. Sequencing the genome of <it>M. acuminata </it>would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated <it>Musa </it>polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.</p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species-2

hypothetical genes are represented in white. The probe used to identify the BAC clones is indicated in brackets. Conserved genes between the two regions are connected by shaded areas. (A) Dot plot analysis of the two pairs of homeologous BACs from and .(B) Diagram of the syntenic regions between the two BAC clones.<p><b>Copyright information:</b></p><p>Taken from "Insights into the Musa genome: Syntenic relationships to rice and between Musa species"</p><p>http://www.biomedcentral.com/1471-2164/9/58</p><p>BMC Genomics 2008;9():58-58.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270835.</p><p></p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species-3

Extensive event pre-dating the ginger-or rice-divergences.<p><b>Copyright information:</b></p><p>Taken from "Insights into the Musa genome: Syntenic relationships to rice and between Musa species"</p><p>http://www.biomedcentral.com/1471-2164/9/58</p><p>BMC Genomics 2008;9():58-58.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270835.</p><p></p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species-0

hypothetical genes are represented in white. The probes used to identify the BAC clones are indicated in brackets. Conserved genes between and rice regions are connected by shaded areas. (A) Syntenic relationship between MBP_91N22 BAC clone and rice chromosome 1. (B) Syntenic relationship between MA4_25J11 BAC clone and rice chromosome 1 and 5. The numbers above the genes correspond to the locus numbers used for phylogenetic analyses. (C) Syntenic relationship between MA4_8L21 BAC clone and rice chromosome 3.<p><b>Copyright information:</b></p><p>Taken from "Insights into the Musa genome: Syntenic relationships to rice and between Musa species"</p><p>http://www.biomedcentral.com/1471-2164/9/58</p><p>BMC Genomics 2008;9():58-58.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270835.</p><p></p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species-1

Rs are taken from Figure 5B. Stars indicate duplication events in the most recent common ancestor of major grain lineages (i.e. rice, wheat and maize). MA4_25J11 BAC clone was isolated by the SbRPG132 probe.<p><b>Copyright information:</b></p><p>Taken from "Insights into the Musa genome: Syntenic relationships to rice and between Musa species"</p><p>http://www.biomedcentral.com/1471-2164/9/58</p><p>BMC Genomics 2008;9():58-58.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270835.</p><p></p