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

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.

Figure 1

Current understanding of relationships among monocot orders [118]. Families are shown in bold caps and genera with EST sequences in dbEST [119]. The number of sequences in GenBank (as of 10/08/07) are shown in parentheses for each order and the shaded box highlights Commelinid orders. The nodes with < 75% bootstrap support are grey.

Figure 2

Chromosome preparations of M. acuminata cv. Calcutta-4 (2n = 22) stained with DAPI after FISH of BAC. (A) MA4_78I12 (detected with Texas red). (B) MA4_54N07 (detected FITC). Scale bar = 10 microns.

Figure 3

Distribution of GC content in Musa and its comparison with other plant species. (A) All TCs/ESTs from the named species. (B) All annotated CDS from 17 Musa BACs (this data set) and the complete genomes of Arabidopsis and rice.

Figure 4

Mean GC content from 5' to 3' across 129 bp sliding windows. (A) for 77 Musa genes with a "rice-like" gradient. (B) for 180 Musa genes with an "Aradidopsis-like" pattern

Figure 5

Musa-rice syntenic regions. Predicted genes and their orientation are shown as boxed areas. Genes annotated such as hypothetical genes are represented in white. The probes used to identify the Musa BAC clones are indicated in brackets. Conserved genes between Musa and rice regions are connected by shaded areas. (A) Syntenic relationship between Musa MBP_91N22 BAC clone and rice chromosome 1. (B) Syntenic relationship between Musa 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 Musa MA4_8L21 BAC clone and rice chromosome 3.

Figure 6

Phylogenetic analyses on three of the ten M. acuminata genes from MA4_25J11 BAC clone. These three Musa genes have homologous genes in rice chromosomes 1 and 5 and the locus numbers 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.

Figure 7

Comparison between M. acuminata MA4_82I11 BAC clone and M. balbisiana MBP_81C12 BAC clone. Predicted genes and their orientation are shown as boxed areas. Genes annotated such as hypothetical genes are represented in white. The probe used to identify the Musa BAC clones is indicated in brackets. Conserved genes between the two Musa regions are connected by shaded areas. (A) Dot plot analysis of the two pairs of homeologous BACs from M. acuminata and M. balbisiana.(B) Diagram of the syntenic regions between the two BAC clones.

Figure 8

Frequency of synonymous substitution (K_s) in different pairwise species comparisons. These results reveal the existence of whole genome duplications within Musa and revealed an extensive event pre-dating the ginger-Musa or rice-Musa divergences.