"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids".

Mark W Davey,Norzulaani Khalid,Johan Keulemans,Jennifer Ann Harikrishna,Ranganath Gudimella,Lee Wan Sin

doi:10.1186/1471-2164-14-683

Abstract

BackgroundModern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been associated with improved vigour and tolerance to biotic and abiotic stresses and is thus a target for Musa breeding programs. However, while a reference M. acuminata genome has recently been released (Nature 488:213–217, 2012), little sequence data is available for the corresponding B-genome.To address these problems we carried out Next Generation gDNA sequencing of the wild diploid M. balbisiana variety ‘Pisang Klutuk Wulung’ (PKW). Our strategy was to align PKW gDNA reads against the published A-genome and to extract the mapped consensus sequences for subsequent rounds of evaluation and gene annotation.ResultsThe resulting B-genome is 79% the size of the A-genome, and contains 36,638 predicted functional gene sequences which is nearly identical to the 36,542 of the A-genome. There is substantial sequence divergence from the A-genome at a frequency of 1 homozygous SNP per 23.1 bp, and a high degree of heterozygosity corresponding to one heterozygous SNP per 55.9 bp. Using expressed small RNA data, a similar number of microRNA sequences were predicted in both A- and B-genomes, but additional novel miRNAs were detected, including some that are unique to each genome. The usefulness of this B-genome sequence was evaluated by mapping RNA-seq data from a set of triploid AAA and AAB hybrids simultaneously to both genomes. Results for the plantains demonstrated the expected 2:1 distribution of reads across the A- and B-genomes, but for the AAA genomes, results show they contain regions of significant homology to the B-genome supporting proposals that there has been a history of interspecific recombination between homeologous A and B chromosomes in Musa hybrids.ConclusionsWe have generated and annotated a draft reference Musa B-genome and demonstrate that this can be used for molecular genetic mapping of gene transcripts and small RNA expression data from several allopolyploid banana cultivars. This draft therefore represents a valuable resource to support the study of metabolism in inter- and intraspecific triploid Musa hybrids and to help direct breeding programs.

Highlights

Modern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes
The resulting consensus Pisang Klutuk Wulung’ (PKW) genome sequences derived from these mappings were on average 78.9% of the length of the A-genome, with the greatest difference being found for chromosome 10 which was only 74.9% of the size of the corresponding ‘Pahang’ chromosome 10 (Table 1)
The higher number of miRNA loci in the B-genome may be related to a higher number of transposable elements present as these are thought to have contributed to the generation of species-specific miRNA genes in plants [69]

Summary

Introduction

Modern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. While a reference M. acuminata genome has recently been released (Nature 488:213–217, 2012), little sequence data is available for the corresponding B-genome To address these problems we carried out Generation gDNA sequencing of the wild diploid M. balbisiana variety ‘Pisang Klutuk Wulung’ (PKW). Bananas and plantains (Musaceae, Zingiberlaes, Musa ssp., ‘bananas’) are giant monocotoyledenous herbs, which originated in Southeast Asia and the western Pacific They were one of the first crops to be domesticated, and are widely distributed throughout the subtropics where they constitute a major staple food for millions of people [1]. Members of the Australimusa sections have a basic chromosome number of 2n = 20, and comprise seven species one of which contains edible parthenocarpic types known as ‘Fe’i’ bananas. Members of this Fe’i group are notable for their upright fruit and in some cases exceptionally high fruit provitamin A carotenoid contents [8,9]

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Conclusion