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

• Authors : Davey, M.W.; Gudimella, R.; Harikrishna, J.A.; Sin, L.W.; Khalid, N.; Keulemans, J.


• Document type : Journal article


• Year of publication : 2013


• Journal title : BMC Genomics


• Volume (number) : 14 (1)




• Pages : 683


• Peer-reviewed : Yes


• ISSN : 1471-2164


• Language(s) : English


• Abstract : Background 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 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. Results The 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. Conclusions We 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.


• Keywords : PLANTAIN; POLYPLOIDY; GENOMES; MUSA ACUMINATA; MUSA BALBISIANA; HYBRIDS; MOLECULAR GENETICS; GENETIC DIVERSITY; RNA; GENETIC MAPS; WILD SPECIES; GENE SEQUENCE; ITC CODE


• Open access : Yes


• Document on publisher's site : View article on publisher's site


• Musalit document ID : IN130359

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