“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”
Identifieur interne : 000136 ( Main/Merge ); précédent : 000135; suivant : 000137“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”
Auteurs : Mark W. Davey [Belgique] ; Ranganath Gudimella [Malaisie] ; Jennifer Ann Harikrishna [Malaisie] ; Lee Wan Sin [Malaisie] ; Norzulaani Khalid [Malaisie] ; Johan Keulemans [Belgique]Source :
- BMC Genomics [ 1471-2164 ] ; 2013.
Abstract
Modern banana cultivars are primarily interspecific triploid hybrids of two species,
To address these problems we carried out Next Generation gDNA sequencing of the wild diploid
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
We have generated and annotated a draft reference
Url:
DOI: 10.1186/1471-2164-14-683
PubMed: 24094114
PubMed Central: 3852598
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PMC:3852598Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">“A draft <italic>Musa balbisiana</italic>
genome sequence for molecular genetics in polyploid, inter- and intra-specific <italic>Musa</italic>
hybrids”</title>
<author><name sortKey="Davey, Mark W" sort="Davey, Mark W" uniqKey="Davey M" first="Mark W" last="Davey">Mark W. Davey</name>
<affiliation wicri:level="4"><nlm:aff id="I1">Laboratory of Fruit Breeding and Biotechnology, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, box 2427B-3001, Heverlee, Leuven, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Laboratory of Fruit Breeding and Biotechnology, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, box 2427B-3001, Heverlee, Leuven</wicri:regionArea>
<orgName type="university">Katholieke Universiteit Leuven</orgName>
<placeName><settlement type="city">Louvain</settlement>
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<region type="district" nuts="2">Province du Brabant flamand</region>
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<author><name sortKey="Harikrishna, Jennifer Ann" sort="Harikrishna, Jennifer Ann" uniqKey="Harikrishna J" first="Jennifer Ann" last="Harikrishna">Jennifer Ann Harikrishna</name>
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<author><name sortKey="Sin, Lee Wan" sort="Sin, Lee Wan" uniqKey="Sin L" first="Lee Wan" last="Sin">Lee Wan Sin</name>
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<author><name sortKey="Keulemans, Johan" sort="Keulemans, Johan" uniqKey="Keulemans J" first="Johan" last="Keulemans">Johan Keulemans</name>
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<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Modern banana cultivars are primarily interspecific triploid hybrids of two species, <italic>Musa acuminata</italic>
and <italic>Musa balbisiana</italic>
, which respectively contribute the A- and B-genomes. The <italic>M. balbisiana</italic>
genome has been associated with improved vigour and tolerance to biotic and abiotic stresses and is thus a target for <italic>Musa</italic>
breeding programs. However, while a reference <italic>M. acuminata</italic>
genome has recently been released (Nature 488:213–217, 2012), little sequence data is available for the corresponding B-genome.</p>
<p>To address these problems we carried out Next Generation gDNA sequencing of the wild diploid <italic>M</italic>
. <italic>balbisiana</italic>
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.</p>
</sec>
<sec><title>Results</title>
<p>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 <italic>Musa</italic>
hybrids.</p>
</sec>
<sec><title>Conclusions</title>
<p>We have generated and annotated a draft reference <italic>Musa</italic>
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 <italic>Musa</italic>
hybrids and to help direct breeding programs.</p>
</sec>
</div>
</front>
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