“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”
Identifieur interne : 000183 ( Ncbi/Checkpoint ); précédent : 000182; suivant : 000184“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
Affiliations:
- Belgique, Malaisie
- Province du Brabant flamand, Région flamande
- Louvain
- Katholieke Universiteit Leuven
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PMC:3852598Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">“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><region>Région flamande</region><region type="district" nuts="2">Province du Brabant flamand</region></placeName></affiliation></author><author><name sortKey="Gudimella, Ranganath" sort="Gudimella, Ranganath" uniqKey="Gudimella R" first="Ranganath" last="Gudimella">Ranganath Gudimella</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603</wicri:regionArea><wicri:noRegion>Kuala Lumpur 50603</wicri:noRegion></affiliation></author><author><name sortKey="Harikrishna, Jennifer Ann" sort="Harikrishna, Jennifer Ann" uniqKey="Harikrishna J" first="Jennifer Ann" last="Harikrishna">Jennifer Ann Harikrishna</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Centre for Research in Biotechnology for Agriculture and 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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><region>Région flamande</region><region type="district" nuts="2">Province du Brabant flamand</region></placeName></affiliation></author><author><name sortKey="Gudimella, Ranganath" sort="Gudimella, Ranganath" uniqKey="Gudimella R" first="Ranganath" last="Gudimella">Ranganath Gudimella</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603</wicri:regionArea><wicri:noRegion>Kuala Lumpur 50603</wicri:noRegion></affiliation></author><author><name sortKey="Harikrishna, Jennifer Ann" sort="Harikrishna, Jennifer Ann" uniqKey="Harikrishna J" first="Jennifer Ann" last="Harikrishna">Jennifer Ann Harikrishna</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603</wicri:regionArea><wicri:noRegion>Kuala Lumpur 50603</wicri:noRegion></affiliation></author><author><name sortKey="Sin, Lee Wan" sort="Sin, Lee Wan" uniqKey="Sin L" first="Lee Wan" last="Sin">Lee Wan Sin</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603</wicri:regionArea><wicri:noRegion>Kuala Lumpur 50603</wicri:noRegion></affiliation></author><author><name sortKey="Khalid, Norzulaani" sort="Khalid, Norzulaani" uniqKey="Khalid N" first="Norzulaani" last="Khalid">Norzulaani Khalid</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603</wicri:regionArea><wicri:noRegion>Kuala Lumpur 50603</wicri:noRegion></affiliation></author><author><name sortKey="Keulemans, Johan" sort="Keulemans, Johan" uniqKey="Keulemans J" first="Johan" last="Keulemans">Johan Keulemans</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><region>Région flamande</region><region type="district" nuts="2">Province du Brabant flamand</region></placeName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="De, Le" uniqKey="De L">LE De</name></author><author><name sortKey="Vrydaghs, L" uniqKey="Vrydaghs L">L Vrydaghs</name></author><author><name sortKey="De Maret, P" uniqKey="De Maret P">P De Maret</name></author><author><name sortKey="Xavier, P" uniqKey="Xavier P">P Xavier</name></author><author><name sortKey="Denham, T" uniqKey="Denham T">T Denham</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Raboin, L" uniqKey="Raboin L">L Raboin</name></author><author><name sortKey="Carreel, F" uniqKey="Carreel F">F Carreel</name></author><author><name sortKey="Noyer, J" uniqKey="Noyer J">J 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uniqKey="Tripathi J">J Tripathi</name></author><author><name sortKey="Tusiime, G" uniqKey="Tusiime G">G Tusiime</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perrier, X" uniqKey="Perrier X">X Perrier</name></author><author><name sortKey="De Langhe, E" uniqKey="De Langhe E">E De Langhe</name></author><author><name sortKey="Donohue, M" uniqKey="Donohue M">M Donohue</name></author><author><name sortKey="Lentfer, C" uniqKey="Lentfer C">C Lentfer</name></author><author><name sortKey="Vrydaghs, L" uniqKey="Vrydaghs L">L Vrydaghs</name></author><author><name sortKey="Bakry, F" uniqKey="Bakry F">F Bakry</name></author><author><name sortKey="Carreel, F" uniqKey="Carreel F">F Carreel</name></author><author><name sortKey="Hippolyte, I" uniqKey="Hippolyte I">I Hippolyte</name></author><author><name sortKey="Horry, J P" uniqKey="Horry J">J-P Horry</name></author><author><name sortKey="Jenny, C" uniqKey="Jenny C">C Jenny</name></author><author><name sortKey="Lebot, V" uniqKey="Lebot V">V Lebot</name></author><author><name sortKey="Risterucci, A M" uniqKey="Risterucci A">A-M Risterucci</name></author><author><name sortKey="Tomekpe, K" uniqKey="Tomekpe K">K Tomekpe</name></author><author><name sortKey="Doutrelepont, H" uniqKey="Doutrelepont H">H Doutrelepont</name></author><author><name sortKey="Ball, T" uniqKey="Ball T">T Ball</name></author><author><name sortKey="Manwaring, J" uniqKey="Manwaring J">J Manwaring</name></author><author><name sortKey="De Maret, P" uniqKey="De Maret P">P De Maret</name></author><author><name sortKey="Denham, T" uniqKey="Denham T">T Denham</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Belgique</li><li>Malaisie</li></country><region><li>Province du Brabant flamand</li><li>Région flamande</li></region><settlement><li>Louvain</li></settlement><orgName><li>Katholieke Universiteit Leuven</li></orgName></list><tree><country name="Belgique"><region name="Région flamande"><name sortKey="Davey, Mark W" sort="Davey, Mark W" uniqKey="Davey M" first="Mark W" last="Davey">Mark W. Davey</name></region><name sortKey="Keulemans, Johan" sort="Keulemans, Johan" uniqKey="Keulemans J" first="Johan" last="Keulemans">Johan Keulemans</name></country><country name="Malaisie"><noRegion><name sortKey="Gudimella, Ranganath" sort="Gudimella, Ranganath" uniqKey="Gudimella R" first="Ranganath" last="Gudimella">Ranganath Gudimella</name></noRegion><name sortKey="Harikrishna, Jennifer Ann" sort="Harikrishna, Jennifer Ann" uniqKey="Harikrishna J" first="Jennifer Ann" last="Harikrishna">Jennifer Ann Harikrishna</name><name sortKey="Khalid, Norzulaani" sort="Khalid, Norzulaani" uniqKey="Khalid N" first="Norzulaani" last="Khalid">Norzulaani Khalid</name><name sortKey="Sin, Lee Wan" sort="Sin, Lee Wan" uniqKey="Sin L" first="Lee Wan" last="Sin">Lee Wan Sin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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