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

Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J - BMC Genomics (2013)

Bottom Line: 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.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 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. mark.davey@biw.kuleuven.be.

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.

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Overview of distribution of mapped 100 bp RNA reads across individual chromosomes of the combined A- and B-genome sets. RNA reads derived from fruit of each cultivar individually mapped. Ygi, AAA cultivar ‘Yangambi-km5’; GM, AAA cultivar ‘Gros Michel’; Mbk-3, AAB cultivar ‘Mbouroukou-3’; Btd, AAB cultivar ‘Batard’; Iho, AAB cultivar ‘Iholena lele’; Karat, diploid Fe’I cultivar ‘Karat’.
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Figure 4: Overview of distribution of mapped 100 bp RNA reads across individual chromosomes of the combined A- and B-genome sets. RNA reads derived from fruit of each cultivar individually mapped. Ygi, AAA cultivar ‘Yangambi-km5’; GM, AAA cultivar ‘Gros Michel’; Mbk-3, AAB cultivar ‘Mbouroukou-3’; Btd, AAB cultivar ‘Batard’; Iho, AAB cultivar ‘Iholena lele’; Karat, diploid Fe’I cultivar ‘Karat’.

Mentions: As expected, the proportion of mapped 100 bp reads generally decreased with the predicted genetic distance of the cultivar from the reference A-genome, with ‘Karat’ (Fe’i) having the lowest value (74.8%) and ‘Yangambi-km5’ (AAA) having the highest proportion at 90.7% (Additional file 8: Table S8). Although reads from the AAA cultivars should theoretically map only to the A-genome, we can see that 23 – 27% of the reads from the two triploid AAA cultivars preferentially map (have a higher homology) to regions of the B-genome, despite the apparent absence of a B-genome in these cultivars (Figure 4, Additional file 9: Table S9). This could reflect the different sub-group origins of these M. acuminata genomes. i.e. ‘Yangambi-km5’ , and ‘Gros Michel’ belong to the ‘Ibota’ and ‘Gros Michel’ M. acuminata subgroups respectively, whereas the reference ‘Pahang’ belongs to the Malaccencis subgroup. Also, differences between orthologous genes in these M. acuminata subgroup genomes could mean that only minor sequence divergence from ‘Pahang’ could lead to higher homology to the orthologous sequences present in the B-genome, particularly for highly-conserved ‘core’ genes. Alternatively the presence of foreign chromosomal fragments as a result of historical recombinations between the A- and B- genomes as demonstrated by Jeridi et al. [13], could result in the mapping of reads/transcripts to homologous regions of the homeologous B-chromosomes. By comparison, in the AAB plantains, we see that 36.4 – 40.7% of the reads from the three plantains preferentially map to the B-genome. This is in accordance with the presence of a single B-genome in these triploids, and confirms the utility of our PKW consensus B-genome sequence for this type of study. Finally, reads from the diploid Fe’i banana cultivar (Musa, Australimusa, 2n = 20), and a species which is probably most closely related to the wild species M. maclayi, M. peekelii and M. lolodensis[78], mapped nearly equally to both genomes (48.6 : 51.4, A B).


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

Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J - BMC Genomics (2013)

Overview of distribution of mapped 100 bp RNA reads across individual chromosomes of the combined A- and B-genome sets. RNA reads derived from fruit of each cultivar individually mapped. Ygi, AAA cultivar ‘Yangambi-km5’; GM, AAA cultivar ‘Gros Michel’; Mbk-3, AAB cultivar ‘Mbouroukou-3’; Btd, AAB cultivar ‘Batard’; Iho, AAB cultivar ‘Iholena lele’; Karat, diploid Fe’I cultivar ‘Karat’.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852598&req=5

Figure 4: Overview of distribution of mapped 100 bp RNA reads across individual chromosomes of the combined A- and B-genome sets. RNA reads derived from fruit of each cultivar individually mapped. Ygi, AAA cultivar ‘Yangambi-km5’; GM, AAA cultivar ‘Gros Michel’; Mbk-3, AAB cultivar ‘Mbouroukou-3’; Btd, AAB cultivar ‘Batard’; Iho, AAB cultivar ‘Iholena lele’; Karat, diploid Fe’I cultivar ‘Karat’.
Mentions: As expected, the proportion of mapped 100 bp reads generally decreased with the predicted genetic distance of the cultivar from the reference A-genome, with ‘Karat’ (Fe’i) having the lowest value (74.8%) and ‘Yangambi-km5’ (AAA) having the highest proportion at 90.7% (Additional file 8: Table S8). Although reads from the AAA cultivars should theoretically map only to the A-genome, we can see that 23 – 27% of the reads from the two triploid AAA cultivars preferentially map (have a higher homology) to regions of the B-genome, despite the apparent absence of a B-genome in these cultivars (Figure 4, Additional file 9: Table S9). This could reflect the different sub-group origins of these M. acuminata genomes. i.e. ‘Yangambi-km5’ , and ‘Gros Michel’ belong to the ‘Ibota’ and ‘Gros Michel’ M. acuminata subgroups respectively, whereas the reference ‘Pahang’ belongs to the Malaccencis subgroup. Also, differences between orthologous genes in these M. acuminata subgroup genomes could mean that only minor sequence divergence from ‘Pahang’ could lead to higher homology to the orthologous sequences present in the B-genome, particularly for highly-conserved ‘core’ genes. Alternatively the presence of foreign chromosomal fragments as a result of historical recombinations between the A- and B- genomes as demonstrated by Jeridi et al. [13], could result in the mapping of reads/transcripts to homologous regions of the homeologous B-chromosomes. By comparison, in the AAB plantains, we see that 36.4 – 40.7% of the reads from the three plantains preferentially map to the B-genome. This is in accordance with the presence of a single B-genome in these triploids, and confirms the utility of our PKW consensus B-genome sequence for this type of study. Finally, reads from the diploid Fe’i banana cultivar (Musa, Australimusa, 2n = 20), and a species which is probably most closely related to the wild species M. maclayi, M. peekelii and M. lolodensis[78], mapped nearly equally to both genomes (48.6 : 51.4, A B).

Bottom Line: 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.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 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. mark.davey@biw.kuleuven.be.

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.

Show MeSH
Related in: MedlinePlus