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Overview
 DH-Pahang is a doubled-haploid of the germplasm collection accession named Pahang (2n=22). Pahang was collected in Malaysia’s Pahang province in the late 1940s. It is a wild accession that belongs to subspecies Musa acuminata ssp. malaccensis, whose genetic signature is commonly found in dessert and cooking bananas. The Musa acuminata reference genome sequence results from collaboration between Genoscope and CIRAD (UMR AGAP) funded by ANR. The sequence was analyzed in collaboration with several teams within the Global Musa Genomics Consortium (GMGC) and was published as version 1 in:
D’Hont A, Denoeud F, Aury JM., Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 10.1038/nature11241.
The reference sequence was then improved by a combination of methods and datasets, leading the release of the version 2 of the assembly and gene annotation, which are described in the following publication:
Martin G, Baurens FC, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Dolezel J, Aury JM, Alberti A, Carreel F, D’Hont A (2016) Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatic methods. BMC Genomics.
If you have any question, please don’t hesitate to contact us Assembly statistics version 1
1. Sequencing MethodGenomic sequence was generated using a whole genome shotgun approach using Sanger technology sequencing (ABI 3730xl) and next generation sequencers (Roche/454 GSFLX and Illumina GAIIx)
Table 1. Raw sequencing data overview. 2. Assembly MethodSanger and 454 were assembled with Newbler. We obtained 29,251 contigs that were linked into 7,513 scaffolds. The contig N50 was 28.3 kb, and the scaffold N50 was 1.3 Mb.
Table 2. Global statistics on the sequence of Musa acuminata (DH-Pahang) 3. Anchoring the assembly on a genetic map
180 individuals were derived from "Musa acuminata 'Pahang' self-fertilization and used to build the genetic map.
652 markers were used for the anchoring (589 SSRs + 63 DArt) 4. Genome Size / LociThe cumulative scaffold size was 472.9 Mb, about 10% smaller than the estimated genome size of 523 Mb.
Table 3. Genome Statistics. Assembly statistics version 2
1. Sequencing MethodGenomic sequence was generated using a whole genome shotgun approach using Sanger technology sequencing (ABI 3730xl) and next generation sequencers (Roche/454 GSFLX and Illumina GAIIx)
Table 1. Raw sequencing data overview. 2. Assembly MethodSanger and 454 were assembled with Newbler. We obtained 29,251 contigs that were linked into 7,513 scaffolds. The contig N50 was 28.3 kb, and the scaffold N50 was 1.3 Mb.
Table 2. Global statistics on the sequence of Musa acuminata (DH-Pahang) 3. Anchoring the assembly on a genetic map
268 individuals were derived from "Musa acuminata 'Pahang' self-fertilization and used to build the genetic map.
23,430 markers were used for the anchoring (609 SSRs + 75 DArt, 20,919 DArtSeq) 4. Genome Size / LociThe cumulative scaffold size was 450.8 Mb, about 13.8 % smaller than the estimated genome size of 523 Mb.
Table 3. Genome Statistics. Feature Browser
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