Summary
Abbreviation
DH-Pahang
Genus
Musa
Species
acuminata
Common Name
DH Pahang
Description

DH-Pahang (doi:10.18730/9MZSP) is a doubled-haploid of the germplasm collection accession named Pahang (doi:10.18730/9K93B). 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.

DH stands for Doubled Haploid which refers to the induced doubling of the chromosomes in a haploid cell (which has one set of chromosomes). In this case, the haploid cell was pollen. The doubled-haploid (DH Pahang) was produced through anther culture and spontaneous chromosomes doubling.
 

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.

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Infraspecific Taxon
subspecies malaccensis
Organism Image
Publication
  1. Martin G, Baurens FC, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Doležel J, Aury JM, Alberti A, Carreel F, D'Hont A. Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.. BMC genomics. 2016 Mar 16; 17:243.
  2. D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quétier F, Yahiaoui N, Wincker P. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.. Nature. 2012 Aug 09; 488(7410):213-7.
Analyses
NameProgramDate Constructed
InterPro (5.34) Annotations of DH PahangInterProScanMay 15th, 2019
Whole Genome Annotation of M. acuminata DH Pahang (v2)Consensus annotationMar 28th, 2016
Whole Genome Assembly of M. acuminata DH Pahang (v2)8 successive steps based on Scaffremodler and ScaffhunterOct 28th, 2019
OrthofinderDiamond, mafft, fasttreeNov 11th, 2019
Statistics
Statistics of genome assembly

Value

Estimated genome size (Mb)

594

Assembled genome size (Mb)

450.6

Unknown bases (Ns, Mb)

 

Contig N50 (Mb)

 

Scaffold N50 (Mb)

3.05

GC_rate (%)

 

Gene number

35,264