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). It was published in version 1:

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.
 
The latest version corresponds to the version 4 (version 3 was skipped) described in
 
Belser, C., Baurens, FC., Noel, B. et al. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. Commun Biol 4, 1047 (2021). https://doi.org/10.1038/s42003-021-02559-3

 

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Infraspecific Taxon
subspecies malaccensis
Organism Image
Publication
  1. Belser C, Baurens FC, Noel B, Martin G, Cruaud C, Istace B, Yahiaoui N, Labadie K, Hřibová E, Doležel J, Lemainque A, Wincker P, D'Hont A, Aury JM. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing.. Communications biology. 2021 09 07; 4(1):1047.
  2. 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.
  3. 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
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
InterPro (5.48-83.0) Annotations of DH PahangInterProScanMar 1st, 2021
Whole Genome Annotation of M. acuminata DH Pahang (v4.3)GmoveMar 23rd, 2021
InterPro (5.48-83.0) Annotations of DH Pahang (v4.3)InterProScanApr 18th, 2021
Statistics

Statistics of genome assembly

Version 1

Version 2

Version 3

Estimated genome size (Mb)

523

523

523

Assembled genome size (Mb)

472.2

450.6

485

Unknown bases (Ns, %)

17.3

10

0.17

Contig (scaffold) N50 (Mb)

0.028 (1.3)

0.043 (3)

32

Chromosome Number

11+ 1

11 + 1

11

Contig (scaffold) number

24,425 (7,513)

24,425 (1,532)

124

Gene number

36,542

35,276

36,769