Help Login Create account

Data released on February 28, 2014

Genomic

Genomic data of the chickpea (Cicer arietinum).

Varshney,RK; Song,C; Saxena,RK; Azam,S; Yu,S; Sharpe,AG; Cannon,S; Baek,J; Rosen,BD; Taran,B; Millan,T; Zhang,X; Ramsay,LD; Iwata,A; Wang,Y; Nelson,W; Farmer,AD; Gaur,PM; Soderlund,C; Penmetsa,RV; Xu,C; Bharti,AK; He,W; Winter,P; Zhao,S; Hane,JK; Carrasquilla-Garcia,N; Condie,JA; Upadhyaya,HD; Luo,M; Thudi,M; Gowda,CLL; Singh,NP; Lichtenzveig,J; Gali,KK; Rubio,J; Nadarajan,N; Dolezel,J; Bansal,KC; Xu,X; Edwards,D; Zhang,G; Kahl,G; Gil,J; Singh,KB; Datta,SK; Jackson,SA; Wang, J; Cook, DR (2014): Genomic data of the chickpea (Cicer arietinum). GigaScience Database. http://dx.doi.org/10.5524/100076 RIS BibTeX Text

Chickpea (Cicer arietinum) is one of the world's most consumed pulses. The Chickpea plant has finely divided leaves, giving it a feathery appearance. The pods are oblong (2 to 3 by 1 to 2 cm) and contain one or two beaked seeds which may be white, yellow, red, brown, or nearly black. They do well in a cool, dry climate and are grown in India as a winter crop.
The draft of the chickpea genome is based on genotype CDC Frontier, a Canadian kabuli chickpea variety.

DNA from the chickpea was collected and e sequenced the 0.74 Gb genome to a depth of approximately 207 x with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 153 Gb, with the contig and scaffold N50 values of 645 kb and 39.9 Mb respectively. We identified 28,256 protein-coding genes with an mean coding length of 1,166 bp.

Related manuscripts:

doi:10.1038/nbt.2491

Accessions (data included in GigaDB):

BioProject: PRJNA175619

Samples:

Sample ID Taxonomic ID Common name Genbank name Scientific name Sample attributes
Chickpea-CDC Frontier 3827 Cicer arietinum chickpea Cicer arietinum tissue_type="etiolated seedlings"
ploidy="diploid"
geographical_location(country_and/or_region)="not recorded"
geographical_location(latitude_and_longitude)="not recorded"
cultivar="CDC Frontier"

Files (FTP site) (Aspera):Aspera user name: gigadb , password: gigadb Table Settings
Items per page:

File Name Sample ID File Type File Format Size Release Date

README.txt

Readme TEXT 1 3 5220.51 KB 2014-02-28

Cicer_arietinum_GA_v1.0.fa

Chickpea-CDC Frontier Genome assembly FASTA 2 9 537799657512.89 MB 2014-02-28

Cicer_arietinum_GA_v1.0.gene.cds.fa

Chickpea-CDC Frontier coding sequence FASTA 2 8 3480958733.2 MB 2014-02-28

Cicer_arietinum_GA_v1.0.gene.gff

Chickpea-CDC Frontier annotation GFF 2 7 98638169.41 MB 2014-02-28

Cicer_arietinum_GA_v1.0.gene.pep.fa

Chickpea-CDC Frontier protein sequnce FASTA 2 8 1314995612.54 MB 2014-02-28