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Data released on May 23, 2014

Genomic

Genomic data of the green sea turtle (Chelonia mydas).

Wang,Z; Pascual-Anaya,J; Zadissa,A; Li,W; Niimura,Y; Huang,Z; Li,C; White,S; Xiong,Z; Fang,D; Wang,B; Ming,Y; Chen,Y; Zheng,Y; Kuraku,S; Pignatelli,M; Herrero,J; Beal,K; Nozawa,M; Li,Q; Wang,J; Zhang,H; Yu,L; Shigenobu,S; Wang,J; Liu,J; Flicek,P; Searle,S; Wang,J; Kuratani,S; Yin,Y; Aken, B; Zhang, G; Irie, N (2014): Genomic data of the green sea turtle (Chelonia mydas). GigaScience Database. http://dx.doi.org/10.5524/100085 RIS BibTeX Text

Green turtles are long-lived and may take up to 59 years to reach sexual maturity. Undertaking tremendous feats of navigation, adults return to the same beach to breed each season.
DNA from the green sea turtle was collected in Hong Kong. We sequenced the 2.24 Gb genome to a depth of approximately 82.3 X with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb,20kb and 40kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 180.94 Gb, with the contig and scaffold N50 values of 20.4 kb and 3.78 Mb respectively. We identified 19,633 protein-coding genes with an mean length of 1456 bp.Experimental procedures and animal care were conducted in strict accordance with guidelines approved by the RIKEN Animal Experiments Committee (Approval IDs H14-23 and H16-10).

Related manuscripts:

doi:10.1038/ng.2615 (PubMed: 23624526)

Accessions (data included in GigaDB):

PROJECT: PRJNA104937
SRA: SRP011574

Projects:


Samples:

Sample ID Taxonomic ID Common name Genbank name Scientific name Sample attributes
SRS301450 8469 Chelonia mydas green seaturtle tissue_type="blood"
ploidy="diploid"
geographical_location(country_and/or_region)="Hong Kong"
geographical_location(latitude_and_longitude)="not recorded"
sex="female"
IUNC_Red_List="Endangered"

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

Cmyd.v1.1.gff

SRS301450 annotation GFF 2 8 1171062411.17 MB 2013-02-20

Cmyd.v1.1.fa

SRS301450 Genome assembly FASTA 3 10 22434345162.09 GB 2013-02-20

Cmyd.v1.1.cds

SRS301450 coding sequence FASTA 2 8 2961386128.24 MB 2013-02-20

Cmyd.v1.1.pep

SRS301450 protein sequnce FASTA 2 8 1070995110.21 MB 2013-02-20

README.txt

Readme TEXT 1 3 3450.34 KB 2013-02-20