Genomic data of the soft shell turtle (Pelodiscus sinensis).
Dataset type: Genomic
Data released on May 23, 2014
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 soft shell turtle (Pelodiscus sinensis). GigaScience Database. http://dx.doi.org/10.5524/100086
The soft shell turtle can reach a carapace length of 1 ft (0.30 m). It has webbed feet for swimming. They are called "softshell" because their carapace lacks horny scutes (scales). The carapace is leathery and pliable, particularly at the sides. It is commercially farmed in vast numbers for the food trade.
DNA from the soft shell turtle was collected in Japan. We sequenced the 2.21 Gb genome to a depth of approximately 105.6 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 221.7 Gb, with the contig and scaffold N50 values of 21.9 kb and 3.33 Mb respectively. We identified 19,327 protein-coding genes with an mean length of ~1500bp. 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).
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Accessions (data generated as part of this study):
Accessions (data referenced by this study):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|Soft Shell Turtle Daiwa-1||13735||Chinese softshell turtle||Chinese soft-shelled turtle||Pelodiscus sinensis|| Geographic location (country and/or sea,region):Ja...|
Geographic location (latitude and longitude):not r...
... Geographic location (country and/or sea,region):Japan, Saga
Geographic location (latitude and longitude):not recorded
IUCN Red List:VU