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Data released on May 23, 2014

Genomic data of the soft shell turtle (Pelodiscus sinensis).

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

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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Read the peer-reviewed publication(s):

Wang, Z., Pascual-Anaya, J., Zadissa, A., Li, W., Niimura, Y., Huang, Z., … Irie, N. (2013). The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics, 45(6), 701–706. doi:10.1038/ng.2615 (PubMed: 23624526)

Accessions (data included in GigaDB):

BioProject: PRJNA68233

Accessions (data not in GigaDB):

DRA: DRA000567
DRA: DRA000639



Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Soft Shell Turtle Daiwa-113735Chinese softshell turtleChinese soft-shelled turtlePelodiscus sinensis Geographic location (country and/or sea,region):Ja...
Geographic location (latitude and longitude):not r...
Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings


File Description
Sample ID
Data Type
File Format
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
Soft Shell Turtle Daiwa-1Coding sequenceFASTA29.67 MB2013-02-20
Soft Shell Turtle Daiwa-1AnnotationGFF15.04 MB2013-02-20
Soft Shell Turtle Daiwa-1Protein sequenceFASTA10.84 MB2013-02-20
Soft Shell Turtle Daiwa-1Sequence assemblyFASTA2.08 GB2013-02-20
ReadmeTEXT0.34 KB2013-02-20
Displaying 1-5 of 5 File(s).

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