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On-line Access: 2013-01-08

Received: 2012-08-16

Revision Accepted: 2012-11-09

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Journal of Zhejiang University SCIENCE B 2013 Vol.14 No.1 P.58-67

http://doi.org/10.1631/jzus.B1200219


De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology*#


Author(s):  Wei Wang, Cai-yan Li, Chu-tian Ge, Lei Lei, You-ling Gao, Guo-ying Qian

Affiliation(s):  Zhejiang Provincial Top Key Discipline of Modern Microbiology and Application, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China; more

Corresponding email(s):   qiangy@zwu.edu.cn

Key Words:  Pelodiscus sinensis, Illumina RNA-Seq, Transcriptome, Gene expression


Wei Wang, Cai-yan Li, Chu-tian Ge, Lei Lei, You-ling Gao, Guo-ying Qian. De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology*#[J]. Journal of Zhejiang University Science B, 2013, 14(1): 58-67.

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author="Wei Wang, Cai-yan Li, Chu-tian Ge, Lei Lei, You-ling Gao, Guo-ying Qian",
journal="Journal of Zhejiang University Science B",
volume="14",
number="1",
pages="58-67",
year="2013",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B1200219"
}

%0 Journal Article
%T De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology*#
%A Wei Wang
%A Cai-yan Li
%A Chu-tian Ge
%A Lei Lei
%A You-ling Gao
%A Guo-ying Qian
%J Journal of Zhejiang University SCIENCE B
%V 14
%N 1
%P 58-67
%@ 1673-1581
%D 2013
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1200219

TY - JOUR
T1 - De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology*#
A1 - Wei Wang
A1 - Cai-yan Li
A1 - Chu-tian Ge
A1 - Lei Lei
A1 - You-ling Gao
A1 - Guo-ying Qian
J0 - Journal of Zhejiang University Science B
VL - 14
IS - 1
SP - 58
EP - 67
%@ 1673-1581
Y1 - 2013
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1200219


Abstract: 
The soft-shelled turtle Pelodiscus sinensis is a high-profile turtle species because of its nutritional and medicinal value in Asian countries. However, little is known about the genes that are involved in formation of their nutritional quality traits, especially the molecular mechanisms responsible for unsaturated fatty acid and collagen biosynthesis. In the present study, the transcriptomes from six tissues from Pelodiscus sinensis were sequenced using an Illumina paired-end sequencing platform. We obtained more than 47 million sequencing reads and 73 954 unigenes with an average size of 754 bp by de-novo assembly. In total, 55.19% of the unigenes (40 814) had significant similarity with proteins in the National Center of Biotechnology Information (NCBI) non-redundant protein database and Swiss-Prot database (E-value <10−5). Of these annotated unigenes, 9 156 and 11 947 unigenes were assigned to 52 gene ontology categories (GO) and 25 clusters of orthologous groups (COG), respectively. In total, 26 496 (35.83%) unigenes were assigned to 242 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we found a number of highly expressed genes involved in the regulation of P. sinensis unsaturated fatty acid biosynthesis and collagen formation, including desaturases, growth factors, transcription factors, and extracellular matrix components. Our data represent the most comprehensive sequence resource available for the Chinese soft-shelled turtle and could provide a basis for new research on this turtle as well as the molecular genetics and functional genomics of other terrapins. To our knowledge, we report for the first time, the large-scale RNA sequencing (RNA-Seq) of terrapin animals and would enrich the knowledge of turtles for future research.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

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[53]List of electronic supplementary materials

[54]Table S1 KEGG pathways for Pelodiscus sinensis

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