Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea

Chuankun Zhu; Lei Zhang; Huaiyu Ding; Zhengjun Pan

doi:10.7717/peerj.7770

Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea

PeerJ. 2019 Oct 22:7:e7770. doi: 10.7717/peerj.7770. eCollection 2019.

Authors

Chuankun Zhu^{1

2}, Lei Zhang^{2

3}, Huaiyu Ding^{1

2}, Zhengjun Pan^{1

2}

Affiliations

¹ Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai'an, Jiangsu, China.
² Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China.
³ Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai'an City, Huai'an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an, China.

Abstract

The Asian clam, Corbicula fluminea, is a commonly consumed small freshwater bivalve in East Asia. However, available genetic information of this clam is still limited. In this study, the transcriptome of female C. fluminea was sequenced using the Illumina HiSeq 2500 platform. A total of 89,563 unigenes were assembled with an average length of 859 bp, and 36.7% of them were successfully annotated. Six members of Sox gene family namely SoxB1, SoxB2, SoxC, SoxD, SoxE and SoxF were identified. Based on these genes, the divergence time of C. fluminea was estimated to be around 476 million years ago. Furthermore, a total of 3,117 microsatellites were detected with a distribution density of 1:12,960 bp. Fifty of these microsatellites were randomly selected for validation, and 45 of them were successfully amplified with 31 polymorphic ones. The data obtained in this study will provide useful information for future genetic and genomic studies in C. fluminea.

Keywords: Corbicula fluminea; Microsatellite; Sox gene family; Transcriptome.

Grants and funding

This study was supported by the Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai’an City, Huai’an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences (HASBSY201303) and the Start-up Funds of Scientific Research from Huaiyin Normal University (31ZCK00). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.