Wang Jiajia, Ge Qianqian, Li Jitao, Gao Haiyu, Li Jian, Zhao Fazhen
Fisheries College, Ocean University of China, Qingdao, 266003, People's Republic of China.
Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China.
Genes Genomics. 2018 Feb;40(2):207-215. doi: 10.1007/s13258-017-0571-2. Epub 2017 Nov 2.
The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of 14273 SSR loci were identified from 130,082 assembled transcripts, with 6590 pairs of PCR primers designed. A total of 12,155 sequences containing SSR were predicted; and 2764 (22.74%) transcripts had significant matches to the NCBI non redundant protein (Nr) database. 11,563 transcripts were assigned into gene ontology (GO) categories. A set of 200 primers selected randomly were synthesized, of which 152 (76.0%) were successfully amplified. Further test with 60 pairs of polymorphic SSR primers to evaluate the genetic diversity of 30 wild populations and 43 loci were polymorphic, which had a polymorphic information content between 0.204 and 0.911. The results enriched genomic resources of E. carinicauda and provided powerful information for future conservation and breeding researches.
脊尾白虾（Exopalaemon carinicauda）是中国东部主要的海水养殖商业品种之一。然而，由于缺乏基因组信息，目前可用的分子标记有限，这阻碍了其遗传和育种研究。在本研究中，我们通过Illumina Hiseq 2500平台从转录组序列中鉴定了新的简单序列重复序列。从130,082条组装转录本中总共鉴定出14273个SSR位点，设计了6590对PCR引物。总共预测了12155个包含SSR的序列；2764个（22.74%）转录本与NCBI非冗余蛋白质（Nr）数据库有显著匹配。11563个转录本被归入基因本体（GO）类别。随机选择并合成了一组200对引物，其中152对（76.0%）成功扩增。用60对多态性SSR引物进一步测试以评估30个野生群体的遗传多样性，43个位点具有多态性，其多态信息含量在0.204至0.911之间。这些结果丰富了脊尾白虾的基因组资源，并为未来的保护和育种研究提供了有力信息。
