Lv Jianjian, Liu Ping, Gao Baoquan, Wang Yu, Wang Zheng, Chen Ping, Li Jian
Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
PLoS One. 2014 Apr 10;9(4):e94055. doi: 10.1371/journal.pone.0094055. eCollection 2014.
The swimming crab, Portunus trituberculatus, is an important farmed species in China, has been attracting extensive studies, which require more and more genome background knowledge. To date, the sequencing of its whole genome is unavailable and transcriptomic information is also scarce for this species. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for major tissues of Portunus trituberculatus by the Illumina paired-end sequencing technology.
Total RNA was isolated from eyestalk, gill, heart, hepatopancreas and muscle. Equal quantities of RNA from each tissue were pooled to construct a cDNA library. Using the Illumina paired-end sequencing technology, we generated a total of 120,137 transcripts with an average length of 1037 bp. Further assembly analysis showed that all contigs contributed to 87,100 unigenes, of these, 16,029 unigenes (18.40% of the total) can be matched in the GenBank non-redundant database. Potential genes and their functions were predicted by GO, KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes with fundamental roles in growth and muscle development, including actin, myosin, tropomyosin, troponin and other potentially important candidate genes were identified for the first time in this specie. Furthermore, 22,673 SSRs and 66,191 high-confidence SNPs were identified in this EST dataset.
The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in Portunus trituberculatus. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will be essential for accelerating aquaculture breeding programs with this species.
三疣梭子蟹是中国重要的养殖蟹类，吸引了广泛研究，这需要越来越多的基因组背景知识。迄今为止，该物种的全基因组测序尚未完成，转录组信息也很匮乏。在本研究中，我们采用Illumina双末端测序技术进行了从头转录组测序，以生成三疣梭子蟹主要组织的全面转录本数据集。
从眼柄、鳃、心脏、肝胰腺和肌肉中分离出总RNA。将每个组织等量的RNA混合构建cDNA文库。利用Illumina双末端测序技术，我们共生成了120,137个转录本，平均长度为1037 bp。进一步的组装分析表明，所有重叠群构成了87,100个单基因，其中16,029个单基因（占总数的18.40%）可在GenBank非冗余数据库中匹配。通过GO、KEGG通路映射和COG分析预测了潜在基因及其功能。基于我们的序列分析和已发表的文献，首次在该物种中鉴定出许多在生长和肌肉发育中起重要作用的假定基因，包括肌动蛋白、肌球蛋白、原肌球蛋白、肌钙蛋白和其他潜在重要的候选基因。此外，在该EST数据集中鉴定出22,673个SSR和66,191个高可信度SNP。
该转录组为三疣梭子蟹的功能基因组学资源和未来生物学研究提供了宝贵的新数据。这些数据还将指导未来的功能研究，以操纵或选择影响生长的基因，这些基因应在水产养殖育种计划中找到实际应用。本研究中鉴定的分子标记将为未来的遗传连锁和数量性状位点分析提供物质基础，对于加速该物种的水产养殖育种计划至关重要。
