East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China.
Sci Rep. 2019 Feb 27;9(1):2910. doi: 10.1038/s41598-019-39070-z.
Scylla paramamosain is one of the most economically important crabs in China. In this study, the first genome survey sequencing of this crab was performed, and the results revealed that the estimated genome size was 1.21 Gb with high heterozygosity (1.3%). Then, RAD technology was used to construct a high-resolution linkage map for this species. A total of 24,444 single nucleotide polymorphism (SNP) makers were grouped into 47 linkage groups. The total length of the linkage groups was 3087.53 cM with a markers interval of 0.92 cM. With the aid of transcriptome and genome scaffold data, 4,271 markers were linked to genes, including several important growth-related genes such as transforming growth factor-beta regulator I, immune related-gene C-type lectin and ecdysone pathway gene broad-complex-like protein. Further, 442 markers, representing 279 QTLs, associated with 24 traits were identified, and of these markers, 78 were linked to genes. Some interesting genes, such as dedicator of cytokinesis protein 3, tenascin-X and DNA helicase MCM8, were believed to have important relationship with specific traits and merit further exploration. The results of this study will accelerate the genetic improvement and genome sequencing analysis of the mud crab.
拟穴青蟹是中国最重要的经济蟹类之一。本研究对该蟹进行了首次基因组调查测序，结果表明其估计基因组大小为 1.21Gb，杂合度较高（1.3%）。随后，利用 RAD 技术构建了该物种的高分辨率连锁图谱。共获得 24444 个单核苷酸多态性（SNP）标记，分为 47 个连锁群。连锁群总长度为 3087.53cM，标记间隔为 0.92cM。借助转录组和基因组支架数据，将 4271 个标记与基因相连，其中包括转化生长因子-β调节剂 I、免疫相关基因 C 型凝集素和蜕皮激素途径基因宽复合体样蛋白等几个重要的生长相关基因。进一步鉴定出 442 个与 24 个性状相关的标记，代表 279 个 QTL，其中 78 个标记与基因相连。一些有趣的基因，如胞质分裂蛋白 3、腱生蛋白 X 和 DNA 解旋酶 MCM8，被认为与特定性状有重要关系，值得进一步研究。本研究结果将加速泥蟹的遗传改良和基因组测序分析。
