Genome survey and identification of polymorphic microsatellites provide genomic information and molecular markers for the red crab Charybdis feriatus (Linnaeus, 1758) (Decapoda: Brachyura: Portunidae)
文献类型： 外文期刊
作者： Fang, Shaobin 1 ; Wu, Renxie 3 ; Shi, Xi 1 ; Zhang, Yin 1 ; Ikhwanuddin, Mhd 4 ; Lu, Jianxue 5 ; Xia, Lianjun 5 ; Wu, Qin 1 ;
作者机构： 1.Shantou Univ, Guangdong Prov Key Lab Marine Biotechnol, Shantou 515063, Peoples R China
2.Shantou Univ, STU UMT Joint Shellfish Res Lab, Shantou 515063, Peoples R China
3.Guangdong Ocean Univ, Coll Fisheries, Zhanjiang 524088, Peoples R China
4.Univ Malaysia Terengganu, Inst Trop Aquaculture, Kuala Terengganu 21030, Malaysia
5.Chinese Acad Fishery Sci, East China Sea Fisheries Res Inst, Shanghai 200090, Peoples R China
关键词： genome characteristics; next generation sequencing (NGS)
期刊名称：JOURNAL OF CRUSTACEAN BIOLOGY （ 影响因子：1.43； 五年影响因子：1.501 ）
ISSN： 0278-0372
年卷期： 2020 年 40 卷 1 期
页码：
收录情况： SCI
摘要： We conducted a whole genome survey in the portunid crab Charybdis feriatus (Linnaeus, 1758) using Illumina sequencing platform and developed a set of polymorphic microsatellite loci. A total of 117.7 Gb of clean reads were generated, with 74x coverage of the estimated genome size of 1.4 Gb. The GC content, heterozygosity rate, and repeat sequence rate of the genome were estimated to be 40%, 1.1%, and 51%, respectively. A total of 3,779,209 microsatellites were identified from the genome. Sixty microsatellite loci were evaluated in a wild population of 40 individuals. As a result, 14 polymorphic microsatellite loci (23.3%) were obtained. The number of alleles (3 to 15), polymorphism information content (0.365 to 0.884), observed heterozygosity (0.050 to 0.975), and expected heterozygosity (0.450 to 0.907) per locus averaged 6.8, 0.652, 0.691, and 0.707, respectively. We show that the genome of C. feriatus has a high heterozygosity and repeat sequence rates, and provide a novel insight into the genome profile of marine crabs. The genetic markers developed in this study are potentially useful for studies on population dynamics and conservation genetics of C. feriatus and other species of brachyuran crabs.
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