Journal
JOURNAL OF CRUSTACEAN BIOLOGY
Volume 40, Issue 1, Pages 76-81Publisher
OXFORD UNIV PRESS
DOI: 10.1093/jcbiol/ruz074
Keywords
genome characteristics; next generation sequencing (NGS)
Categories
Funding
- National Program for Support of Top-Notch Young Professionals
- Sail Plan Program for the Introduction of Outstanding Talents of Guangdong Province, China
- Program for Innovation and Enhancement of School of Department of Education of Guangdong Province [2017KCXTD014]
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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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