Genome survey, high-resolution genetic linkage map construction, growth-related quantitative trait locus (QTL) identification and gene location in Scylla paramamosain

Abstract

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.

Mapping and validation of sex-linked SNP markers in the swimming crab Portunus trituberculatus

“…In the present study, three genetic linkage maps were constructed for P. trituberculatus using 2b-RAD, covering a total distance of 2,960.5 cM, 2,728.3 cM and 3,237.7 cM for sex-averaged, female, and male maps, respectively. The average marker interval of the sex-averaged map was 0.47 cM, which was comparable to previous reports in many crustacean species (0.4 -1.51 cM), including Litopenaeus vannamei (0.7 cM, Yu et al, 2015); Penaeus monodon (1.51 cM, Guo et al, 2019); Scylla paramamosain (0.81 -0.92 cM, Waiho et al, 2019;Zhao et al, 2019); Eriocheir sinensis (0.49 -0.81 cM, Cui et al, 2015;Qiu et al, 2017) and P. trituberculatus (0.51 cM, Lv et al, 2017). The high resolution of the new SNP-based linkage map will facilitate further studies of detailed QTL mapping.…”

A chromosome‐level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean

“…The insert size distribution of one paired‐end library was consistent with the estimated insert sizes (Figure S2). Genome contiguity was also confirmed via correlation analysis between the assembly and the high‐density linkage map (Zhao et al, 2019). Pearson's correlation between assembly distances and genetic distances ranged from 0.740 to 0.967, with a mean value of 0.853 (Figure S3).…”

“…The genome size estimated on the basis of the k ‐mer distribution was greatly affected by k ‐mer size. Previously, the mud crab genome size was estimated to be 1.21 Gb, with a k ‐mer size of 17 (Zhao et al, 2019). In our study, the mud crab genome size ranged from 1.2 to 1.6 Gb with different k ‐mer sizes.…”

“…The mud crab chromosomes were generated by the integration of Hi‐C data and a high‐density genetic linkage map (Zhao et al, 2019). HiCUP (Wingett et al, 2015) was used to process the Hi‐C reads and retain valid pairs.…”

Effects of berberine hydrochloride on immune response in the crab Charybdis japonica

“…For example, transcriptomics technology has revealed the biological mechanism behind multiple pathogenic microorganisms affecting crustaceans, such as WSSV and Vibrio species. Many immune-related genes and polymorphic microsatellite markers have been identified in crabs [12][13][14], providing important genetic information, essential for further understanding the molecular mechanisms of innate immunity.…”