Aims To identify the intestinal microbial diversity in mud crab and to investigate the bacterial difference in the intestinal microbiology between wild crabs (WC), pond‐raised healthy and diseased crabs (DC). Methods and Results The intestinal microbial community of mud crab Scylla paramamosain from WC, pond‐raised healthy crabs (HC) and DC were examined by Denaturing Gradient Gel Electrophoresis (DGGE) and clone library analysis of 16S rDNA gene. Eight of 21 representative DGGE bands were affiliated with unidentified or unclassified bacteria. Vibrio, Pseudoalteromonas and Shewanella were also found from the DGGE gel. Analysis of clone libraries revealed that all sequenced clones were grouped into either of the following phyla: Proteobacteria, Firmicutes, Tenericutes, Bacteroidetes, Fusobacteria, Cyanobacteria and unidentified or unclassified bacteria. The phylotypes affiliated with Firmicutes were not found in DC library, yet DC had a little portion of Cyanobacteria which did not exist in both WC and HC library. Real‐time PCR showed that the abundance of the total bacterial load in WC were significantly three times higher than that in healthy and DC, the abundance of Bacteriodes in healthy and WC were as much four times, three times as that in DC, respectively. Conclusions Statistical analysis showed that the bacterial communities in intestine of the mud crab from these three populations were significantly different. The phylotypes of the Bacteriodes and Tenericutes were the dominant population in the gut of the mud crab. Significance and Impact of the Study This study demonstrated significant differences in the intestinal bacterial composition of three crab populations. This knowledge will increase our understanding of the effect of growth conditions on bacterial community composition in the crab gut and provide necessary data for further development of probiotic products for diseases prevention in crab farming.

The noble scallop Chlamys nobilis Reeve displays polymorphism in shell and muscle colors. Previous research showed that the orange scallops with orange shell and muscle had a significantly higher carotenoid content than the brown ones with brown shell and white muscle. There is currently a need to identify candidate genes associated with carotenoid-based coloration. In the present study, 454 GS-FLX sequencing of noble scallop transcriptome yielded 1,181,060 clean sequence reads, which were assembled into 49,717 isotigs, leaving 110,158 reads as the singletons. Of the 159,875 unique sequences, 11.84% isotigs and 9.35% singletons were annotated. Moreover, 3,844 SSRs and over 120,000 high confidence variants (SNPs and INDELs) were identified. Especially, one class B scavenge receptor termed SRB-like-3 was discovered to express only in orange scallops and absent in brown ones, suggesting a significant association with high carotenoid content. Down-regulation of SRB-like-3 mRNA by RNA interference remarkably decreased blood carotenoid, providing compelling evidence that SRB-like-3 is an ideal candidate gene controlling carotenoid deposition and determining orange coloration. Transcriptome analysis of noble scallop reveals a novel scavenger receptor significantly associated with orange scallop rich in carotenoid content. Our findings pave the way for further functional elucidation of this gene and molecular basis of carotenoid deposition in orange scallop.

Mud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is extremely essential in aquaculture. However, the sex determination mechanism is still unclear. Development of sex-specific genetic markers based on next-generation sequencing proved to be an effective tool for discovering sex determination system in various animals. Restriction-site associated DNA sequencing (RAD-seq) was employed to isolate sex-specific SNP markers for S. paramamosain. A total of 335.6 million raw reads were obtained from 20 individuals, of which 204.7 million were from 10 females and 130.9 million from 10 males. After sequence assembly and female-male comparison, 20 SNP markers were identified to be sex-specific. Furthermore, ten SNPs in a short sequence (285 bp) were confirmed heterozygous in females and homozygous in males in a large population by PCR amplification and sequencing. Subsequently, a female-specific primer was successfully designed according to the female-specific nucleotide which could amplify an expected band from females but not from males. Thus, a rapid and effective method for molecular sexing in S. paramamosain was developed, meanwhile, this method could successfully identify the sex of S. tranquebarica and S. serrata. Finally, nine and four female-specific SNP markers were detected in S. tranquebarica and S. serrata, respectively. Sex-specific SNP markers were firstly identified in crab species and showed female heterogamety and male homogamety, which provided strong genetic evidence for a WZ/ZZ sex determination system in mud crabs S. paramamosain, S. tranquebarica and S. serrata. These findings will lay a solid foundation for the study of sex determination mechanism, sex chromosome evolution, and the development of mono-sex population in crustaceans.