In-Depth Transcriptome Analysis of the Red Swamp Crayfish Procambarus clarkii

Abstract

The red swamp crayfish Procambarus clarkii is a highly adaptable, tolerant, and fecund freshwater crayfish that inhabits a wide range of aquatic environments. It is an important crustacean model organism that is used in many research fields, including animal behavior, environmental stress and toxicity, and studies of viral infection. Despite its widespread use, knowledge of the crayfish genome is very limited and insufficient for meaningful research. This is the use of next-generation sequencing techniques to analyze the crayfish transcriptome. A total of 324.97 million raw reads of 100 base pairs were generated, and a total of 88,463 transcripts were assembled de novo using Trinity software, producing 55,278 non-redundant transcripts. Comparison of digital gene expression between four different tissues revealed differentially expressed genes, in which more overexpressed genes were found in the hepatopancreas than in other tissues, and more underexpressed genes were found in the testis and the ovary than in other tissues. Gene ontology (GO) and KEGG enrichment analysis of differentially expressed genes revealed that metabolite- and immune-related pathway genes were enriched in the hepatopancreas, and DNA replication-related pathway genes were enriched in the ovary and the testis, which is consistent with the important role of the hepatopancreas in metabolism, immunity, and the stress response, and with that of the ovary and the testis in reproduction. It was also found that 14 vitellogenin transcripts were highly expressed specifically in the hepatopancreas, and 6 transcripts were highly expressed specifically in the ovary, but no vitellogenin transcripts were highly expressed in both the hepatopancreas and the ovary. These results provide new insight into the role of vitellogenin in crustaceans. In addition, 243,764 SNP sites and 43,205 microsatellite sequences were identified in the sequencing data. We believe that our results provide an important genome resource for the crayfish.

Transcriptomic response to ammonia-N stress in the hepatopancreas of swimming crab Portunus trituberculatus

“…Compared with traditional sequencing technologies, next-generation sequencing technologies can provide a large amount of sequence data with a wider range and depth by spending less time and cost (Huse et al 2007). Recently, digital gene expression (DGE) analysis has become an effective and convenient method for monitoring differences in the transcriptomic response of tissues or organs under environmental stress in aquatic crustaceans, such as P. trituberculatus (Lv et al 2013), Eriocheir sinensis (Li et al 2013a;Sun et al 2014), Sinopotamon henanense (Sun et al 2016), Macrobrachium rosenbergii (Rao et al 2015), Procambarus clarkii (Shen et al 2014), Litopenaeus vannamei (Guo et al 2016) and Fenneropenaeus chinensis (Li et al 2013b). Lu et al (2016) performed a comparative transcriptome analysis of the hepatopancreas between controls and an ammoniatreated group of L. vannamei.…”

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

“…Transcriptomics using NGS technology has revealed genes involved in stress response, reproduction, development, molting and growth, limb regeneration, immune response, endocrinology, and nutrition and digestion in decapod crustaceans (Sagi et al 2013; Tom et al 2013; Durica et al 2014; Ghaffari et al 2014; Hao et al 2014; Lv et al, 2014, 2015; Shen et al 2014; Song et al 2014; Tom et al 2014; Wei et al 2014a, 2014b; Abehsera et al 2015; Chandler et al 2015; Christiaens et al 2015; Huang et al 2015; Johnson et al 2015; Li et al 2015a, 2015b; Ventura et al 2014, 2015; Verbruggen et al 2015; Wang et al 2015; Das et al 2016a). It is clear from the input received at the SICB meeting and the ten symposium papers in this issue (Armstrong and Stillman 2016; Chandler et al 2016; Clark and Greenwood 2016; Das and Mykles 2016; Das et al 2016b; Havird and Santos 2016a, 2016b; Johnson et al 2016; Powell et al 2016; Tarrant et al 2016) that a greater understanding of the relationship between transcriptomic and phenotypic change in decapod crustaceans will not be achieved until more powerful and applicable “-omic” tools and resources are developed.…”

Transcriptomics in aquaculture: current status and applications

“…Detailed transcriptomic analysis of the Procambarus clarkii has identified 243,764 SNPs and 43,205 microsatellites that will form a valuable genome resource for the crayfish (Shen et al . ).…”