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.
Highlights
The red swamp crayfish Procambarus clarkii is a freshwater crayfish species that is native to parts of Mexico and the United States [1], but is commonly found outside its natural range in Asia, Africa, Europe, and elsewhere in the Americas, where it is often considered to be an invasive pest [2]
All raw sequence data were deposited in the NCBI Sequence Read Archive (SRA) under accession code SRP044128
A total of 324.97 million paired-end reads were generated with a read length of 100 bp, of which 102.46 million reads were from the hepatopancreas, 83.51 million reads were from muscle, 84.94 million reads were from the ovary, and 36.06 million reads were from the testis
Summary
The red swamp crayfish Procambarus clarkii is a freshwater crayfish species that is native to parts of Mexico and the United States [1], but is commonly found outside its natural range in Asia, Africa, Europe, and elsewhere in the Americas, where it is often considered to be an invasive pest [2]. P. clarkii is a highly adaptable, tolerant, and fecund freshwater crayfish that can inhabit a wide range of aquatic environments, including those with moderate salinity, low oxygen levels, extreme temperatures, and pollution [2,5]. Because of these characteristics, in addition to its economic role, the crayfish has become an important crustacean model organism in research on viral infection [6,7,8,9,10], animal behavior [11,12,13,14,15,16,17], and environmental stress and toxicity [18,19,20,21,22,23]
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