Abstract
BackgroundThe swimming crab, Portunus trituberculatus, is an important farmed species in China, has been attracting extensive studies, which require more and more genome background knowledge. To date, the sequencing of its whole genome is unavailable and transcriptomic information is also scarce for this species. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for major tissues of Portunus trituberculatus by the Illumina paired-end sequencing technology.ResultsTotal RNA was isolated from eyestalk, gill, heart, hepatopancreas and muscle. Equal quantities of RNA from each tissue were pooled to construct a cDNA library. Using the Illumina paired-end sequencing technology, we generated a total of 120,137 transcripts with an average length of 1037 bp. Further assembly analysis showed that all contigs contributed to 87,100 unigenes, of these, 16,029 unigenes (18.40% of the total) can be matched in the GenBank non-redundant database. Potential genes and their functions were predicted by GO, KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes with fundamental roles in growth and muscle development, including actin, myosin, tropomyosin, troponin and other potentially important candidate genes were identified for the first time in this specie. Furthermore, 22,673 SSRs and 66,191 high-confidence SNPs were identified in this EST dataset.ConclusionThe transcriptome provides an invaluable new data for a functional genomics resource and future biological research in Portunus trituberculatus. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will be essential for accelerating aquaculture breeding programs with this species.
Highlights
Portunus trituberculatus (Crustacea: Decapoda: Brachyura), commonly known as the swimming crab, is widely distributed in the coastal waters of Korea, Japan, China, and southeast Asia [1]
Commercial crab farming largely depended on wild seed stock and the commercial characteristics of the cultured stocks have declined after many years of culturing [4], and wild populations of Portunus trituberculatus have dramatically declined for the last decades due to over-exploitation and the deterioration of environmental conditions in China [5]
Illumina Draft Reads and Sequence Assembly In order to achieve a comprehensive Portunus trituberculatus transcriptome, total RNA was extracted from a variety of tissues, including the eyestalk, gill, heart, hepatopancreas, and muscle
Summary
Portunus trituberculatus (Crustacea: Decapoda: Brachyura), commonly known as the swimming crab, is widely distributed in the coastal waters of Korea, Japan, China, and southeast Asia [1]. This species inhabits estuaries and coastal waters, which belong to typical euryhaline crab species. Commercial crab farming largely depended on wild seed stock and the commercial characteristics (growth rate, flesh quality and disease resistance) of the cultured stocks have declined after many years of culturing [4], and wild populations of Portunus trituberculatus have dramatically declined for the last decades due to over-exploitation and the deterioration of environmental conditions in China [5]. The swimming crab, Portunus trituberculatus, is an important farmed species in China, has been attracting extensive studies, which require more and more genome background knowledge. We performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for major tissues of Portunus trituberculatus by the Illumina paired-end sequencing technology
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