Abstract
BackgroundThe oriental river prawn, Macrobrachium nipponense, is an economically and nutritionally important species of the Palaemonidae family of decapod crustaceans. To date, the sequencing of its whole genome is unavailable as a non-model organism. Transcriptomic information is also scarce for this species. In this study, we performed de novo transcriptome sequencing to produce the first comprehensive expressed sequence tag (EST) dataset for M. nipponense using high-throughput sequencing technologies.Methodology and Principal FindingsTotal RNA was isolated from eyestalk, gill, heart, ovary, testis, hepatopancreas, muscle, and embryos at the cleavage, gastrula, nauplius and zoea stages. Equal quantities of RNA from each tissue and stage were pooled to construct a cDNA library. Using 454 pyrosequencing technology, we generated a total of 984,204 high quality reads (338.59Mb) with an average length of 344 bp. Clustering and assembly of these reads produced a non-redundant set of 81,411 unique sequences, comprising 42,551 contigs and 38,860 singletons. All of the unique sequences were involved in the molecular function (30,425), cellular component (44,112) and biological process (67,679) categories by GO analysis. Potential genes and their functions were predicted by KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes involved in sex determination, including DMRT1, FTZ-F1, FOXL2, FEM1 and other potentially important candidate genes, were identified for the first time in this prawn. Furthermore, 6,689 SSRs and 18,107 high-confidence SNPs were identified in this EST dataset.ConclusionsThe transcriptome provides an invaluable new data for a functional genomics resource and future biological research in M. nipponense. 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
The oriental river prawn Macrobrachium nipponense, a member of the Palaemonidae family of decapod crustaceans, is widely distributed in freshwater and low-salinity regions of estuaries [1]
Roche 454 Genome Sequencing (GS) FLX sequencing and reads assembly In order to achieve a whole-body M. nipponense transcriptome, total RNA was extracted from a variety of adult organs and tissues, including the eyestalk, gill, heart, ovary, testis, hepatopancreas, muscle, and embryos at the cleavage, gastrula, nauplius and zoea stages
We identified other putative genes related to sex determination/differentiation in M. nipponense for the first time, such as cytochrome P450 aromatase (P450) [65], steroidogenic acute regulatory protein (STAR) [66], Zinc finger Y-chromosomal protein 1 (ZFY1) [67], Wilms’ tumor protein 1 (WT1) [68] and Tudor [69]
Summary
The oriental river prawn Macrobrachium nipponense, a member of the Palaemonidae family of decapod crustaceans, is widely distributed in freshwater and low-salinity regions of estuaries [1]. This prawn is a useful model organism for studying reproduction and development in decapod species for multiple reasons. It produces large numbers of eggs due to its high fecundity. The oriental river prawn, Macrobrachium nipponense, is an economically and nutritionally important species of the Palaemonidae family of decapod crustaceans. We performed de novo transcriptome sequencing to produce the first comprehensive expressed sequence tag (EST) dataset for M. nipponense using high-throughput sequencing technologies
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