Dataset Information

Integrated analysis of microRNA and mRNA expression profiles during the sex-differentiation sensitive period in oriental river prawn, Macrobrachium nipponense.

ABSTRACT: Male oriental river prawns (Macrobrachium nipponense) grow faster than females, and therefore, reach larger sizes by harvest time. Histological observations have indicated that the sex-differentiation sensitive period (which includes the formation of the androgenic gland, the testis, and the ovary) is from post-larvae (PL) developmental stage for M. nipponense. In this study, we prepared four microRNA (miRNA) and mRNA libraries using samples collected from sex-differentiation sensitive period (PL7 to PL16) to perform RNA-sequencing for identifying sex-related candidate miRNAs, genes, and metabolic pathways. A total of nine intersection miRNAs were identified, of which three were highly expressed in the androgenic gland, and their expression was verified by quantitative Real-Time PCR (qPCR). These three miRNAs and their 11 predicted target genes may be strong candidates for sex-related miRNAs and sex-related genes in M. nipponense. Five vital sex-related metabolic pathways were also identified that may regulate other sex-differentiation and sex-determination mechanisms. Finding of the study provide important insights to enhance our understanding on sex-differentiation and sex-determination mechanisms for M. nipponense.

SUBMITTER: Jin S

PROVIDER: S-EPMC5607309 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Integrated analysis of microRNA and mRNA expression profiles during the sex-differentiation sensitive period in oriental river prawn, Macrobrachium nipponense.

Jin Shubo S Fu Hongtuo H Sun Shengming S Jiang Sufei S Xiong Yiwei Y Gong Yongsheng Y Qiao Hui H Zhang Wenyi W Wu Yan Y

Scientific reports 20170920 1

Male oriental river prawns (Macrobrachium nipponense) grow faster than females, and therefore, reach larger sizes by harvest time. Histological observations have indicated that the sex-differentiation sensitive period (which includes the formation of the androgenic gland, the testis, and the ovary) is from post-larvae (PL) developmental stage for M. nipponense. In this study, we prepared four microRNA (miRNA) and mRNA libraries using samples collected from sex-differentiation sensitive period (P ...[more]

PMID: 28931848

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Project description:BackgroundThe oriental river prawn (Macrobrachium nipponense) is the most prevalent aquaculture species in China. The sexual precocity in this species has received considerable attention in recent years because more and more individuals matured at a small size, which devalues the commercial production. In this study, we developed deep-coverage transcriptomic sequencing data for the ovaries of sexually precocious and normal sexually mature M. nipponense using next-generation RNA sequencing technology and attempted to provide the first insight into the molecular regulatory mechanism of sexual precocity in this species.ResultsA total of 63,336 unigenes were produced from the ovarian cDNA libraries of sexually precocious and normal sexually mature M. nipponense using Illumina HiSeq 2500 platform. Through BLASTX searches against the NR, STRING, Pfam, Swissprot and KEGG databases, 15,134 unigenes were annotated, accounting for 23.89% of the total unigenes. 5,195 and 3,227 matched unigenes were categorized by GO and COG analysis respectively. 15,908 unigenes were consequently mapped into 332 KEGG pathways, and many reproduction-related pathways and genes were identified. Moreover, 26,008 SSRs were identified from 18,133 unigenes. 80,529 and 80,516 SNPs were yielded from ovarian libraries of sexually precocious and normal sexually mature prawn, respectively, and 29,851 potential SNPs between these two groups were also predicted. After comparing the ovarian libraries of sexually precocious and normal sexually mature prawn, 549 differentially expressed genes (DEGs) and 9 key DEGs that may be related to sexual precocity of M. nipponense were identified. 20 DEGs were selected for validation by quantitative real-time PCR (QPCR) and 19 DEGs show consistent expression between QPCR and RNAseq-based differential expression analysis datasets.ConclusionThis is the first report on the large-scale RNA sequencing of ovaries of sexually precocious and normal sexually mature M. nipponense. The annotated transcriptome data will provide fundamental support for future research into the reproduction biology of M. nipponense. The large number of candidate SNPs and SSRs detected in this study could be used as genetic markers for population genetics and functional genomics in this species. More importantly, many DEGs, especially nine key DEGs between sexually precocious and normal sexually mature prawns were identified, which will dramatically improve understanding of molecular regulatory mechanism of sexual precocity of this species.

Dataset Information

Integrated analysis of microRNA and mRNA expression profiles during the sex-differentiation sensitive period in oriental river prawn, Macrobrachium nipponense.

Publications

Integrated analysis of microRNA and mRNA expression profiles during the sex-differentiation sensitive period in oriental river prawn, Macrobrachium nipponense.

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