Insights into Sexual Precocity of Female Oriental River Prawn Macrobrachium nipponense through Transcriptome Analysis.
BACKGROUND
The 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.


RESULTS
A 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.


CONCLUSIONS
This 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.
College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People's Republic of China.|Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People's Republic of China.|College of Fisheries, Henan Normal University, Xinxiang, Henan, People's Republic of China.
Hongxia
H
Jiang
Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People's Republic of China.
Xilian
X
Li
College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People's Republic of China.
Yuhang
Y
Sun
College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People's Republic of China.
Fujun
F
Hou
Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People's Republic of China.
Yufei
Y
Zhang
Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People's Republic of China.
Fei
F
Li
Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People's Republic of China.
Zhimin
Z
Gu
College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People's Republic of China.
Xiaolin
X
Liu
D000818:Animals; D005260:Female; D005786:Gene Expression Regulation / Q000502:physiology*; D010053:Ovary / Q000378:metabolism*; D033541:Palaemonidae / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome / Q000502:physiology*