Jiang Hongxia, Li Xilian, Sun Yuhang, Hou Fujun, Zhang Yufei, Li Fei, Gu Zhimin, Liu Xiaolin
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.
PLoS One. 2016 Jun 9;11(6):e0157173. doi: 10.1371/journal.pone.0157173. eCollection 2016.
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.
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.
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.
日本沼虾是中国最主要的水产养殖品种。近年来，该物种的性早熟现象受到了广泛关注，因为越来越多的个体在体型较小时就达到性成熟，这降低了商业生产价值。在本研究中，我们利用新一代RNA测序技术，对性早熟和正常性成熟日本沼虾的卵巢进行了深度转录组测序，试图首次深入了解该物种性早熟的分子调控机制。
利用Illumina HiSeq 2500平台，从性早熟和正常性成熟日本沼虾的卵巢cDNA文库中总共获得了63,336个单基因。通过对NR、STRING、Pfam、Swissprot和KEGG数据库进行BLASTX搜索，注释了15,134个单基因，占单基因总数的23.89%。分别通过GO和COG分析对5,195个和3,227个匹配的单基因进行了分类。15,908个单基因被映射到332条KEGG通路中，并鉴定出许多与生殖相关的通路和基因。此外，从18,133个单基因中鉴定出26,008个简单序列重复（SSR）。性早熟和正常性成熟对虾的卵巢文库分别产生了80,529个和80,516个单核苷酸多态性（SNP），还预测了这两组之间29,851个潜在的SNP。比较性早熟和正常性成熟对虾的卵巢文库后，鉴定出549个差异表达基因（DEG）和9个可能与日本沼虾性早熟相关的关键DEG。选择20个DEG通过定量实时PCR（QPCR）进行验证，19个DEG在QPCR和基于RNAseq的差异表达分析数据集中显示出一致的表达。
这是关于性早熟和正常性成熟日本沼虾卵巢大规模RNA测序的首次报道。注释的转录组数据将为未来日本沼虾生殖生物学的研究提供基础支持。本研究中检测到的大量候选SNP和SSR可作为该物种群体遗传学和功能基因组学的遗传标记。更重要的是，鉴定出了许多DEG，特别是性早熟和正常性成熟对虾之间的9个关键DEG，这将极大地提高对该物种性早熟分子调控机制的理解。
