Nguyen Thanh Hai, Zhao Liangjie, Liu Qigen
Key Laboratory of Freshwater Fishery Germplasm Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai City, P. R. China; Vietnam Institute of Fisheries Economics and Planning, Directorate of Fisheries, Ministry of Agriculture and Rural Development of Viet Nam, Hanoi City, S.R. Vietnam.
Key Laboratory of Freshwater Fishery Germplasm Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai City, P. R. China.
PLoS One. 2014 Oct 20;9(10):e109656. doi: 10.1371/journal.pone.0109656. eCollection 2014.
Giant freshwater prawn (GFP; Macrobrachium rosenbergii) is an exotic species that was introduced into China in 1976 and thereafter it became a major species in freshwater aquaculture. However the gene discovery in this species has been limited to small-scale data collection in China. We used the next generation sequencing technology for the experiment; the transcriptome was sequenced of samples of hepatopancreas organ in individuals from 4 GFP groups (A1, A2, B1 and B2). De novo transcriptome sequencing generated 66,953 isogenes. Using BLASTX to search the Non-redundant (NR), Search Tool for the Retrieval of Interacting Genes (STRING), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases; 21,224 unigenes were annotated, 9,552 matched unigenes with the Gene Ontology (GO) classification; 5,782 matched unigenes in 25 categories of Clusters of Orthologous Groups of proteins (COG) and 20,859 unigenes were consequently assigned to 312 KEGG pathways. Between the A and B groups 147 differentially expressed genes (DEGs) were identified; between the A1 and A2 groups 6,860 DEGs were identified and between the B1 and B2 groups 5,229 DEGs were identified. After enrichment, the A and B groups identified 38 DEGs, but none of them were significantly enriched. The A1 and A2 groups identified 21,856 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function and the KEGG pathway defined 2,459 genes had a KEGG Ortholog-ID (KO-ID) and could be categorized into 251 pathways, of those, 9 pathways were significantly enriched. The B1 and B2 groups identified 5,940 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function, and the KEGG pathway defined 1,543 genes had a KO-ID and could be categorized into 240 pathways, of those, 2 pathways were significantly enriched. We investigated 99 queries (GO) which related to growth of GFP in 4 groups. After enrichment we identified 23 DEGs and 1 KEGG PATHWAY 'ko04711' relation with GFP growth.
罗氏沼虾（GFP；Macrobrachium rosenbergii）是一种外来物种，于1976年引入中国，此后成为淡水养殖的主要品种。然而，该物种的基因发现仅限于中国的小规模数据收集。我们使用下一代测序技术进行实验；对4个罗氏沼虾组（A1、A2、B1和B2）个体的肝胰腺器官样本进行转录组测序。从头转录组测序产生了66,953个同基因。使用BLASTX搜索非冗余（NR）、相互作用基因检索工具（STRING）和京都基因与基因组百科全书（KEGG）数据库；对21,224个单基因进行了注释，9,552个匹配的单基因进行了基因本体（GO）分类；5,782个匹配的单基因属于25类蛋白质直系同源簇（COG），20,859个单基因因此被分配到312条KEGG通路。在A组和B组之间鉴定出147个差异表达基因（DEG）；在A1组和A2组之间鉴定出6,860个DEG，在B1组和B2组之间鉴定出5,229个DEG。富集后，A组和B组鉴定出38个DEG，但均未显著富集。A1组和A2组基于功能组在三个主要类别中鉴定出21,856个DEG：生物过程、细胞成分和分子功能，KEGG通路定义的2,459个基因具有KEGG直系同源物ID（KO-ID），可分为251条通路，其中9条通路显著富集。B1组和B2组基于功能组在三个主要类别中鉴定出5,940个DEG：生物过程、细胞成分和分子功能，KEGG通路定义的1,543个基因具有KO-ID，可分为240条通路，其中2条通路显著富集。我们研究了4组中与罗氏沼虾生长相关的99个查询（GO）。富集后，我们鉴定出23个DEG和1条与罗氏沼虾生长相关的KEGG通路“ko04711”。
