title: De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China.
abstract: 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.
authors.affiliation: 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.
authors.forename: Hai
authors.initials: H
authors.lastname: Nguyen Thanh
authors.affiliation: Key Laboratory of Freshwater Fishery Germplasm Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai City, P. R. China.
authors.forename: Liangjie
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Freshwater Fishery Germplasm Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai City, P. R. China.
authors.forename: Qigen
authors.initials: Q
authors.lastname: Liu
mesh_terms: D000818:Animals; D002681:China; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D033541:Palaemonidae / Q000235:genetics* / Q000254:growth & development; D017423:Sequence Analysis, RNA