De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China

Hai Nguyen Thanh; Liangjie Zhao; Qigen Liu

doi:10.1371/journal.pone.0109656

De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China

PLoS One. 2014 Oct 20;9(10):e109656. doi: 10.1371/journal.pone.0109656. eCollection 2014.

Authors

Hai Nguyen Thanh¹, Liangjie Zhao², Qigen Liu²

Affiliations

¹ 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.
² Key Laboratory of Freshwater Fishery Germplasm Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai City, P. R. 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.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

Animals
China
Gene Expression Profiling*
High-Throughput Nucleotide Sequencing*
Molecular Sequence Annotation
Palaemonidae / genetics*
Palaemonidae / growth & development
Sequence Analysis, RNA

Associated data

SRA/SRP045800

Grants and funding

This study was supported by Special Fund for Agro-scientific Research in the Public Interest, State Agriculture Ministry of China (201203083), by Shanghai University Knowledge Service Platform Project (ZF1206) and by Shanghai Universities First-class Disciplines Project of Fisheries. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.