Transcriptome analysis of gonad and eyestalk reveals mechanisms of growth difference among various male morphotypes of the giant freshwater prawn Macrobrachium rosenbergii

The giant freshwater prawn (GFP) Macrobrachium rosenbergii is an economically important species for aquaculture in China. In culture, it is very common that males show different morphotypes which exhibit distinct heterogenous individual growth. At present, very little information is available regarding mechanisms of growth difference among various male morphotypes of GFP. Transcriptome sequencing technology plays an increasingly prominent role in studying gene expression. In this study, transcriptome analyses were performed using RNA-Seq for comparison among various male morphotypes of GFP, including orange claw males (OC), old blue claw males (OBC) and small males (SM). A total of 97.44 Gb clean data was obtained, which were assembled into1,857,760 unigenes annotated by alignment with pubic protein databases. We then performed differential expression analysis and identified 2,072 differentially expressed genes (DEGs) from eyestalk and 18,402 DEGs from gonad. In Gene Ontology (GO) analysis, the biological process categories of system process and multicellular organismal process were the highest DEG enrichment in eyestalk and gonad, respectively. Furthermore, Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to analyse the functional significance of DEGs, and the results suggest that the pathways associated with gene regulation may play a key role in the course of GFP growth. This work provides a valuable resource of novel transcripts for various male morphotypes of GFP and further understanding of the molecular mechanism of the growth difference of GFP.