A preliminary study on differential gene expression in hemocyte of the mantis shrimp Harpiosquilla raphidea by next generation sequencing technique

Abstract

This study aims to determine gene expression profiling in hemocyte of Harpiosquilla raphidea by using bioinformatics technology and Next Generation Sequencing (NGS) technique. The De novo RNA-sequencing was performed using Illumina HiSeq2000. In total, 93,344 assembly consensus sequences were identified by using Trinity software. These 93,344 transcripts were estimated the expression level of each transcript in the hemocyte of H. raphidea (both infected by Vibrio parahemolyticus for 24 hours and normal condition) in terms of FPKM (Frackments Per Kilobase of target transcript length per Million reads mapped). The 219 differential expression of transcripts were classified into 4 clusters, i.e., down regulated expression levels (cluster 1/1 and 2/1) and up regulated expression levels (cluster 1/2 and 2/2). Clusters were further functional and annotation analyzed by using Blast2GO software. The important genes that relevant in the immune system of H. raphidea were found this study. These included histone H1-delta-like, Cyclooxygenases, 5-aminolevulinate erythroid-mitochondrial, electron transfer flavo-ubiquinone mitochondrial and CCR4-NOT transcription complex subunit 7isoform X1 gene. The basic information related to these immune genes in H. raphidea was investigated in this study and will be the guidance for further studies on the important process in the immune system of H. raphidea and for its commercial culture in the future.