Transcriptome analysis and discovery of genes involved in immune pathways in Solen strictus (Gould, 1861) under Vibrio anguillarum

Abstract

The Solen strictus (Gould, 1861) has been recognized as an important marine economic bivalve in Eastern and Southeast Asia. To gain a better understanding of the S. strictus immune system and its related genes in response to bacterial infections, we performed a comparative gene transcription analysis from S. strictus with Vibrio anguillarum through RNA-Seq technology, meanwhile the differentially expressed genes (DEGs) were investigated. After assembly, a total of 195,774 transcripts with an average length of 996 bp were obtained. Total 153,038 unigenes were annotated in the nr, Swiss-Prot, KEGG, COG, KOG, GO and Pfam databases, and 56,597 unigenes (36.98%) were annotated in at least one database. After bacterial challenge, there were 1588 significant differentially expressed genes (DEGs) between the challenged and control groups, including 999 up-regulated and 589 down-regulated genes. All the DEGs were classified into three gene ontology categories, and allocated to 225 KEGG pathways. Immune-related genes were detected from immune system pathways among the top 20 enriched pathways, such as Toll-like receptor signaling, RIG-I-like receptor signaling and NOD-like receptor signaling pathway. In addition, 56,079 potential simple sequence repeats (SSRs) and 1,031,521 candidate single nucleotide polymorphisms (SNPs) were detected and identified in the S. strictus transcriptome. Results of the present study will provide valuable theoretical resources for future genetic and genomic research on S. strictus. The research results will be helpful for improving the efficiency and quality of artificial breeding, establishing genetic linkage map, and enhancing health management for this species.