Comparative transcriptome analysis between strong and weak strains of the ridgetail white prawn, Exopalaemon carinicauda (Decapoda, Caridea) resistant to Vibrio parahaemolyticus

Abstract To explore the differentially expressed genes in the different strains of Exopalaemon carinicauda resistant to Vibrio parahaemolyticus , as in this study, we used RNA-Seq technology to analyse the transcriptome of the F1 generation surviving the infection stress of V. parahaemolyticus . The differentially expressed genes (DEGs) between strongly resistant and weakly resistant strains were screened out. The results showed that a total of 646 differentially expressed genes were identified between strongly resistant and weakly resistant strains. Compared to the weakly resistant strains, 309 genes were up-regulated and 337 genes were down-regulated in the strongly resistant strains. The expression trends of the 20 differentially expressed genes verified by qRT-PCR were consistent with the transcriptome data. The GO functional annotation indicated that the differentially expressed genes are mainly related to functions such as cellular processes, metabolic regulation, and biocatalytic activities. KEGG pathway analysis showed that, compared to the weakly resistant strains, in the strongly resistant strains, such as the one-carbon pool by folate, metabolism pathways, and lysosome were the core disease-resistant regulatory pathways. Among these, in the one-carbon pool by folate, strongly resistant strains may enhance nucleotide metabolism by upregulating the expression of the MTR gene, support the expansion of immune cells and damage repair, and further improve disease resistance. In the metabolic pathway, genes such as HMBS and MIF were significantly upregulated. We speculated that after exposure to Vibrio stress, compared to the weakly resistant strains, immune cells in the strongly resistant strains carried out highenergy- consumption activities such as phagocytosis and antimicrobial peptide synthesis, and the up-regulation of energy metabolism genes to meet ATP requirements. At the same time, multiple genes such as aspC and RDH12 were significantly downregulated. Thus, the strongly resistant strain may inhibit growth and prioritize the allocation of metabolic functions towards immune defense to resist Vibrio infection. The high expression of lysosomal pathway genes such as SPAM1 and LCP2 suggested that the strongly resistant strains enhance their resistance by strengthening the pathogen degradation ability. The screened candidate genes may help with the development of disease-resistant molecular markers and the breeding of stress-resistant varieties of E. carinicauda .