Transcriptome and Expression Profiling Analysis of the Hemocytes Reveals a Large Number of Immune-Related Genes in Mud Crab Scylla paramamosain during Vibrio parahaemolyticus Infection

Abstract

BackgroundMud crab Scylla paramamosain is an economically important marine species in China. However, frequent outbreaks of infectious diseases caused by marine bacteria, such as Vibrio parahaemolyticus, result in great economic losses.Methodology/Principal FindingsComparative de novo transcriptome analysis of S. paramamosain infected with V. parahaemolyticus was carried out to investigate the molecular mechanisms underlying the immune response to pathogenic bacteria by using the Illumina paired-end sequencing platform. A total of 52,934,042 clean reads from the hemocytes of V. parahaemolyticus-infected mud crabs and controls were obtained and assembled into 186,193 contigs. 59,120 unigenes were identified from 81,709 consensus sequences of mud crabs and 48,934 unigenes were matched proteins in the Nr or Swissprot databases. Among these, 10,566 unigenes belong to 3 categories of Gene Ontology, 25,349 to 30 categories of KEGG, and 15,191 to 25 categories of COG database, covering almost all functional categories. By using the Solexa/Illumina's DGE platform, 1213 differentially expressed genes (P<0.05), including 538 significantly up-regulated and 675 down-regulated, were detected in V. parahaemolyticus-infected crabs as compared to that in the controls. Transcript levels of randomly-chosen genes were further measured by quantitative real-time PCR to confirm the expression profiles. Many differentially expressed genes are involved in various immune processes, including stimulation of the Toll pathway, Immune Deficiency (IMD) pathway, Ras-regulated endocytosis, and proPO-activating system.Conclusions/SignificanceAnalysis of the expression profile of crabs under infection provides invaluable new data for biological research in S. paramamosain, such as the identification of novel genes in the hemocytes during V. parahaemolyticus infection. These results will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection and will be helpful for diseases prevention in crab aquaculture.

Comparative transcriptomic analysis of surf clams (Paphia undulate) infected with two strains of Vibrio spp. reveals the identity of key immune genes involved in host defense

“…To characterize the immune response among V. parahaemolyticus- infected groups of clams and to compare it with the control and V . alginolyticus -infected group, quantitative gene expression analysis for all the three groups of clams was performed using the Illumina RNA-seq technology on HiSeq 2000 platform [47, 48].…”

“…For GO analysis, the DEGs obtained from Illumina platform were mapped to terms in GO database version GO slim (http://www.geneontology.org) using Amigo (http://amigo.geneontology.org/) software. GO based functional analysis gave us a broad overview of the ontology content with respect to biological processes, cellular components and molecular functions [6, 9, 10, 47]. Default parameters were used to execute the analysis and the biological process ontology level 2 was selected [2, 13].…”

“…Default parameters were used to execute the analysis and the biological process ontology level 2 was selected [2, 13]. The up- and down-regulated genes from the annotated genes in GO database were identified using DAVID [47].…”

Genome survey, high-resolution genetic linkage map construction, growth-related quantitative trait locus (QTL) identification and gene location in Scylla paramamosain

“…We have been devoted to studying the genetic breeding and aquaculture industry for many years, keeping ahead of the artificial breeding of this crab. Currently, there are no genome assembly datasets for this crab, and only several transcriptome libraries have been reported 15–19 . The only genetic linkage map for the mud crab was constructed by our team using 212 microsatellite and amplified fragment length polymorphism (AFLP) markers, and the mean spacing was 18.68 cM 20 .…”

Enhanced Immune Protection of Mud Crab Scylla paramamosain in Response to the Secondary Challenge by Vibrio parahaemolyticus

“…V. parahaemolyticus is a primary bacterial pathogen of S. paramamosain. It has been reported to cause "milky disease" with high mortality and has led to major losses in the mud-crab aquaculture industry (42)(43)(44). However, due to a lack of research into disease prevention, the culture of S. paramamosain has been hampered by infection by various pathogens, which has restricted the development of the breeding industry.…”