title: 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: BACKGROUND
  Mud 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.
  
  
  RESULTS
  Comparative 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
  Analysis 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.
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Chuping
authors.initials: C
authors.lastname: Xie
authors.affiliation: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Wanwei
authors.initials: W
authors.lastname: Sun
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Ding
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Lizhen
authors.initials: L
authors.lastname: Zhou
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Shasha
authors.initials: S
authors.lastname: Wang
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Shuqi
authors.initials: S
authors.lastname: Wang
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Yueling
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Dashi
authors.initials: D
authors.lastname: Zhu
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Wen
authors.affiliation: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.affiliation: Guangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Shengkang
authors.initials: S
authors.lastname: Li
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism*; D003386:Brachyura / Q000235:genetics* / Q000382:microbiology*; D002478:Cells, Cultured; D020869:Gene Expression Profiling; D015723:Gene Library; D063990:Gene Ontology; D006434:Hemocytes / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014735:Vibrio Infections / Q000235:genetics* / Q000382:microbiology*; D014736:Vibrio parahaemolyticus / Q000502:physiology
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger