title: Characterization of microRNAs in mud crab Scylla paramamosain under Vibrio parahaemolyticus infection.
abstract: BACKGROUND
  Infection of bacterial Vibrio parahaemolyticus is common in mud crab farms. However, the mechanisms of the crab's response to pathogenic V. parahaemolyticus infection are not fully understood. MicroRNAs (miRNAs) are a class of small noncoding RNAs that function as regulators of gene expression and play essential roles in various biological processes. To understand the underlying mechanisms of the molecular immune response of the crab to the pathogens, high-throughput Illumina/Solexa deep sequencing technology was used to investigate the expression profiles of miRNAs in S. paramamosain under V. parahaemolyticus infection.
  
  
  RESULTS
  Two mixed RNA pools of 7 tissues (intestine, heart, liver, gill, brain, muscle and blood) were obtained from V. parahaemolyticus infected crabs and the control groups, respectively. By aligning the sequencing data with known miRNAs, we characterized 421 miRNA families, and 133 conserved miRNA families in mud crab S. paramamosain were either identical or very similar to existing miRNAs in miRBase. Stem-loop qRT-PCRs were used to scan the expression levels of four randomly chosen differentially expressed miRNAs and tissue distribution. Eight novel potential miRNAs were confirmed by qRT-PCR analysis and the precursors of these novel miRNAs were verified by PCR amplification, cloning and sequencing in S. paramamosain. 161 miRNAs (106 of which up-regulated and 55 down-regulated) were significantly differentially expressed during the challenge and the potential targets of these differentially expressed miRNAs were predicted. Furthermore, we demonstrated evolutionary conservation of mud crab miRNAs in the animal evolution process.
  
  
  CONCLUSIONS
  In this study, a large number of miRNAs were identified in S. paramamosain when challenged with V. parahaemolyticus, some of which were differentially expressed. The results show that miRNAs might play some important roles in regulating gene expression in mud crab under V. parahaemolyticus infection, providing a basis for further investigation of miRNA-modulating networks in innate immunity of mud crab.
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China.
authors.forename: Shengkang
authors.initials: S
authors.lastname: Li
authors.forename: Shuo
authors.initials: S
authors.lastname: Zhu
authors.forename: Chuanbiao
authors.initials: C
authors.lastname: Li
authors.forename: Zhao
authors.initials: Z
authors.lastname: Zhang
authors.forename: Lizhen
authors.initials: L
authors.lastname: Zhou
authors.forename: Shijia
authors.initials: S
authors.lastname: Wang
authors.forename: Shuqi
authors.initials: S
authors.lastname: Wang
authors.forename: Yueling
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Wen
mesh_terms: D000818:Animals; D001483:Base Sequence; D003386:Brachyura / Q000235:genetics* / Q000382:microbiology*; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D055029:Inverted Repeat Sequences / Q000235:genetics; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014735:Vibrio Infections / Q000235:genetics* / Q000382:microbiology*; D014736:Vibrio parahaemolyticus / Q000502:physiology*
chemical_list: D035683:MicroRNAs
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