title: Transcriptome analysis and discovery of genes involved in immune pathways from hepatopancreas of microbial challenged mitten crab Eriocheir sinensis.
abstract: BACKGROUND
  The Chinese mitten crab Eriocheir sinensis is an important economic crustacean and has been seriously attacked by various diseases, which requires more and more information for immune relevant genes on genome background. Recently, high-throughput RNA sequencing (RNA-seq) technology provides a powerful and efficient method for transcript analysis and immune gene discovery.
  
  
  RESULTS
  A cDNA library from hepatopancreas of E. sinensis challenged by a mixture of three pathogen strains (Gram-positive bacteria Micrococcus luteus, Gram-negative bacteria Vibrio alginolyticus and fungi Pichia pastoris; 10(8) cfu·mL(-1)) was constructed and randomly sequenced using Illumina technique. Totally 39.76 million clean reads were assembled to 70,300 unigenes. After ruling out short-length and low-quality sequences, 52,074 non-redundant unigenes were compared to public databases for homology searching and 17,617 of them showed high similarity to sequences in NCBI non-redundant protein (Nr) database. For function classification and pathway assignment, 18,734 (36.00%) unigenes were categorized to three Gene Ontology (GO) categories, 12,243 (23.51%) were classified to 25 Clusters of Orthologous Groups (COG), and 8,983 (17.25%) were assigned to six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Potentially, 24, 14, 47 and 132 unigenes were characterized to be involved in Toll, IMD, JAK-STAT and MAPK pathways, respectively.
  
  
  CONCLUSIONS
  This is the first systematical transcriptome analysis of components relating to innate immune pathways in E. sinensis. Functional genes and putative pathways identified here will contribute to better understand immune system and prevent various diseases in crab.
authors.affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Xihong
authors.initials: X
authors.lastname: Li
authors.forename: Zhaoxia
authors.initials: Z
authors.lastname: Cui
authors.forename: Yuan
authors.initials: Y
authors.lastname: Liu
authors.forename: Chengwen
authors.initials: C
authors.lastname: Song
authors.forename: Guohui
authors.initials: G
authors.lastname: Shi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D003445:Crustacea / Q000235:genetics* / Q000276:immunology; D018076:DNA, Complementary; D005260:Female; D043143:Hepatopancreas / Q000276:immunology / Q000378:metabolism*; D007107:Immune System / Q000378:metabolism; D008969:Molecular Sequence Data; D017386:Sequence Homology, Amino Acid; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary