Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Hepatopancreas of Microbial Challenged Mitten Crab <i>Eriocheir sinensis</i>

<div><p>Background</p><p>The Chinese mitten crab <i>Eriocheir sinensis</i> 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.</p><p>Methods/Principal Findings</p><p>A cDNA library from hepatopancreas of <i>E. sinensis</i> challenged by a mixture of three pathogen strains (Gram-positive bacteria <i>Micrococcus luteus</i>, Gram-negative bacteria <i>Vibrio alginolyticus</i> and fungi <i>Pichia pastoris</i>; 10⁸ 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.</p><p>Conclusions/Significance</p><p>This is the first systematical transcriptome analysis of components relating to innate immune pathways in <i>E. sinensis</i>. Functional genes and putative pathways identified here will contribute to better understand immune system and prevent various diseases in crab.</p>