Transcriptome Profiling Analysis on Whole Bodies of Microbial Challenged <i>Eriocheir sinensis</i> Larvae for Immune Gene Identification and SNP Development

<div><p>To study crab immunogenetics of individuals, newly hatched <i>Eriocheir sinensis</i> larvae were stimulated with 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). A total of 44,767,566 Illumina clean reads corresponding to 4.52 Gb nucleotides were generated and assembled into 100,252 unigenes (average length: 1,042 bp; range: 201-19,357 bp). 17,097 (26.09%) of 65,535 non-redundant unigenes were annotated in NCBI non-redundant protein (Nr) database. Moreover, 23,188 (35.38%) unigenes were assigned to three Gene Ontology (GO) categories, 15,071 (23.00%) to twenty-six Clusters of orthologous Groups (COG) and 8,574 (13.08%) to six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. Numerous genes were further identified to be associated with multiple immune pathways, including Toll, immune deficiency (IMD), janus kinase (JAK)-signal transducers and activators of transcription (STAT) and mitogen-activated protein kinase (MAPK) pathways. Some of them, such as tumor necrosis factor receptor associated factor 6 (TRAF6), fibroblast growth factor (FGF), protein-tyrosine phosphatase (PTP), JNK-interacting protein 1 (JIP1), were first identified in <i>E. sinensis</i>. TRAF6 was even first discovered in crabs. Additionally, 49,555 single nucleotide polymorphisms (SNPs) were developed from over 13,309 unigenes. This is the first transcriptome report of whole bodies of <i>E. sinensis</i> larvae after immune challenge. Data generated here not only provide detail information to identify novel genes in genome reference-free <i>E. sinensis</i>, but also facilitate our understanding on host immunity and defense mechanism of the crab at whole transcriptome level.</p>