title: Transcriptome profiling analysis on whole bodies of microbial challenged Eriocheir sinensis larvae for immune gene identification and SNP development.
abstract: To study crab immunogenetics of individuals, newly hatched Eriocheir sinensis larvae were stimulated with 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)). 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 E. sinensis. 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 E. sinensis larvae after immune challenge. Data generated here not only provide detail information to identify novel genes in genome reference-free E. sinensis, but also facilitate our understanding on host immunity and defense mechanism of the crab at whole transcriptome level.
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ; National & Local Joint Engineering Laboratory for Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors: Zhaoxia
authors: Z
authors: Cui
authors: Xihong
authors: X
authors: Li
authors: Yuan
authors: Y
authors: Liu
authors: Chengwen
authors: C
authors: Song
authors: Min
authors: M
authors: Hui
authors: Guohui
authors: G
authors: Shi
authors: Danli
authors: D
authors: Luo
authors: Yingdong
authors: Y
authors: Li
mesh_terms: D000818:Animals; D003386:Brachyura / Q000235:genetics / Q000276:immunology* / Q000382:microbiology*; D005260:Female; D020869:Gene Expression Profiling; D063990:Gene Ontology; D005819:Genetic Markers; D007814:Larva / Q000235:genetics / Q000276:immunology / Q000382:microbiology; D020935:MAP Kinase Signaling System / Q000235:genetics; D016982:Micrococcus luteus / Q000502:physiology*; D058977:Molecular Sequence Annotation; D010843:Pichia / Q000502:physiology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D014733:Vibrio / Q000502:physiology*
chemical_list: D005819:Genetic Markers; D011506:Proteins