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.
PLoS One. 2013 Dec 4;8(12):e82156. doi: 10.1371/journal.pone.0082156. eCollection 2013.
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.
为了研究个体螃蟹的免疫遗传学，我们用三种病原体菌株（革兰氏阳性菌微球菌、革兰氏阴性菌溶藻弧菌和真菌毕赤酵母；10（8）cfu·mL（-1））混合物刺激刚孵化的中华绒螯蟹幼虫。共产生 44767566 个 Illumina 清洁读数，对应 4.52Gb 核苷酸，并组装成 100252 个非冗余基因（平均长度：1042bp；范围：201-19357bp）。在 NCBI 非冗余蛋白（Nr）数据库中注释了 65535 个非冗余基因中的 17097 个（26.09%）。此外，23188 个（35.38%）基因被分配到三个基因本体（GO）类别，15071 个（23.00%）到 26 个直系同源群（COG），8574 个（13.08%）到六个京都基因与基因组百科全书（KEGG）途径。进一步鉴定了许多与多种免疫途径相关的基因，包括 Toll、免疫缺陷（IMD）、Janus 激酶（JAK）-信号转导和转录激活因子（STAT）和丝裂原激活蛋白激酶（MAPK）途径。其中一些基因，如肿瘤坏死因子受体相关因子 6（TRAF6）、成纤维细胞生长因子（FGF）、蛋白酪氨酸磷酸酶（PTP）、JNK 相互作用蛋白 1（JIP1），在中华绒螯蟹中首次被鉴定。TRAF6 甚至是在螃蟹中首次发现的。此外，从 13309 个基因中开发了 49555 个单核苷酸多态性（SNP）。这是中华绒螯蟹幼虫免疫挑战后全基因组的首次转录组报告。这里产生的数据不仅为在中华绒螯蟹无基因组参考的基因组中鉴定新基因提供了详细信息，而且有助于我们在全转录组水平上了解螃蟹的宿主免疫和防御机制。
