Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
PLoS One. 2013 Jul 17;8(7):e68233. doi: 10.1371/journal.pone.0068233. Print 2013.
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.
METHODS/PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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.
中华绒螯蟹（Eriocheir sinensis）是一种重要的经济甲壳类动物，受到各种疾病的严重侵袭，这就需要在基因组背景下获取更多与免疫相关的基因信息。最近，高通量 RNA 测序（RNA-seq）技术为转录本分析和免疫基因发现提供了一种强大而高效的方法。
方法/主要发现：构建了中华绒螯蟹肝胰腺在混合三种病原体（革兰氏阳性菌微球菌（Micrococcus luteus）、革兰氏阴性菌溶藻弧菌（Vibrio alginolyticus）和真菌巴斯德毕赤酵母（Pichia pastoris）；10(8) cfu·mL(-1)）刺激下的 cDNA 文库，并使用 Illumina 技术进行随机测序。总共获得了 3976 万条清洁读段，组装成 70300 条非冗余基因。在排除短序列和低质量序列后，对 52074 条非冗余基因进行了同源性搜索，与 NCBI 非冗余蛋白质（Nr）数据库中的序列进行比较，其中 17617 条基因与 NCBI Nr 数据库中的序列具有高度相似性。为了进行功能分类和途径分配，将 18734 条（36.00%）基因分为三个基因本体论（GO）类别，将 12243 条（23.51%）基因分为 25 个同源簇（COG），将 8983 条（17.25%）基因分为 6 个京都基因与基因组百科全书（KEGG）途径。推测 24、14、47 和 132 条基因分别参与了 Toll、IMD、JAK-STAT 和 MAPK 途径。
结论/意义：这是首次系统地分析中华绒螯蟹先天免疫途径相关成分的转录组。鉴定的功能基因和潜在途径将有助于更好地了解免疫系统并预防蟹类的各种疾病。
