文献类型：期刊文献

中文题名：马氏珠母贝(Pinctada fucata)血细胞转录组测序数据中SNP标记的开发及其功能注释分析

英文题名：SNP DISCOVERY AND FUNCTIONAL ANNOTATION IN TRANSCRIPTOME DATASETS FROM HEMOCYTES OF PINCTADA FUCATA

作者：王忠良[1,2];丁燏[1];许尤厚[3];王蓓[1];张健东[1,2]

机构：[1]广东海洋大学水产学院,湛江524088;[2]南海水产经济动物增养殖广东省普通高校重点实验室,湛江524088;[3]广西北部湾海洋生物多样性养护重点实验室(钦州学院),钦州535000

年份：2018

卷号：49

期号：2

起止页码：403

中文期刊名：海洋与湖沼

外文期刊名：Oceanologia Et Limnologia Sinica

收录：CSTPCD、、北大核心2017、Scopus、CSCD2017_2018、北大核心、CSCD

基金：广东省省级科技计划项目;2015A020209169号;广东海洋大学优秀青年骨干教师特别资助计划项目;GDOU2015050214号;国家自然科学基金项目;31202023号;广西北部湾海洋生物多样性养护重点实验室(钦州学院)开放课题;2017KB03号

语种：中文

中文关键词：马氏珠母贝;单核苷酸多态性标记;转录组;分子标记

外文关键词：Pinctadafucata;single nucleotide polymorphism;transcriptome;molecular marker

中文摘要：本文基于马氏珠母贝(Pinctada fucata)血细胞比较转录组学数据进行单核苷酸多态性标记(SNP)的开发和关联基因的功能注释分析,以期为SNP标记的利用提供有效信息。在转录组测序获得的67632条SNP-unigenes中共获得962995个SNP位点,位点平均发生频率约为1个SNP/100bp;转换SNP数目与颠换SNP数目比值约为0.5,与理论比率相符;而6种单核苷酸变异类型中,以A/T颠换SNP最多。SNP-unigene功能注释分析表明,30376条unigenes(44.91%)匹配到GO分类条目;18150条unigenes(26.84%)获得COG注释信息,并以"一般功能预测"类最多;10981条unigenes(16.24%)富集到32条KEGG子集,其中以"信号转导"子集中富集的SNP-unigene最多。进一步富集分析显示629个SNP-unigenes注释到"Platelet activation"等多条免疫防御相关信号通路中;同时,根据SNP位点分布情况筛选到123个溶藻弧菌感染前、后转录组中特异分布的免疫防御相关候选SNP位点。基于标准化的基因表达水平分析,在17个差异表达免疫防御相关基因中共检测到1594个SNP位点。

外文摘要：To enrich more SNP markers for prospective genetic studies in Pinctada fueata, SNPs were predicted and characterized by analyzing reads from hemocytes transcriptome. A total of 962995 SNPs of high quality were predicted from 67632 SNP-unigenes. The average SNP frequency was one SNP per 100 bp and the estimated ratio of transition to transversion was 0.5, which is in coincidence with the theoretical ratio. A/T was the most abundant SNP type among the six SNP mutation types. By matching GO, COG and KEGG databases, 30376 （44.91%）, 18150 （26.84%, ＂general function prediction only＂ was the most dominant group） and 10981 （16.24%, ＂signal transduction＂ was the largest group） SNP-unigenes were annotated, respectively. Further enrichment and SNP distribution analysis indicated that 629 SNP-unigenes were enriched in some well-known immune-related signal pathways, and 36 and 87 specific immune-related SNPs （123 SNPs in total） were detected from pre-and post-challenged transcriptomes, respectively. Additionally, 1594 SNPs were predicted in 17 differentially expressed immune-related unigenes based on the analysis on normalized gene expressed level.