| 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。 |
| 关键词: 马氏珠母贝 单核苷酸多态性标记 转录组 分子标记 |
| DOI：10.11693/hyhz20171000264 |
| 分类号:Q789 |
| 基金项目: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。 |
附件 |
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| SNP DISCOVERY AND FUNCTIONAL ANNOTATION IN TRANSCRIPTOME DATASETS FROM HEMOCYTES OF PINCTADA FUCATA |
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WANG Zhong-Liang1,2, DING Yu1, XU You-Hou3, WANG Bei1, ZHANG Jian-Dong1,2
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1.Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China;2.Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Zhanjiang 524088, China;3.Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou University, Qinzhou 535000, China
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| Abstract: |
| To enrich more SNP markers for prospective genetic studies in Pinctada fucata, 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. |
| Key words: Pinctada fucata single nucleotide polymorphism transcriptome molecular marker |
