文章摘要
邓素贞,韩兆方,陈小明,李庆昌,肖世俊,李佳凯,刘贤德.大黄鱼高温适应的转录组学分析[J].水产学报,2018,42(11):1673~1683
大黄鱼高温适应的转录组学分析
Transcriptome analysis of high-temperature adaptation in large yellow croaker (Larimichthys crocea)
投稿时间:2017-11-07  修订日期:2018-03-12
DOI:10.11964/jfc.20171111029
中文关键词: 大黄鱼  转录组测序  差异表达基因  qRT-PCR
英文关键词: Larimichthys crocea  transcriptome sequencing  differentially expressed genes  qRT-PCR
基金项目:国家自然科学基金(31172397);福建省高校新世纪优秀人才支持计划(JA14167)
作者单位E-mail
邓素贞 集美大学水产学院, 农业部东海海水健康养殖重点实验室, 福建 厦门 361021  
韩兆方 集美大学水产学院, 农业部东海海水健康养殖重点实验室, 福建 厦门 361021  
陈小明 集美大学水产学院, 农业部东海海水健康养殖重点实验室, 福建 厦门 361021  
李庆昌 集美大学水产学院, 农业部东海海水健康养殖重点实验室, 福建 厦门 361021  
肖世俊 集美大学水产学院, 农业部东海海水健康养殖重点实验室, 福建 厦门 361021  
李佳凯 集美大学水产学院, 农业部东海海水健康养殖重点实验室, 福建 厦门 361021  
刘贤德 集美大学水产学院, 农业部东海海水健康养殖重点实验室, 福建 厦门 361021 xdliu@jmu.edu.cn 
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中文摘要:
      为了探究大黄鱼高温胁迫条件下基因表达水平的变化,实验利用Illumina Hiseq 2 500的125 pair-ended测序模式分别对大黄鱼高温处理组和常温对照组进行了转录组测序。对照组(3个生物学重复)和高温处理组(3个生物学重复)分别获得15.28和13.92 Gb测序数据,GC含量平均值约为51%。过滤后的高质量测序reads使用Bowtie2软件比对到大黄鱼参考转录组序列上估计基因表达量,进而进行基因表达差异统计学检验。以常温对照组为参比,高温处理组中阈值设为|log2(FC)| > 2和FDR < 0.05,共检测到1 259条显著差异表达基因。其中,821条基因为高表达,438条基因为低表达。随机选取12条差异表达基因,运用实时荧光定量PCR(qRT-PCR)进行了验证,结果证实转录组分析可靠。进一步将所有差异表达的基因进行GO功能注释和KEGG通路富集分析,结果发现大量差异表达基因的功能与氧化还原反应、蛋白质折叠和去折叠、糖和脂代谢以及某些疾病的发生相关。该研究结果为下一步深入研究大黄鱼高温适应的调控机制提供了重要的参考材料。
英文摘要:
      In order to investigate the variations of gene expression of Larimichthys crocea under high temperature stress, two libraries of high temperature treatment group and control group were constructed and sequenced using the Illumina HiSeq 2500 platform (paired-end). High temperature treatment group (heat1, heat2, heat3) and control group (control1, control2, control3) obtained 15.28 Gb and 13.92 Gb raw data respectively, and the average GC content of each library was 51%. After strict filtering, clean reads were then mapped to the Larimichthys crocea reference transcriptome using the Bowtie 2 software, the amount of gene expression were also estimated according to the reads mapped to genes. EdgeR software package was then used to determine the differential gene expression of 2 groups of samples with a threshold criteria FDR < 0.05 and |log2(FC)| > 2. Totally 1259 differentially expressed genes (DEGs) were identified under high temperature stress, among which 821 genes were up-regulated and 438 genes were down-regulated. Twelve DEGs were random selected for quantitative RT-PCR (qRT- PCR) analysis, and the results confirmed that the transcriptome analysis was reliable. Furthermore, the DEGs were subject to GO and KEGG enrichment analysis, the results showed that most of the DEGs were involved in oxidation-reduction, reduction reactions, protein folding and defolding, glucose and lipid metabolism, and the occurrence of certain diseases. The results above mentioned provide foundation information for further study on the molecular mechanism of high temperature tolerance in Larimichthys crocea.
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