基于转录组测序的红萍SSR和SNP特征分析  

Characteristic Analysis of SSR and SNP in Azolla imbircata Basedon Transcriptome Sequencing

作　　者：秦煜 郑向丽 林钟员 QIN Yu;ZHENG Xiang-li;LIN Zhong-yuan(College of Geography and Oceanography,Minjiang University,Fuzhou,Fujian 350002,China;College of Future Technology,Fujian Agriculture and Forestry University,Fuzhou,Fujian 350002,China;Institute of Agricultural Ecology,Fujian Academy of Agricultural Sciences,Fuzhou,Fujian 350002,China;Fuzhou Technological Innovation Center of Seawater Planting Industry,Fuzhou,Fujian 350002,China)

机构地区：[1]闽江学院地理与海洋学院,福建福州350002 [2]福建农林大学未来技术学院,福建福州350002 [3]福建农业科学院农业生态研究所,福建福州350002 [4]福州海水种植行业技术创新中心,福建福州350002

出　　处：《福建农业科技》2023年第6期44-48,共5页Fujian Agricultural Science and Technology

基　　金：福建省自然科学基金项目(2020J01862)。

摘　　要：为了解红萍在不同氮浓度胁迫下红萍转录组中SSR、SNP分子标记的详细情况,分析转录组数据中分布的SSR和SNP位点。通过提取红萍根和叶的RNA,构建cDNA文库并利用二代测序平台进行高通量测序,利用MISA对测序数据进行SSR特征分析,同时采用软件STAR进行比对并通过GATK进行SNP识别。结果表明:红萍转录组共有9009个SSR位点,SSR位点频率为30.12%。其中,以三核苷酸重复和单核苷酸重复为主,分别占总比例的43.66%和26.41%。SNP位点有439217个,包括转换类型(282532个)和颠换类型(156685个);转换类型占比(64.33%)显著大于颠换类型(35.67%)。C/T在所有变异类型中所占比率最高,占总量的17.33%;G/A位居其次(17.01%)。红萍转录组SSR和SNP位点丰富,可为红萍遗传多样性、遗传结构与分化以及功能基因的开发利用等研究提供依据。In order to understand the detailed information of SSR and SNP molecular markers in the transcriptome of Azolla imbircata under different nitrogen concentration stress,the SSR and SNP loci distributed in the transcriptomic data were analyzed.By extracting RNA from the roots and leaves of Azolla imbircata,the cDNA library was constructed and the high-throughput sequencing was performed using the next generation sequencing platform.The SSR characteristics of the sequencing data were analyzed using MISA,and the software STAR was used for the comparison and the SNP identification was performed by GATK.The results showed that:there were a total of 9009 SSR loci in the transctiptome group of Azolla imbircata,and the frequency of SSR loci was 30.12%.Among them,the trinucleotide and mononucleotide repeats were the two most SSR type,which accounted for 43.66%and 26.41%of the total repeats,respectively.There were 439217 SNP loci,including the conversion types(282532)and transversion types(156685).The proportion of conversion types(64.33%)was significantly higher than that of transversion types(35.67%).Among all the variation types,C/T had the highest proportion,accounting for 17.33%of the total SNP loci,followed by G/A with 17.01%.The transcription group of Azolla imbircata had abundant SSR and SNP loci,which could provide a basis for the study of genetic diversity and the genetic structure and differentiation,as well as the development and utilization of functional genes.

关 键 词：红萍 转录组 SSR SNP 

分 类 号：S511[农业科学—作物学]