基于RNA-seq技术的北草蜥转录组中SSR位点信息分布  

Distribution of SSR Loci in the Transcriptome of the Northern Grass lizard(Takydromus septentrionalis)Based on RNA-seq Technology

作　　者：刘其则 陈忠荫 廖征蓝 夏岩 郭坤 杜宇 林炽贤 LIU Qize;CHEN Zhongyin;LIAO Zhenglan;XIA Yan;GUO Kun;DU Yu;LIN Chixian(College of Fisheries Life Science,Hainan Tropical Ocean University,Sanya Hainan 572022,China;Hainan Key Laboratory of Herpetological Research,Hainan Tropical Ocean University,Sanya Hainan 572022,China;Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources,Ministry of Education,Hainan Tropical Ocean University,Sanya Hainan 572022,China;College of Life and Environmental Sciences,Wenzhou University,Wenzhou Zhejiang 325035,China)

机构地区：[1]海南热带海洋学院水产与生命学院,海南三亚572022 [2]海南热带海洋学院海南省两栖爬行动物研究重点实验室,海南三亚572022 [3]海南热带海洋学院热带海洋生物资源利用与保护教育部重点实验室,海南三亚572022 [4]温州大学生命与环境科学学院,浙江温州325035

出　　处：《海南热带海洋学院学报》2021年第5期32-36,共5页Journal of Hainan Tropical Ocean University

基　　金：海南省两栖爬行动物研究重点实验室开放课题(HKLHR202001);海南省重点科技计划项目(ZDXM20110008);三亚市院地科技合作项目(2013YD08)。

摘　　要：北草蜥(Takydromus septentrionalis)是蜥蜴科草蜥属的一种爬行动物,为中国特有种,分布广泛。不同分布种群的北草蜥的体色存在差别。为了获得北草蜥皮肤组织内的简单序列重复(Simple sequence repeat,SSR)标记,以备后续对其不同生境中的体色进行差异性分析,基于转录组测序(RNAseq)组装了417190条转录本序列,合计全长479055094 bp。共识别到60968个SSR位点,含有SSR位点的转录本数目为56456条,占总转录本数目的13.53%。其中:有1个以上的SSR位点的Unigenes有10644个,存在复合形式SSR位点的数量有4513个。在SSR位点中包含1~6个核苷酸重复的所有类型,不同核苷酸重复类型的含量差异较大。单核苷酸重复型有27028个(44.33%);2核苷酸重复型和3核苷酸重复型分别有17876个(29.31%)和13332个(21.87%);4~6核苷酸重复型含量极少,位点总数占比只有4.48%。其中:4核苷酸重复型有2580个(4.23%),5核苷酸重复型和6核苷酸重复型分别只有112个(0.18%)和40个(0.07%)。从整体上看,在北草蜥转录组中,平均约7.86 kb出现1个SSR位点。The northern grass lizard(Takydromus septentrionalis)is a reptile of the genus Takydromus,which is endemic to China and widely distributed.There are differences in body color among different populations.In order to obtain simple sequence repeat(SSR)markers in the skin tissues of the northern grass lizards for subsequent analysis of body color differences in various habitats,417,190 transcript sequences with a total length of 479,055,094 bp were assembled based on transcriptome sequencing(RNAseq).A total of 60,968 SSR sites were identified,of which the number of transcripts containing SSR sites was 56,456,accounting for 13.53% of the total number of transcripts.Thereinto,there were 10,644 unigenes with more than one SSR site and 4,513 SSR sites with compound form.There existed all types of one to six nucleotide repeats,and the content of different types of nucleotide repeats varies greatly.27,028—namely 44.33%—were single nucleotide repeats.There were 17,876—namely 29.31%—of dinucleotide repeats and 13,332—namely 21.87%—of trinucleotide repeats.The content of four to six nucleotide repetitions was extremely low,and the total number of sites accounted for just 4.48%,among which there were 2,580—namely 4.23%—tetranucleotide repeats,112—namely 0.18%—pentanucleotide repeats and 40—namely 0.07%—hexanucleotide repeats.On the whole,in an average of 7.86 kb of the transcriptome exists one SSR site in northern grass lizards.

关 键 词：北草蜥 转录组 微卫星 筛选 皮肤 

分 类 号：Q3-3[生物学—遗传学] Q953