文献类型：期刊文献

中文题名：珍贵树种火力楠转录组SSR特征分析

英文题名：Characteristic Analysis of Microsatellites in the Transcriptome of Michelia macclurei of Rare Tree Species

作者：李清莹[1] 仲崇禄[1] 姜清彬[1] 张勇[1] 陈羽[1] 魏永成[1] 陈珍[1]

第一作者：李清莹

机构：[1]中国林业科学研究院热带林业研究所热带林业研究国家林业局重点实验室,广州510520

年份：2019

卷号：38

期号：4

起止页码：1674-1682

中文期刊名：基因组学与应用生物学

外文期刊名：Genomics and Applied Biology

收录：CSTPCD;;北大核心:【北大核心2017】；CSCD:【CSCD2019_2020】；

基金：中央公益性科研院所基金项目(RITFYWZX201506;CAFYBB2016SZ002);"十三五"国家重点研发计划项目任务共同资助

语种：中文

中文关键词：火力楠;转录组;SSR特征;多态性

外文关键词：Michelia macclurei;Transcriptome;SSR characteristics;Polymorphism

分类号：S792.99;Q943.2

摘要：为了全面了解珍贵乡土树种火力楠转录组SSR位点的分布及序列特征,为火力楠遗传资源的保存和合理开发利用提供遗传学资料,为同属植物及近缘种SSR标记的开发及遗传研究提供便利。利用Illumina Hiseq2000高通量测序平台对火力楠进行转录组测序,再通过MISA软件对测序所得Unigenes进行SSR位点的发掘和分析。分析的结果显示发现含SSR的序列21 218条,共得到27 379个SSR,出现频率为28.08%,平均约每3 kb出现1个SSR。单碱基和二碱基重复为火力楠SSR主要重复单元类型,分别占SSR总数的42.18%和35.66%,所有重复基元共85种,其中(A/T) n所占比例最高41.65%,然后是(AG/CT)n(29.47%)、(AAG/CTT)n (6.83%)和(AC/GT)n (4.11%)。在SSR和CDS的交集基因中,共发现24 668个SSR位点,其中3 805个位于编码区,出现频率为0.099 SSR/kb,而非编码区为0.287 SSR/kb,在基因编码区中出现频率最高的是三碱基重复(2 030, 53.35%)。在SSR序列长度方面,长度变化范围最大的为单碱基重复SSR,其次是二碱基重复。火力楠转录组SSR位点的出现频率高、分布密度大、基元类型丰富、重复次数较高、长片段较多,具有较高的多态性潜能,用于遗传分析的潜力很大,能满足该物种的保护遗传学研究。
To comprehensively understand the distribution and sequence characteristics of SSR loci in the Michelia macclurei transeriptome,and to provide a theoretical basis for further development of high efficient SSR markers.Transcriptome sequencing was conducted on M.macclurei by using Illumina Hiseq 2000.Then the SSR loci were sought and analyzed using MIS A software from the obtained unigenes.The results of the analysis showed that 21 218 SSR containing sequences were found,27 379 SSRs were obtained,with a frequency of28.08%and an average of about 1 SSR per 3 kb.Mononu cleotide and dinucleotide repeat were the main SSR types,accounting for 42.18%and 35.66%of all SSRs,respectively.Among all the 85 repeat motifs,(A/T)n was the most frequent repeat motif(41.65%),followed by(AG/CT)n(29.47%),(AAG/CTT)n(6.83%)and(AC/GT)n(4.11%).A total of 24 668 SSRs occurred in the intersection of SSR and CDS,only 3 805 of which occurred in protein-coding regions of these sequences.The density of SSRs was 0.099 SSR/kb in coding regions which was significantly lower than(0.287 SSR/kb).Moreover,trinucleotide repeat was the most abundant in coding regions(2 030,53.35%).In terms of different length repeat units,the variation of the length of mononucleotide repeat SSR was the most abundant,followed by the dinucleotide.The SSR loci in the M.macclurei transcriptome showed high frequency and density of distribution,rich repeat motifs,high repeat times,more long fragment and significant potential of polymorphism.The SSR loci could be applied in genetic analysis and conservation genetics of M.macclurei in the future.