银杏转录组SSR位点分布及其序列特征分析  

Distribution and sequence characterization of SSR in Ginkgo biloba transcriptions

作　　者：范雪娇 汪贵斌[1] 杨晓明 周婷婷[1] 任重 FAN Xuejiao;WANG Guibin;YANG Xiaoming;ZHOU Tingting;REN Zhong(College of Forestry,Nanjing Forestry University,Nanjing 210037,Jiangsu,China)

机构地区：[1]南京林业大学,江苏南京210037

出　　处：《经济林研究》2021年第2期63-73,共11页Non-wood Forest Research

基　　金：国家自然科学基金项目“银杏叶类黄酮代谢关键基因挖掘及分子调控机制研究”(31971689)。

摘　　要：【目的】为了探究银杏叶片转录组中简单重复序列(Simple sequence repeats,SSR)的位点信息,以丰富银杏分子标记库,为日后银杏SSR分子标记的筛选和开发、SSR遗传多样性分析、遗传图谱构建和品种鉴定及种质资源保护奠定理论基础。【方法】利用Illumina HiSeq^(TM)2500高通量测序平台获得银杏叶片转录组数据,然后采用MicroSAtellite(MISA)软件对测序获得的299 373条Unigenes序列SSR位点的分布特征进行分析;再利用转录组数据开发SSR分子标记,对6份不同品种(单株)的银杏叶片材料进行扩增和筛选。【结果】通过组装得到了299 373条Unigenes序列,其总长为232 983.457 kb,其中,G+C的占比为42.82%。通过检测,共搜索到SSR位点17 821个,SSR位点的出现频率为5.95%,即平均长为13.07 kb的序列中就含有1个SSR位点,其中,有16 163条Unigenes序列含有1个以上的SSR位点;SSR位点重复类型中最主要的类型是二核苷酸和三核苷酸,分别占SSR位点总数的74.46%和23.37%,其中的AG/CT、AAG/TTC分别是二核苷酸、三核苷酸的优势重复单元,分别占SSR位点总数的31.19%和4.65%;对5种不同SSR位点重复类型的重复次数的统计结果表明,重复次数为5~11次的不同SSR位点类型占SSR位点总数的90.21%;基序长度为10~20 bp的SSR位点数占SSR位点总数的83.17%。利用6个不同品种(单株)的银杏叶片材料对所有引物进行筛选,得到了条带清晰、稳定且多态性好的引物。【结论】根据转录组测序数据中不同SSR位点的分析结果可知,转录组中SSR位点的出现频率相对较高、平均距离较短,说明转录组中SSR位点的数量和种类均较多。随着重复次数的增加,SSR位点的出现频率随之降低。重复次数和基序长度也都说明了转录组测序所得的SSR位点大部分具有多态性的潜能。试验筛选出了条带清晰、稳定且多态性好的引物,其不仅适用于后续的银杏遗传多样性分析,还可以用于�【Objective】In order to explore the site information of simple sequence repeats(SSRs) in transcriptome of Ginkgo biloba leaves, enrich the molecular marker Library of G. biloba, provide a theoretical basis for future development and selection of Ginkgo SSR molecular markers, SSR genetic diversity analysis, genetic map construction and variety identification, and protection of germplasm resources.【Method】The transcriptome data of G. biloba leaves were obtained by 2500 high-throughput sequencing platform Illumina hiseq^(TM), and then the SSR loci of 299 373 Unigenes obtained by sequencing were deeply mined and analyzed by microsatellite(MISA). Using transcriptome data to develop SSR molecular markers, amplify and screen 6 G. biloba leaf materials of different varieties(single plant).【Result】The 299373 Unigenes obtained through assembly were 232 983.457 kb in length, of which G + C accounts for 42.82%. Through the search and detection of SSR loci, a total of 17820 SSR loci were searched. The frequency of SSR loci was 5.95%, and there was 1 SSR loci at 13.07 kb on average. Among them, 16 163 Unigenes contained more than 1 SSR site;the main repeat types in SSR sequences were dinucleotide and trinucleotide, which accounted for 74.46% and 23.37% of the total number of SSR locis, respectively. Among them, AG/CT and AAG/TTC were the dominant repeating units of dinucleotide and trinucleotide, accounted for 31.19% and 4.65% of the total SSR respectively;in the statistics of the repetition times of 5 different SSR repetition types, the different SSR types whose repetition times were concentrated in 5-11 times accounted for 90.21% of the total SSR locis number;the motif length was concentrated in the 10-20 bp site, accounted for 83.17% of the total SSR. Using 6G. biloba leaf materials of different varieties(single plant) to screen all the primers, primers with clear, stable and polymorphic bands were obtained.【Conclusion】From the analysis of different SSR sites in the transcriptome sequencing data, it can be se

关 键 词：银杏 转录组 SSR 特征分析 

分 类 号：S603.2[农业科学—园艺学] S792.95