摘要
【目的】基于黄地老虎转录组测序结果,对其SSR及SNP位点信息进行分析。【方法】对黄地老虎总RNA进行提取,使用Illumina平台对转录组进行测序,利用MISA和GATK软件分别对黄地老虎转录组的SSR和SNP位点特征信息进行分析。【结果】黄地老虎转录组数据库包含66469条Unigene序列。利用MISA对Unigene序列进行搜索,得到SSR位点4438个,分布于4048条Unigene序列上,占总序列的6.09%。其中,以单碱基和三碱基重复为主,分别占总重复类型的54.73%和29.29%。A/T基元是黄地老虎SSR的优势基元。SSR基元包含4~24次重复,以5次重复(21.67%)为主。SSR位点序列长度为12~127 bp,包含3493个中等多态性位点、820个高度多态性位点。利用GATK对Unigene序列SNP位点进行搜索,得到转换类型(237619个)和颠换类型(133529个)共371148个。C/T占SNP位点总数的18.61%,比率最高;G/A位居其次(18.28%),均属于转换类型。转换类型(64.02%)显著高于颠换类型(35.98%)。【结论】黄地老虎转录组数据库中SSR位点分布频率较高、种类较多且多态性丰富,转换类型是主要的SNP变异类型,可为今后开展黄地老虎种群遗传结构与分化、遗传进化关系、迁飞规律及该害虫综合防治等研究提供重要科学依据。
【Objective】Based on transcriptome dataset of Agrotis segetum,the SSR and SNP loci were analyzed.【Method】Total RNA of A.segetum was extracted and the transcriptomes were sequenced with Illumina sequencing platform.SSR and SNP information in total unigene sequences were separately analyzed by MISA and GATK.【Result】In the study,the A.segetum tra nscriptome database contained 66469 unigene sequences.MISA was used to search the Unigene sequences and 4438 SSR loci were obtained,which were distributed on 4048 Unigene sequences,accounting for 6.09%of the total sequences.Mononucleotide and trinucleotide repeats accounted for 54.73%and 29.29%of the total repeats,respectively.The A/T motifs were the dominant microsatellite loci of A.segetum SSR.SSR motifs contained 4 to 24 repeats,with 5 repetitions(21.67%)as the dominant repetitions.The length of SSR loci sequence ranged from 12 bp to 127 bp,including 3493 moderately polymorphic loci and 820 highly polymorphic loci.GATK was used to search SNP loci in Unigene sequence,and 371148 SNP loci were successfully searched,inculding 237619 conversion types and 133529 transversion types.C/T accounted for 18.61%of the total SNP sites,with the highest ratio,followed by G/A accounting for 18.28%,and all of which belonged to conversion types.The ratio of conversion type(64.02%)was significantly higher than that of transversion type(35.98%).【Conclusion】The SSR loci in the transcriptome database of A.segetum have higher distribution frequency,more species and richer polymorphism;and the conversion type is the main type of SNP variation,which can provide a very important scientific basis for future studies on the genetic structure and differentiation,genetic evolution,migratory rule and integrated control of A.segetum population.
作者
常虹
高燕
王思威
王潇楠
刘艳萍
孙海滨
CHANG Hong;GAO Yan;WANG Siwei;WANG Xiaonan;LIU Yanping;SUN Haibin(Plant Protection Research Institute,Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of High Technology for Plant Protection,Guangzhou 510640,China)
出处
《广东农业科学》
CAS
2022年第2期118-125,共8页
Guangdong Agricultural Sciences
基金
广东省农业科学院青年导师制项目(R2020QD-021)
广东省农业科学院院长基金(202026)
广东省重点领域研发计划项目(2020B020223004)。
关键词
黄地老虎
转录组
微卫星
简单重复序列
单核苷酸多态性
Agrotis segetum
transcriptome
microsatellite
simple sequence repeat(SSR)
single nucleotide polymorphism(SNP)
