| 常 虹，高 燕，王思威，王潇楠，刘艳萍，孙海滨.基于黄地老虎转录组测序的 SSR 和 SNP 特征分析[J].广东农业科学,2022,49(2):118-125 |
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基于黄地老虎转录组测序的 SSR 和 SNP 特征分析 |
| Analysis of SSR and SNP Loci in Agrotis segetum Based on Transcriptome Sequencing |
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| DOI：10.16768/j.issn.1004-874X.2022.02.014 |
| 中文关键词: 黄地老虎 转录组 微卫星 简单重复序列 单核苷酸多态性 |
| 英文关键词: Agrotis segetum transcriptome microsatellite simple sequence repeat (SSR) single nucleotide polymorphism (SNP) |
| 基金项目: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） |
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| 中文摘要: |
| 【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66 469条Unigene序列。利用MISA对Unigene序
列进行搜索，得到SSR位点4 438个，分布于4 048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3 493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（237 619个）和颠换类型（133 529个）
共371 148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。 |
| 英文摘要: |
| 【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 66 469 unigene sequences. MISA was used to search the
Unigene sequences and 4 438 SSR loci were obtained, which were distributed on 4 048 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 3 493 moderately polymorphic loci and 820 highly polymorphic loci. GATK was used to search SNP loci in Unigene sequence, and 371 148 SNP loci were successfully searched, inculding 237 619 conversion types and 133
529 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. |
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