热带臭虫转录组分析

李婷, 廖嵩, 徐业, 王常禄, 王建国

doi:10.11853/j.issn.1003.8280.2022.01.010

中国媒介生物学及控制杂志 >

2022 , Vol. 33 >Issue 1: 54 - 61

DOI: https://doi.org/10.11853/j.issn.1003.8280.2022.01.010

实验研究

热带臭虫转录组分析

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1. 江西农业大学入侵生物实验室, 江西南昌 330045;
2. Department of Entomology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA

李婷,女,在读硕士,从事农业昆虫与害虫防治研究,E-mail:tinglilsy@qq.com

收稿日期: 2021-08-16

网络出版日期: 2022-02-17

基金资助

江西省2018年“双千人才”计划（jxsq2018102116）；江西省国家外国专家项目（G20200222010，G2021022002）

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Transcriptome analysis of Cimex hemipterus （Hemiptera： Cimicidae）

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1. Laboratory of Invasion Biology, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China;
2. Department of Entomology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA

Received date: 2021-08-16

Online published: 2022-02-17

Supported by

Jiangxi Province 2018＂Double Thousand Talents＂Plan (No. jxsq2018102116); Jiangxi Province National Foreign Experts Program (No. G20200222010, G2021022002)

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摘要

目的获得热带臭虫转录组数据，为后续基因功能研究奠定基础。方法基于Illumina NovaSeq 6000高通量测序平台，对热带臭虫混合样本进行测序，采用Trinity软件组装有效测序数据获得unigenes。将unigenes分别与非冗余蛋白数据库（NR）、基因本体论（GO）、京都基因和基因组百科全书（KEGG）、直系同源蛋白分组比对数据库（eggNOG）和注释蛋白数据库（Swiss-Prot）进行比对和功能注释，利用MISA软件对热带臭虫的unigenes进行简单重复序列位点分析，使用Samtools和GATK软件检测热带臭虫单核苷酸多态性（SNP）。结果转录组测序数据质控后获得5.49 Gb高质量数据，组装后获得21 619个unigenes，总长度为29 322 540 bp，平均长度为1 356 bp。将unigenes序列与5个公共数据库进行比对和功能注释，得到45 362个有功能注释的unigenes，预测发现10 906条编码区序列，检测到7 754个简单重复序列（SSR）位点信息和33 144个SNP位点信息。结论报道并构建了热带臭虫转录组数据库，并对21 619个unigenes进行组装和功能注释分析，该数据的获得可为后期热带臭虫的功能基因研究、SSR和SNP分子标记开发、遗传多样性分析以及遗传图谱构建等奠定基础。

关键词： 热带臭虫; 转录组; 生物信息学; 微卫星; 单核苷酸多态性

本文引用格式

李婷, 廖嵩, 徐业, 王常禄, 王建国 . 热带臭虫转录组分析[J]. 中国媒介生物学及控制杂志, 2022 , 33(1) : 54 -61 . DOI: 10.11853/j.issn.1003.8280.2022.01.010

Abstract

Objective To obtain the transcriptome data of Cimex hemipterus and to provide a basis for subsequent functional genomic studies. Methods The mixed sample of C. hemipterus was sequenced on the Illumina NovaSeq 6000 high-throughput sequencing platform. Unigenes were obtained by assembling the sequencing data using the Trinity software for alignment and functional annotation against the databases of non-redundant protein sequence (NR), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (eggNOG), and Swiss-Prot. The unigenes were analyzed for simple sequence repeat (SSR) loci with MISA and single nucleotide polymorphism (SNP) loci with Samtools and GATK softwares. Results A total of 5.49 Gb high-quality data were obtained from quality-controlled raw sequencing data. A total of 21 619 unigenes with a total length of 29 322 540 bp and an average length of 1 356 bp were obtained. Alignment and functional annotation of the unigenes sequences with five public databases resulted in 45 362 functional unigenes, 10 906 coding sequences (CDSs), 7 754 SSR loci, and 33 144 SNPs. Conclusion The transcriptome database of C. hemipterus was established and 21 619 unigenes were assembled for functional annotation analysis, which lays a foundation for subsequent studies of C. hemipterus in terms of functional genes, molecular marker development of SSR and SNP, genetic diversity, and genetic maps.

Key words： Cimex hemipterus; Transcriptome; Bioinformatics; Microsatellite; Single nucleotide polymorphism

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