Transcriptome analysis of Cimex hemipterus （Hemiptera： Cimicidae）

doi:10.11853/j.issn.1003.8280.2022.01.010

Abstract

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

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

CLC Number:

R384.9

LI Ting, LIAO Song, XU Ye, WANG Chang-lu, WANG Jian-guo. Transcriptome analysis of Cimex hemipterus （Hemiptera： Cimicidae）[J]. Chinese Journal of Vector Biology and Control, 2022, 33(1): 54-61.

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.

References

[1] 邓国藩,冯兰洲. 温带及热带臭虫Cimex lectularius L.,C. hemiptera F. 在中国的地理分布[J]. 昆虫学报,1953,2(2):253-264. DOI:10.16380/j.kcxb.1953.02.002. Deng GF,Feng LZ. The geographical distribution of the two species of bedbugs,Cimex lectularius L. and C. hemiptera F.,in China[J]. Acta Entomol Sin,1953,2(2):253-264. DOI:10. 16380/j.kcxb.1953.02.002.(in Chinese)
[2] 陆宝麟. 西部开发中的虫媒病传播问题[J]. 寄生虫与医学昆虫学报,2003,10(4):212-217. DOI:10.3969/j.issn.1005-0507. 2003.04.005. Lu BL. The problem of the transmission of insect-borne diseases in the Northwest developmental areas[J]. Acta Parasitol Med Entomol Sin,2003,10(4):212-217. DOI:10.3969/j.issn.1005-0507.2003.04.005.(in Chinese)
[3] Goddard J,deShazo R. Bed bugs (Cimex lectularius) and clinical consequences of their bites[J]. JAMA,2009,301(13):1358-1366. DOI:10.1001/jama.2009.405.
[4] Minocha R,Wang CL,Dang K,et al. Systemic and erythrodermic reactions following repeated exposure to bites from the common bed bug Cimex lectularius (Hemiptera:Cimicidae)[J]. Austral Entomol,2017,56(3):345-347. DOI:10.1111/aen.12250.
[5] Wang CL,Wen XJ. Bed bug infestations and control practices in China:Implications for fighting the global bed bug resurgence[J]. Insects,2011,2(2):83-95. DOI:10.3390/insects2020083.
[6] Wang L,Xu YJ,Zeng L. Resurgence of bed bugs (Hemiptera:Cimicidae) in mainland China[J]. Fla Entomol,2013,96(1):131-136. DOI:10.1653/024.096.0117.
[7] 任东升,吴海霞,郭玉红,等. 2018年全国臭虫监测报告[J]. 中国媒介生物学及控制杂志,2019,30(2):151-153. DOI:10.11853/j.issn.1003.8280.2019.02.008. Ren DS,Wu HX,Guo YH,et al. National vectors surveillance report on bed bugs in China,2018[J]. Chin J Vector Biol Control,2019,30(2):151-153. DOI:10.11853/j.issn.1003.8280. 2019.02.008.(in Chinese)
[8] 任东升,吴海霞,修朋程,等. 2019年全国臭虫监测报告[J]. 中国媒介生物学及控制杂志,2020,31(4):423-425. DOI:10.11853/j.issn.1003.8280.2020.04.008. Ren DS,Wu HX,Xiu PC,et al. National surveillance report on bed bugs in China,2019[J]. Chin J Vector Biol Control,2020,31(4):423-425. DOI:10.11853/j.issn.1003.8280.2020.04.008.(in Chinese)
[9] Wang L,Cai XQ,Xu YJ. Status of urban bed bug infestations in southern China:An analysis of pest control service records in Shenzhen in 2012 and Dongguan in 2013[J]. J Med Entomol,2015,52(1):76-80. DOI:10.1093/jme/tju015.
[10] Zhang JS,Xia YW,Wang CL,et al. Morphological and molecular identification of tropical bed bugs from two cities of the Pearl River Delta in China[J]. J Med Entomol,2021,58(1):471-474. DOI:10.1093/JME/TJAA155.
[11] 沈培谊. 我国臭虫防治现状的研究与展望[J]. 中华卫生杀虫药械,2011,17(4):300-303. DOI:10.19821/j.1671-2781.2011. 04.020. Shen PY. Research and prospect of bedbug control in China[J]. Chin J Hyg Insect Equip,2011,17(4):300-303. DOI:10.19821/j.1671-2781.2011.04.020.(in Chinese)
[12] 郑剑宁,裘炯良. 臭虫防治研究进展[J]. 中华卫生杀虫药械,2011,17(2):145-148. DOI:10.19821/j.1671-2781.2011.02.024. Zheng JN,Qiu JL. Advances in bedbug control research[J]. Chin J Hyg Insect Equip,2011,17(2):145-148. DOI:10.19821/j. 1671-2781.2011.02.024.(in Chinese)
[13] 李兴文,马涛,王蓬,等. 深圳地区臭虫侵害调查研究[J]. 中华卫生杀虫药械,2013,19(3):236-238,241. DOI:10.19821/j.1671-2781.2013.03.023. Li XW,Ma T,Wang P,et al. Bug hazard investigation in Shenzhen[J]. Chin J Hyg Insect Equip,2013,19(3):236-238,241. DOI:10.19821/j.1671-2781.2013.03.023.(in Chinese)
[14] 李敏,王青,陈晨,等. 基于转录组测序的温带臭虫SSR和SNP位点分析[J]. 山西农业大学学报(自然科学版),2019,39(4):52-57. DOI:10.13842/j.cnki.issn1671-8151.201812031. Li M,Wang Q,Chen C,et al. Transcriptome analysis of SSR and SNP loci in Cimex lectularius[J]. J Shanxi Agric Univ(Natl Sci Ed),2019,39(4):52-57. DOI:10.13842/j.cnki.issn1671-8151. 201812031.(in Chinese)
[15] 刘念,周小洁,戚广浩,等. 北京市温带臭虫击倒抗性基因突变检测[J]. 中国媒介生物学及控制杂志,2019,30(5):524-527,544. DOI:10.11853/j.issn.1003.8280.2019.05.010. Liu N,Zhou XJ,Qi GH,et al. Detection of knockdown resistance mutations in a Cimex lectularius field population in Beijing,China[J]. Chin J Vector Biol Control,2019,30(5):524-527,544. DOI:10.11853/j.issn.1003.8280.2019.05.010.(in Chinese)
[16] 贾孝凯,高春花,周丹丹,等. 温带臭虫对常用杀虫剂半数致死剂量的测定[J]. 中国媒介生物学及控制杂志,2020,31(1):46-48. DOI:10.11853/j.issn.1003.8280.2020.01.010. Jia XK,Gao CH,Zhou DD,et al. Measurement of the median lethal dose of several common insecticides against Cimex lectularius[J]. Chin J Vector Biol Control,2020,31(1):46-48. DOI:10.11853/j.issn.1003.8280.2020.01.010.(in Chinese)
[17] Zhao YH,Feng XY,Li M,et al. The double-mutation (M918I+L1014F) kdr allele is fixed in Cimex hemipterus populations in Guangxi,China[J]. Bull Entomol Res,2020,110(4):506-511. DOI:10.1017/S0007485319000877.
[18] Shu SH,Chen B,Zhou MC,et al. De novo sequencing and transcriptome analysis of Wolfiporia cocos to reveal genes related to biosynthesis of triterpenoids[J]. PLoS One,2013,8(8):e71350. DOI:10.1371/journal.pone.0071350.
[19] Flintoft L. Transcriptomics:digging deep with RNA-Seq[J]. Nat Rev Genet,2008,9(8):568. DOI:10.1038/nrg2423.
[20] Anholt RRH,Dilda CL,Chang S,et al. The genetic architecture of odor-guided behavior in Drosophila:Epistasis and the transcriptome[J]. Nat Genet,2003,35(2):180-184. DOI:10. 1038/ng1240.
[21] Vera JC,Wheat CW,Fescemyer HW,et al. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing[J]. Mol Ecol,2008,17(7):1636-1647. DOI:10.1111/j.1365-294X.2008.03666.x.
[22] Gibbons JG,Janson EM,Hittinger CT,et al. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics[J]. Mol Biol Evol,2009,26(12):2731-2744. DOI:10.1093/molbev/msp188.
[23] Malone JH,Oliver B. Microarrays,deep sequencing and the true measure of the transcriptome[J]. BMC Biol,2011,9:34. DOI:10.1186/1741-7007-9-34.
[24] 张棋麟,袁明龙. 基于新一代测序技术的昆虫转录组学研究进展[J]. 昆虫学报,2013,56(12):1489-1508. DOI:10.16380/j.kcxb.2013.12.005. Zhang QL,Yuan ML. Progress in insect transcriptomics based on the next-generation sequencing technique[J]. Acta Entomol Sin,2013,56(12):1489-1508. DOI:10.16380/j.kcxb.2013.12.005.(in Chinese)
[25] Grabherr MG,Haas BJ,Yassour M,et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nat Biotechnol,2011,29(7):644-652. DOI:10.1038/nbt.1883.
[26] Conesa A,Götz S,García-Gómez JM,et al. Blast2GO:A universal tool for annotation,visualization and analysis in functional genomics research[J]. Bioinformatics,2005,21(18):3674-3676. DOI:10.1093/bioinformatics/bti610.
[27] Kanehisa M,Goto S,Kawashima S,et al. The KEGG resource for deciphering the genome[J]. Nucleic Acids Res,2004,32(Database issue):D277-280. DOI:10.1093/nar/gkh063.
[28] Tatusov RL,Galperin MY,Natale DA,et al. The COG database:A tool for genome-scale analysis of protein functions and evolution[J]. Nucleic Acids Res,2000,28(1):33-36. DOI:10.1093/nar/28.1.33.
[29] 蒋月丽,李彤,武予清,等. 基于高通量测序的麦红吸浆虫转录组分析[J]. 环境昆虫学报,2020,42(1):128-136. DOI:10.3969/j.issn.1674-0858.2020.01.16. Jiang YL,Li T,Wu YQ,et al. Transcriptome analysis of Sitodiplosis mosellana Gehin by RNA-Seq[J]. J Environ Entomol,2020,42(11):128-136. DOI:10.3969/j.issn.1674-0858.2020. 01.16.(in Chinese)
[30] 罗梅,张鹤,宾淑英,等. 基于转录组数据高通量发掘扶桑绵粉蚧微卫星引物[J]. 昆虫学报,2014,57(4):395-400. DOI:10.16380/j.kcxb.2014.04.005. Luo M,Zhang H,Bin SY,et al. High-throughput discovery of SSR genetic markers in the mealybug,Phenacoccus solenopsis (Hemiptera:Pseudococcidae),from its transcriptome database[J]. Acta Entomol Sin,2014,57(4):395-400. DOI:10.16380/j.kcxb.2014.04.005.(in Chinese)
[31] Zou DY,Coudron TA,Liu CX,et al. Nutrigenomics in Arma chinensis:Transcriptome analysis of A. chinensis fed on artificial diet and Chinese oak silk moth Antheraea pernyi pupae[J]. PLoS One,2013,8(4):e60881. DOI:10.1371/journal.pone.0060881.
[32] Zhai L,Liu L,Zhu X,et al. Development,characterization and application of novel expressed sequence tag-simple sequence repeat (EST-SSR) markers in radish (Raphanus sativus L.)[J]. Afr J Biotechnol,2013,12(9):921-935. DOI:10.5897/AJB12.918.
[33] Li H,Leavengood JM Jr,Chapman EG,et al. Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs[J]. Proc Roy Soc B:Biol Sci,2017,284(1862):20171223. DOI:10.1098/rspb.2017.1223.