基于转录组测序的温带臭虫SSR和SNP位点分析
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摘要
[目的]温带臭虫(Cimex lectularius)是世界性分布的吸血性寄生虫,主要靠吸食人血为生。探究温带臭虫转录组SSR和SNP分布规律,可为后期温带臭虫的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研究奠定基础。[方法]以转录组数据为基础,利用软件msatcommander v0.8.2和SOAPsnp v1.03系统分析了SSR和SNP位点多态性和分布特征。[结果]温带臭虫转录组数据的25 468条unigene中含有4 758个SSR位点,分布在4 171unigene序列中。其中单核苷酸重复的次数最多,共有2 795个,占总数的58.74%,其次是三核苷酸重复和二核苷酸重复分别是984个(20.68%)和764个(16.06%),四核苷酸重复有195个(4.10%),而五、六核苷酸重复最少,仅出现20次(0.42%)。在温带臭虫的SSR位点中,共出现30个重复基元,其中优势的重复基元类型是A/T,共有2 757个,其次是AT/AT,有474个,ATT/AAT有342个。在25 468个unigene中共发现76 562个simple SNPs,其中转换类型46 634个,占60.91%,颠换类型29 928个,占39.09%。碱基转换类型比例高于颠换类型。6种单碱基变异类型中,C-T发生频率最高,比例为30.69%,其次为A-G,比例为30.22%。[结论]温带臭虫转录组中SSR和SNP位点数量多,出现频率高,且类型丰富。
[Objectives]Cimex lectularius(Bedbugs)are worldwide distribution blood-feeding ectoparasites that preferentially feed on humans.To study the distribution pattern of simple sequence repeat(SSR)and single nucleotide polymorphism(SNP)of C.lectularius would be benefit a lot to the molecular marker development,genetic diversity analysis and genetic map construction study in the further research.[Methods]The SSR and SNP loci were searched and analyzed based on the transcriptomic data of C.lectularius,using the software of msatcommander v0.8.2 and SOAPsnp v1.03,respectively.[Results]A total of 25 468 unigenes were detected.4 758 SSR loci were identified,distributing in 4 171 unigenes.The mononucleotide repeats were the most abundant SSR type with a frequency of 58.74%,followed by trinucleotide repeat (20.68%),dinuclotide repeat (16.06%) and tetranucleotide(4.10%),respectively.Pentonucleotide and hexanucleotide repeats were 20 in all.There were 30 kinds of repeated motif types in C.lectularius transcriptome SSR.A/T was the most advantages repeat motif types (2 757),then AT/AT(474) and ATT/AAT(342).A total of 76 562 candidate simple SNPs in 25 468 unigenes were identified.The transition types of SNPs were 46 634,with the proportion of 60.91%,while the transversion type were 29 928,with the proportion of 39.09%.The number of the transition type was higher than that of the transversion type.The C/T and A/G belonging to the transition type occurred most frequently among six kinds of SNP types with the proportion of 30.69% and 30.22%,respectively.[Conclusion]The SSR and SNP loci in the sequence of the bedbug transcriptome are abundant.The frequencies of the SSR and SNP loci are high and the types of them were rich.
[Objectives]Cimex lectularius(Bedbugs)are worldwide distribution blood-feeding ectoparasites that preferentially feed on humans.To study the distribution pattern of simple sequence repeat(SSR)and single nucleotide polymorphism(SNP)of C.lectularius would be benefit a lot to the molecular marker development,genetic diversity analysis and genetic map construction study in the further research.[Methods]The SSR and SNP loci were searched and analyzed based on the transcriptomic data of C.lectularius,using the software of msatcommander v0.8.2 and SOAPsnp v1.03,respectively.[Results]A total of 25 468 unigenes were detected.4 758 SSR loci were identified,distributing in 4 171 unigenes.The mononucleotide repeats were the most abundant SSR type with a frequency of 58.74%,followed by trinucleotide repeat (20.68%),dinuclotide repeat (16.06%) and tetranucleotide(4.10%),respectively.Pentonucleotide and hexanucleotide repeats were 20 in all.There were 30 kinds of repeated motif types in C.lectularius transcriptome SSR.A/T was the most advantages repeat motif types (2 757),then AT/AT(474) and ATT/AAT(342).A total of 76 562 candidate simple SNPs in 25 468 unigenes were identified.The transition types of SNPs were 46 634,with the proportion of 60.91%,while the transversion type were 29 928,with the proportion of 39.09%.The number of the transition type was higher than that of the transversion type.The C/T and A/G belonging to the transition type occurred most frequently among six kinds of SNP types with the proportion of 30.69% and 30.22%,respectively.[Conclusion]The SSR and SNP loci in the sequence of the bedbug transcriptome are abundant.The frequencies of the SSR and SNP loci are high and the types of them were rich.
引文
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[3]Wang L,Cai X Q,Xu Y J.Status of urban bed bug infestations in southern China:An Analysis of Pest Control Service Records in Shenzhen in 2012and Dongguan in 2013[J].Journal of Medical Entomology,2015,52(1):76-80.
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[15]袁远,张丽芳,吴国星,等.云南切梢小蠹微卫星的高通量发掘[J].环境昆虫学报,2014,36(2):166-170.
[16]孟翔,胡俊杰,李艳华,等.基于转录组数据的荔枝蒂蛀虫SSR位点信息分析[J].环境昆虫学报.201 7,39(6):1219-1224.
[17]李微,张蕾,程云霞,等.应用转录组测序高通量发掘东方粘虫SSR标记[J].植物保护学报,2017,44(3):377-384.
[18]Zhu J Y,Li Y H,Yang S,et al.De novo assembly and characterization of the global transcriptome for Rhyacionia leptotubula using illumina paired-end sequencing[J].Plos One,2013,8(11):e81096.
[19]魏丹丹,石俊霞,张夏瑄,等.基于转录组数据的桔小实蝇微卫星位点信息分析[J].应用生态学报,2014,25(6):1799-1805.
[20]Zou D Y,Coudron T A,Liu C X,et al.Nutrigenomics in Arma chinensis:transcriptome analysis of Arma chinensis fed on artificial diet and Chinese oak silk moth Antheraea pernyi pupae[J].Plos One,2013,8(4):e60881.
[21]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.
[22]段慧生,张安盛,赵传志,等.西花蓟马EST-SSR信息分析、标记筛选及其与Genomic-SSR的多态性比较[J].昆虫学报,2012,55(6):634-640.
[23]胡艳华,李敏,张虎芳,等.粘虫转录组中SSR位点的信息分析[J].山西农业大学学报(自然科学版),2015,35(5):484-489.
[24]唐培安,陶冶心,薛昊,等.基于转录组数据的印度谷螟微卫星位点分析[J].植物保护,2017,43(3):43-48,75.
[25]Cook N,Aziz N,Hedley P E,et al.Transcriptome sequencing of an ecologically important graminivorous sawfly:a resource for marker development[J].Conservation Genetics Resources,2011,3(4):789-795.
[26]Li L T,Zhu Y B,Ma J F,et al.An analysis of the Athetis lepigone transcriptome from four developmental stages[J].Plos One,2013,8(9):e73911.
[27]Sun J T,Zhang Y K,Ge C,et al.Mining and characterization of sequence tagged microsatellites from the brown planthopper Nilaparvata lugens[J].Journal of Insect Science,2011,11(134):1-11.
[28]Zhang F J,Guo H Y,Zheng H J,et al.Massively parallel pyrosequencing-based trancriptome analyses of small brown planthopper(Laodelphax striatellus),a vector insect transmitting rice stripe virus(RSV)[J].BMC Genomics,2010,11(1):303.
[29]Metzgar D,Bytof J,Wills C.Selection against frameshift mutations limits microsatellite expansion in coding DNA[J].Genome Research,2000,10(1):72-80.
[30]Brookes A J.The essence of SNPs[J].Gene,1999,234(2):177-186.
[31]钱荷英,李刚,李龙,等.基于家蚕抗血液型脓病新品种的SNP分子标记开发[J].河北农业大学学报,2018,41(1):76-82.
[2]Wang C L,Wen X J.Bed bug infestations and control practices in China:implications for fighting the global bed bug resurgence[J].Insects,2011,2(2):83-95.
[3]Wang L,Cai X Q,Xu Y J.Status of urban bed bug infestations in southern China:An Analysis of Pest Control Service Records in Shenzhen in 2012and Dongguan in 2013[J].Journal of Medical Entomology,2015,52(1):76-80.
[4]王磊,王常禄,许益镌,等.臭虫的再猖獗、生物学及防治研究进展[J].昆虫学报,2016,59(9):1021-1032.
[5]刘小闪,陈轶岚,靖博彬.铁路旅客列车臭虫防控研究进展[J].铁路节能环保与安全卫生,2017,7(3):137-139.
[6]Tautz D.Hypervariability of simple sequences as a general source for polymorphic DNA markers[J].Nucleic Acids Research,1989,17(16):6463-6471.
[7]Jarne P,Lagoda P J L.Microsatellites,from molecules to populations and back[J].Trends in Ecology and Evolution,1996,11(10):424-429.
[8]Liu S R,An Y L,Li F D,et al.Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers for genetic studies in tea plant(Camellia sinensis)[J].Molecular Breeding,2018,38(5):59.
[9]Moon S,Lee H Y Shim D,et al.Development and molecular characterization of novel polymorphic genomic DNA SSR markers in Lentinula edodes[J].Mycobiology,2017,45(2):105-109.
[10]Mammadov J,Aggarwal R,Buyyarapu R,et al.SNP markers and their impact on plant breeding[J].International Journal of Plant Genomics,2012(3):728398.
[11]Ganal M W,Altmann T,R9der M S.SNP identification in crop plants[J].Current Opinion in Plant Biology,2009,12(2):211-217.
[12]Laosatit K,Tanya P,Somta P,et al.De novo transcriptome analysis of apical meristem of Jatropha spp.using 454pyrosequencing platform,and identification of SNP and EST-SSR markers[J].Plant Molecular Biology Reporter,2015,34(4):786-793.
[13]Faircloth B C.MSATCOMMANDER:detection of microsatellite repeat arrays and automated,locus-specific primer design[J].Molecular Ecology Resources,2008,8(1):92-94.
[14]Li R Q,Li Y R,Kristiansen K,et al.SOAP:short oligonucleotide alignment program[J].Bioinformatics,2008,24(5):713-714.
[15]袁远,张丽芳,吴国星,等.云南切梢小蠹微卫星的高通量发掘[J].环境昆虫学报,2014,36(2):166-170.
[16]孟翔,胡俊杰,李艳华,等.基于转录组数据的荔枝蒂蛀虫SSR位点信息分析[J].环境昆虫学报.201 7,39(6):1219-1224.
[17]李微,张蕾,程云霞,等.应用转录组测序高通量发掘东方粘虫SSR标记[J].植物保护学报,2017,44(3):377-384.
[18]Zhu J Y,Li Y H,Yang S,et al.De novo assembly and characterization of the global transcriptome for Rhyacionia leptotubula using illumina paired-end sequencing[J].Plos One,2013,8(11):e81096.
[19]魏丹丹,石俊霞,张夏瑄,等.基于转录组数据的桔小实蝇微卫星位点信息分析[J].应用生态学报,2014,25(6):1799-1805.
[20]Zou D Y,Coudron T A,Liu C X,et al.Nutrigenomics in Arma chinensis:transcriptome analysis of Arma chinensis fed on artificial diet and Chinese oak silk moth Antheraea pernyi pupae[J].Plos One,2013,8(4):e60881.
[21]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.
[22]段慧生,张安盛,赵传志,等.西花蓟马EST-SSR信息分析、标记筛选及其与Genomic-SSR的多态性比较[J].昆虫学报,2012,55(6):634-640.
[23]胡艳华,李敏,张虎芳,等.粘虫转录组中SSR位点的信息分析[J].山西农业大学学报(自然科学版),2015,35(5):484-489.
[24]唐培安,陶冶心,薛昊,等.基于转录组数据的印度谷螟微卫星位点分析[J].植物保护,2017,43(3):43-48,75.
[25]Cook N,Aziz N,Hedley P E,et al.Transcriptome sequencing of an ecologically important graminivorous sawfly:a resource for marker development[J].Conservation Genetics Resources,2011,3(4):789-795.
[26]Li L T,Zhu Y B,Ma J F,et al.An analysis of the Athetis lepigone transcriptome from four developmental stages[J].Plos One,2013,8(9):e73911.
[27]Sun J T,Zhang Y K,Ge C,et al.Mining and characterization of sequence tagged microsatellites from the brown planthopper Nilaparvata lugens[J].Journal of Insect Science,2011,11(134):1-11.
[28]Zhang F J,Guo H Y,Zheng H J,et al.Massively parallel pyrosequencing-based trancriptome analyses of small brown planthopper(Laodelphax striatellus),a vector insect transmitting rice stripe virus(RSV)[J].BMC Genomics,2010,11(1):303.
[29]Metzgar D,Bytof J,Wills C.Selection against frameshift mutations limits microsatellite expansion in coding DNA[J].Genome Research,2000,10(1):72-80.
[30]Brookes A J.The essence of SNPs[J].Gene,1999,234(2):177-186.
[31]钱荷英,李刚,李龙,等.基于家蚕抗血液型脓病新品种的SNP分子标记开发[J].河北农业大学学报,2018,41(1):76-82.