未知植物病毒分子生物学检测方法的研究现状
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摘要
植物的真菌病原菌可以通过核糖体RNA或者其他通用引物进行鉴定,植物病毒缺乏通用引物,这给植物未知病毒病的鉴定带来较大挑战。随着分子生物学及测序技术的发展,出现了很多直接从植物病料中检测未知病毒的方法,这些方法推进了植物病毒的发掘和病原鉴定,取得了非常好的效果。本文主要阐述近年来应用于检测未知植物病毒的分子生物学方法。
The fungal pathogen in plants can be identified by ribosomal RNA or other universal primers. Due to the lack of universal primers for plant viruses,the diagnosis of unknown viral diseases in plants encountered a great challenge.With the development of molecular biology and sequencing technology,there were many methods for detecting unknown viruses directly from plant diseases. The discovery and identification of plant viruses were promoted by using these methods,and good results were achieved. This paper reviews the application of molecular biological detection methods for unknown plant viruses in recent years.
The fungal pathogen in plants can be identified by ribosomal RNA or other universal primers. Due to the lack of universal primers for plant viruses,the diagnosis of unknown viral diseases in plants encountered a great challenge.With the development of molecular biology and sequencing technology,there were many methods for detecting unknown viruses directly from plant diseases. The discovery and identification of plant viruses were promoted by using these methods,and good results were achieved. This paper reviews the application of molecular biological detection methods for unknown plant viruses in recent years.
引文
[1] STRANGE R N,SCOTT P R. Plant disease:a threat to globalfood security[J]. Annual Review of Phytopathology,2005,43:83-116.
[2] SEIFERT K A. Progress towards DNA barcoding of fungi[J]. Mo-lecular Ecology Resources,2009,9:83-89.
[3] STACKEBRANDT E,GOEBEL B M. Taxonomic note:a place forDNA-DNA reassociation and 16S rRNA sequence analysis in thepresent species definition in bacteriology[J]. International Journalof Systematic and Evolutionary Microbiology,1994,44(4):846-849.
[4] GOLDSMITH C S,MILLER S E. Modern uses of electron micros-copy for detection of viruses[J]. Clinical Microbiology Reviews,2009,22(4):552-563.
[5] BYSTRICKA D,LENZ O,MRAZ I,et al. Oligonucleotide-basedmicroarray:a new improvement in microarray detection of plant vi-ruses[J]. Journal of Virological Methods,2005,128(1/2):176-182.
[6]王莉爽,陈小均,何海永,等.贵州辣椒脉斑驳病毒的检测及株系分化研究[J].南方农业学报,2017,48(7):1220-1224.
[7]马新颖,汪琳,任鲁风,等. 10种植物病毒的基因芯片检测技术研究[J].植物病理学报,2007,37(6):561-565.
[8]孙玉兰,李德新.新病毒鉴定的分子生物学技术[J].病毒学报,2011,27(2):170-175.
[9] LACROIX C,RENNER K,COLE E,et al. Methodological guide-lines for accurate detection of viruses in wild plant species[J].Applied and Environmental Microbiology,2016,82:1966-1975.
[10]张晓婷,吴祖建,林奇英,等.双链RNA技术与植物病毒研究[J].云南农业大学学报,2005,20(4):455-458.
[11] DALE J L. Banana bunchy top:an economically important tropicalplant virus disease[J]. Advances in Virus Research,1987,33:301-326.
[12] ADAMS I P,MIANO D W,KINYUA Z M,et al. Use of next-gen-eration sequencing for the identification and characterization ofMaize chlorotic mottle virus and Sugarcane mosaic virus causingmaize lethal necrosis in Kenya[J]. Plant Pathology,2013,62(4):741-749.
[13] OKADA R,KIYOTA E,MORIYAMA H,et al. A simple and rap-id method to purify viral dsRNA from plant and fungal tissue[J].Journal of General Plant Pathology,2015,81(2):103-107.
[14] LISITSYN N,WIGLER M. Cloning the differences between twocomplex genomes[J]. Science,1993,259(5097):946-951.
[15]战晴晴.柴胡全长c DNA文库和遗传图谱的构建及蚕豆病毒属病毒的鉴定[D].哈尔滨:东北林业大学,2010.
[16] COOPER B,ECKERT D,ANDON N L,et al. Investigative pro-teomics:identification of an unknown plant virus from infectedplants using mass spectrometry[J]. Journal of the American Socie-ty for Mass Spectrometry,2003,14(7):736-741.
[17] REYES G R,KIM J P. Sequence-independent,single-primer am-plification(SISPA)of complex DNA populations[J]. Molecularand Cellular Probes,1991,5(6):473-481.
[18] ALLANDER T,EMERSON S U,ENGLE R E,et al. A virus dis-covery method incorporating DNase treatment and its application tothe identification of two bovine parvovirus species[J]. Proceedingsof the National Academy of Sciences,2001,98(20):11609-11614.
[19] ALLANDER T,TAMMI M T,ERIKSSON M,et al. Cloning of ahuman parvovirus by molecular screening of respiratory tract sam-ples[J]. Proceedings of the National Academy of Sciences,2005,102(36):12891-12896.
[20] ZHANG T,BREITBART M,LEE W H,et al. RNA viral commu-nity in human feces:prevalence of plant pathogenic viruses[J].PLoS Biology,2005,4(1):e3.
[21]赵西梅.地黄和白术病毒病病原检测及病毒全基因组序列测定与分析[D].晋中:山西农业大学,2013.
[22] BADILLO-VARGAS I E,BAKER C A,TURECHEK W W,et al.Genomic and biological characterization of Tomato necrotic streakvirus,a novel subgroup 2 ilarvirus infecting tomato in Florida[J].Plant Disease,2016,100(6):1046-1053.
[23] CIUFFO M,MAMMELLA M,VALLINO M,et al. Molecular i-dentification and biological characterization of a new potyvirus inlettuce[J]. Archives of Virology,2016,161(9):2549-2554.
[24] SHAHID M S,ABOUGHANEM-SABANADZOVIC N,SABA-NADZOVIC S,et al. Genomic characterization and populationstructure of a badnavirus infecting blackberry[J]. Plant Disease,2017,101(1):110-115.
[25] YASAKI M,HIRANO Y,UGA H,et al. Characterization of a newcarmovirus isolated from an Adonis plant[J]. Archives of Virolo-gy,2017,162(2):501-504.
[26]钱亚娟,徐毅,周琦,等.利用深度测序技术发掘植物病毒资源[J].中国科学(生命科学),2014,44(4):351-363.
[27] BARBA M,CZOSNEK H,HADIDI A. Historical perspective,de-velopment and applications of next-generation sequencing in plantvirology[J]. Viruses,2014,6(1):106-136.
[28] ZENGLER K,PALSSON B O. A road map for the development ofcommunity systems(CoSy)biology[J]. Nature Reviews Microbi-ology,2012,10(5):366.
[29] ADAMS I P,GLOVER R H,MONGER W A,et al. Next-genera-tion sequencing and metagenomic analysis:a universal diagnostictool in plant virology[J]. Molecular Plant Pathology,2009,10(4):537-545.
[30] GREEN K J,MOLLOV D,TRAN L T,et al. Characterization of anew tymovirus causing stunting and chlorotic mosaic in naranjilla(Solanum quitoense)[J]. Plant Disease,2018,102(5):911-918.
[31] TANG J,LEBAS B,LIEFTING L,et al. Opium poppy mosaic vi-rus,a new umbravirus isolated from Papaver somniferum in NewZealand[J]. Archives of Virology,2016,161(1):197-201.
[32] PETRZIK K,PRIBYLOVJ,KOLONIUK I,et al. Molecularcharacterization of a novel capillovirus from red currant[J]. Ar-chives of Virology,2016,161(4):1083-1086.
[33] PARDINA P E R,BEJERMAN N,LUQUE A V,et al. Completenucleotide sequence of an Argentinean isolate of sweet potato virusG[J]. Virus Genes,2012,45(3):593-595.
[34] HU Q,HOLLUNDER J,NIEHL A,et al. Specific impact of to-bamovirus infection on the Arabidopsis small RNA profile[J].PLoS ONE,2011,6(5):e19549.
[35] MOLNR A,CSORBA T,LAKATOS L,et al. Plant virus-de-rived small interfering RNAs originate predominantly from highlystructured single-stranded viral RNAs[J]. Journal of Virology,2005,79(12):7812-7818.
[36]朱慧,郭惠珊.植物中病毒来源的小RNA介导的RNA沉默[J].中国科学(生命科学),2012,42(1):29-36.
[37] PANTALEO V,SALDARELLI P,MIOZZI L,et al. Deep sequen-cing analysis of viral short RNAs from an infected Pinot Noir gra-pevine[J].Virology,2010,408:49-56.
[38] LI R,GAO S,HERNANDEZ A G,et al. Deep sequencing ofsmall RNAs in tomato for virus and viroid identification and straindifferentiation[J]. PLoS ONE,2012,7(5):e37127.
[39]何艳.蔷薇科植物上两种未知病毒的基因组克隆及其分子特性分析[D].武汉:华中农业大学,2015.
[40] HE Y,YANG Z,HONG N,et al. Deep sequencing reveals a no-vel closterovirus associated with wild rose leaf rosette disease[J].Molecular Plant Pathology,2015,16(5):449-458.
[41]陈莎.深度测序鉴定玉米病毒及感病玉米组织中小RNA分析[D].杭州:浙江大学,2015.
[42] ROOSSINCK M J. Deep sequencing for discovery and evolutionaryanalysis of plant viruses[J]. Virus Research,2017,239:82-86.
[2] SEIFERT K A. Progress towards DNA barcoding of fungi[J]. Mo-lecular Ecology Resources,2009,9:83-89.
[3] STACKEBRANDT E,GOEBEL B M. Taxonomic note:a place forDNA-DNA reassociation and 16S rRNA sequence analysis in thepresent species definition in bacteriology[J]. International Journalof Systematic and Evolutionary Microbiology,1994,44(4):846-849.
[4] GOLDSMITH C S,MILLER S E. Modern uses of electron micros-copy for detection of viruses[J]. Clinical Microbiology Reviews,2009,22(4):552-563.
[5] BYSTRICKA D,LENZ O,MRAZ I,et al. Oligonucleotide-basedmicroarray:a new improvement in microarray detection of plant vi-ruses[J]. Journal of Virological Methods,2005,128(1/2):176-182.
[6]王莉爽,陈小均,何海永,等.贵州辣椒脉斑驳病毒的检测及株系分化研究[J].南方农业学报,2017,48(7):1220-1224.
[7]马新颖,汪琳,任鲁风,等. 10种植物病毒的基因芯片检测技术研究[J].植物病理学报,2007,37(6):561-565.
[8]孙玉兰,李德新.新病毒鉴定的分子生物学技术[J].病毒学报,2011,27(2):170-175.
[9] LACROIX C,RENNER K,COLE E,et al. Methodological guide-lines for accurate detection of viruses in wild plant species[J].Applied and Environmental Microbiology,2016,82:1966-1975.
[10]张晓婷,吴祖建,林奇英,等.双链RNA技术与植物病毒研究[J].云南农业大学学报,2005,20(4):455-458.
[11] DALE J L. Banana bunchy top:an economically important tropicalplant virus disease[J]. Advances in Virus Research,1987,33:301-326.
[12] ADAMS I P,MIANO D W,KINYUA Z M,et al. Use of next-gen-eration sequencing for the identification and characterization ofMaize chlorotic mottle virus and Sugarcane mosaic virus causingmaize lethal necrosis in Kenya[J]. Plant Pathology,2013,62(4):741-749.
[13] OKADA R,KIYOTA E,MORIYAMA H,et al. A simple and rap-id method to purify viral dsRNA from plant and fungal tissue[J].Journal of General Plant Pathology,2015,81(2):103-107.
[14] LISITSYN N,WIGLER M. Cloning the differences between twocomplex genomes[J]. Science,1993,259(5097):946-951.
[15]战晴晴.柴胡全长c DNA文库和遗传图谱的构建及蚕豆病毒属病毒的鉴定[D].哈尔滨:东北林业大学,2010.
[16] COOPER B,ECKERT D,ANDON N L,et al. Investigative pro-teomics:identification of an unknown plant virus from infectedplants using mass spectrometry[J]. Journal of the American Socie-ty for Mass Spectrometry,2003,14(7):736-741.
[17] REYES G R,KIM J P. Sequence-independent,single-primer am-plification(SISPA)of complex DNA populations[J]. Molecularand Cellular Probes,1991,5(6):473-481.
[18] ALLANDER T,EMERSON S U,ENGLE R E,et al. A virus dis-covery method incorporating DNase treatment and its application tothe identification of two bovine parvovirus species[J]. Proceedingsof the National Academy of Sciences,2001,98(20):11609-11614.
[19] ALLANDER T,TAMMI M T,ERIKSSON M,et al. Cloning of ahuman parvovirus by molecular screening of respiratory tract sam-ples[J]. Proceedings of the National Academy of Sciences,2005,102(36):12891-12896.
[20] ZHANG T,BREITBART M,LEE W H,et al. RNA viral commu-nity in human feces:prevalence of plant pathogenic viruses[J].PLoS Biology,2005,4(1):e3.
[21]赵西梅.地黄和白术病毒病病原检测及病毒全基因组序列测定与分析[D].晋中:山西农业大学,2013.
[22] BADILLO-VARGAS I E,BAKER C A,TURECHEK W W,et al.Genomic and biological characterization of Tomato necrotic streakvirus,a novel subgroup 2 ilarvirus infecting tomato in Florida[J].Plant Disease,2016,100(6):1046-1053.
[23] CIUFFO M,MAMMELLA M,VALLINO M,et al. Molecular i-dentification and biological characterization of a new potyvirus inlettuce[J]. Archives of Virology,2016,161(9):2549-2554.
[24] SHAHID M S,ABOUGHANEM-SABANADZOVIC N,SABA-NADZOVIC S,et al. Genomic characterization and populationstructure of a badnavirus infecting blackberry[J]. Plant Disease,2017,101(1):110-115.
[25] YASAKI M,HIRANO Y,UGA H,et al. Characterization of a newcarmovirus isolated from an Adonis plant[J]. Archives of Virolo-gy,2017,162(2):501-504.
[26]钱亚娟,徐毅,周琦,等.利用深度测序技术发掘植物病毒资源[J].中国科学(生命科学),2014,44(4):351-363.
[27] BARBA M,CZOSNEK H,HADIDI A. Historical perspective,de-velopment and applications of next-generation sequencing in plantvirology[J]. Viruses,2014,6(1):106-136.
[28] ZENGLER K,PALSSON B O. A road map for the development ofcommunity systems(CoSy)biology[J]. Nature Reviews Microbi-ology,2012,10(5):366.
[29] ADAMS I P,GLOVER R H,MONGER W A,et al. Next-genera-tion sequencing and metagenomic analysis:a universal diagnostictool in plant virology[J]. Molecular Plant Pathology,2009,10(4):537-545.
[30] GREEN K J,MOLLOV D,TRAN L T,et al. Characterization of anew tymovirus causing stunting and chlorotic mosaic in naranjilla(Solanum quitoense)[J]. Plant Disease,2018,102(5):911-918.
[31] TANG J,LEBAS B,LIEFTING L,et al. Opium poppy mosaic vi-rus,a new umbravirus isolated from Papaver somniferum in NewZealand[J]. Archives of Virology,2016,161(1):197-201.
[32] PETRZIK K,PRIBYLOVJ,KOLONIUK I,et al. Molecularcharacterization of a novel capillovirus from red currant[J]. Ar-chives of Virology,2016,161(4):1083-1086.
[33] PARDINA P E R,BEJERMAN N,LUQUE A V,et al. Completenucleotide sequence of an Argentinean isolate of sweet potato virusG[J]. Virus Genes,2012,45(3):593-595.
[34] HU Q,HOLLUNDER J,NIEHL A,et al. Specific impact of to-bamovirus infection on the Arabidopsis small RNA profile[J].PLoS ONE,2011,6(5):e19549.
[35] MOLNR A,CSORBA T,LAKATOS L,et al. Plant virus-de-rived small interfering RNAs originate predominantly from highlystructured single-stranded viral RNAs[J]. Journal of Virology,2005,79(12):7812-7818.
[36]朱慧,郭惠珊.植物中病毒来源的小RNA介导的RNA沉默[J].中国科学(生命科学),2012,42(1):29-36.
[37] PANTALEO V,SALDARELLI P,MIOZZI L,et al. Deep sequen-cing analysis of viral short RNAs from an infected Pinot Noir gra-pevine[J].Virology,2010,408:49-56.
[38] LI R,GAO S,HERNANDEZ A G,et al. Deep sequencing ofsmall RNAs in tomato for virus and viroid identification and straindifferentiation[J]. PLoS ONE,2012,7(5):e37127.
[39]何艳.蔷薇科植物上两种未知病毒的基因组克隆及其分子特性分析[D].武汉:华中农业大学,2015.
[40] HE Y,YANG Z,HONG N,et al. Deep sequencing reveals a no-vel closterovirus associated with wild rose leaf rosette disease[J].Molecular Plant Pathology,2015,16(5):449-458.
[41]陈莎.深度测序鉴定玉米病毒及感病玉米组织中小RNA分析[D].杭州:浙江大学,2015.
[42] ROOSSINCK M J. Deep sequencing for discovery and evolutionaryanalysis of plant viruses[J]. Virus Research,2017,239:82-86.