烟草叶际细菌区系检测探针的设计及优化
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- 英文论文题名：Design and optimization of microbial probes for the tobacco leaves bacteria
- 论文作者：赵敏 ; 徐宸 ; 贾凌 ; 程廷才 ; 汪长国 ; 戴亚 ; 夏庆友
- 英文论文作者：ZHAO Min ; XU Chen ; JIA Ling ; CHENG Tingcai ; WANG Changguo ; DAI Ya ; XIA Qingyou ; Chongqing Tobacco Science Research Institute ; State Key Laboratory of Silkworm Genome Biology ; Technical Center ; China Tobacco Chongqing Industrial Corporation
- 年：2016
- 作者机构：重庆烟草科学研究所;家蚕基因组生物学国家重点实验室;重庆中烟工业有限责任公司技术中心;
- 论文关键词：烟草 ; 叶际 ; 探针 ; 细菌种属
- 英文论文关键词：tobacco ; phyllosphere ; probe ; bacterial species
- 会议召开时间：2016-12-01
- 会议录名称：中国烟草学会2016年度优秀论文汇编——烟草农业主题
- 语种：中文
- 分类号：S572;Q93
- 学会代码：ZGYG
- 学会名称：中国烟草学会
- 页数：15
- 文件大小：1183k
- 原文格式：D
摘要
为了快速准确地检测烟草叶面的细菌种群,本研究利用基因芯片技术,采集我国主要烟区主栽品种旺长期叶际微生物进行宏基因组测序,结合生物信息学分析方法,筛选用以检测其中细菌种属特异性的探针。宏基因组数据分析表明,烟草叶面的宏基因组整体质量值较高,Q20、Q30分别占总碱基数99.2%、81.4%,测序长度为100bp,碱基分布均匀,所获得测序数据可用于后续探针设计。Blast比对结果表明共筛选出候选探针200条,属于9种细菌属,其中属于假单胞菌属的探针有165条。该结果为基因芯片技术应用于烟草叶面的细菌种群的检测提供了坚实的基础。
To rapidly and accurately detect the bacterial population on the tobacco leaves, the gene chip was used for screening bacterial species specific probes from metagenomic sequencing data of the main varieties grown in the national tobacco areas. The results showed that the overall quality value of sequencing reads is relatively high, the percentage of Q20 and Q30 was 99.2% and 81.4%, respectively. The sequencing length is 100 bp and the base is well-distributed. Then 200 specific candidate probes were identified from blast comparison results, which belong to 9 kinds of bacteria genera, and 165 probes belong to Pseudomonas. The results showed that gene chip technology can be applied to detect the bacteria population on the tobacco leaves.
To rapidly and accurately detect the bacterial population on the tobacco leaves, the gene chip was used for screening bacterial species specific probes from metagenomic sequencing data of the main varieties grown in the national tobacco areas. The results showed that the overall quality value of sequencing reads is relatively high, the percentage of Q20 and Q30 was 99.2% and 81.4%, respectively. The sequencing length is 100 bp and the base is well-distributed. Then 200 specific candidate probes were identified from blast comparison results, which belong to 9 kinds of bacteria genera, and 165 probes belong to Pseudomonas. The results showed that gene chip technology can be applied to detect the bacteria population on the tobacco leaves.
引文
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[29]陆光涛,唐纪良,何勇强,等.野油菜黄单胞菌野油菜致病变种一个新的致病相关基因的克隆和鉴定[J].浙江大学学报,2003,29(6):591-598.
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[31]雷丽萍,郭荣君,缪作清,等.微生物在烟草生产中应用研究进展[J].中国烟草学报,2006,12(4):47-51.
[32]王晓玲,杨冬,孙冲,等.微生物活菌剂对烤烟生长发育及烟叶品质的影响[J].中国农机化学报,2013,34(1):82-85.
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[35]Zhao Min,Wang Changguo,Liu Jin,et al.Comparison of gene expression profiles in Bacillus megaterium treated tobacco leaves using microarray[J].African Journal of Biotechnology,2013,12(51):7017-7030..
[36]赵敏,汪长国,李宁,等.微生物制剂MP代谢产物的蛋白质组分析[J].中国烟草学报,2013,19(5):108-113.
[37]张万良,翟争光,谢扬军,等.烟草赤星病研究进展[J].《江西农业学报》,2011,23(01):118-120.
[38]王益平,刘森,夏木,等.烟草黑胫病研究进展[J].现代农业科技,2013(22):129-131.
[39]左娟,向金友,程智敏,等.不同药剂对烟草青枯病的防治研究[J].现代农业科技,2011(4):143-143.
[40]王振国,丁伟.烟草野火病发生与防治的研究进展[J].《中国烟草学报》,2012,18(02):101-106.
[41]王远山,王平,胡正嘉.绿针假单胞菌PL9菌株对烟草疫霉的拮抗作用研究[J].《华中农业大学学报》,2002,21(3):66-69.
[42]杨合同,王少杰,许勃.荧光假单胞菌与植物病害生物防治[J].山东科学,1993,6(3):50-56.
[43]翟熙伦.蒙氏假单胞菌(Pseudomonas monteilii)的活性小分子物质对TMV、PVY的抑制作用[D].《中国农业科学院》,2012.
[44]谭周进,肖罗,谢丙炎等.假单胞菌的微生态调节作用[J].核农学报,2004,18(1):72-76.
[45]左静,廖晓兰.应用假单胞菌防治植物真菌性病害研究进展[J].现代农业科技,2011,1(22):164-165.
[46]林海云.青枯雷尔氏菌(Ralstonia solanacearum)致病性差异及其相关基因的分析[D].《福建农林大学》,2012.
[47]Grenier AM,Duport G,Pages S,et al.The phytopathogen Dickeya dadantii(Erwinia chrysanthemi 3937)is a pathogen of the pea aphid[J].Appl Environ Microbiol,2006,72(3):1956-1965.
[48]Coutinho TA,Venter S N.Pantoea ananatis:an unconventional plant pathogen[J].Mol Plant Pathol,2009,10(3):325-335.
[49]Bereswill S,Pahl A,Bellemann P,et al.Sensitive and species-specific detection of Erwinia amylovora by polymerase chain reaction analysis[J].Appl Environ Microbiol,1992,58(11):3522-3526.
[2]Omer Z S,Tombolini R,Gerhardson B.Plant colonization by pink-pigmented facultative methylotrophic bacteria(PPFMs)[J].Fems Microbiology Ecology,2004,47(3):319-326.
[3]Sandhu A,Halverson L J,Beattie G A.Bacterial degradation of airborne phenol in the phyllosphere[J].Environmental Microbiology,2007,9(2):383-392.
[4]潘建刚,呼庆,齐鸿雁,等.叶际微生物研究进展[J].生态学报,2011,31(2):583-592.
[5]Ruppel S,Hecht-Buchholz C,Remus R,et al.Settlement of the diazotrophic,phytoeffective bacterial strain Pantoea agglomerans on and within winter wheat:An investigation using ELISA and transmission electron microscopy[J].Plant&Soil,1992,145(2):261-273.
[6]Ruppel S,Merbach W.Effect of ammonium and nitrate on 15N 2-fixation of Azospirillum spp.and Pantoea agglomerans in association with wheat plants[J].Microbiological Research,1997,152:377-383.
[7]Koenig R L,Morris R O,Polacco J C.t RNA is the source of low-level trans-zeatin production in Methylobacterium spp[J].Journal of Bacteriology.2002,184(7):1832-1842.
[8]Doronina N V,Ivanova E G,Trotsenko Y A.New Evidence for the Ability of Methylobacteria and Methanotrophs to Synthesize Auxins[J].Microbiology,2002,71(1):116-118.
[9]Basile D V,Basile M R,Li Q Y,et al.Vitamin B12-Stimulated Growth and Development of Jungermannia leiantha Grolle and Gymnocolea inflata(Huds.)Dum.(Hepaticae)[J].The Bryologist,1985,88(2):77-81.
[10]Smith R A,Couche G A.The Phylloplane as a Source of Bacillus thuringiensis Variants[J].Applied&Environmental Microbiology,1991,57(1):311-315.
[11]陈福星,王磊,莫湘涛,等.烟叶微生物发酵的探讨[J].湖南微生物学通讯,1990,1(2):37-39.
[12]韩锦峰,朱大恒,刘卫群,等.陈化发酵期间烤烟叶面微生物活性及其应用研究[J].中国烟草科学,1997,1(4):13-14.
[13]汪长国,戴亚,朱立军,等.采收前叶面喷施微生物制剂改善烟叶品质试验[J].烟草科技,2006(4):31-34.
[14]Ye RW,Wang Tao,Bedzyk L,et al.Applications of DNA microarrays in microbial systems[J].J Microbiol Methods,2001,47(3):257-272.
[15]Kellam P.Post-genomic virology:the impact of bioinformatics,microarrays and proteomics on investigating host and pathogen interactions[J].Rev Med Virol,2001,11(5):313-329.
[16]Southern EM.DNA microarrays.History and overview[J].Methods in Molecular Biology,2001,170(170):1-15.
[17]Wang Rong-Fu,Beggs M L,Robertson L H,et al.Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples[J].FEMS Microbiol Lett,2002,213(2):175-182.
[18]Chizhikov V,Rasooly A,Chumakov K,et al.Microarray analysis of microbial virulence factors[J].Appl Environ Microbiol,2001,67(7):3258-3263.
[19]Suzuki S,Ono N,Furusawa C,et al.Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays[J].BMC Genomics,2007,8(20):1-13.
[20]Gomes M,Vieira H,Vale F F.Characterization,validation and application of a DNA microarray for the detection of mandatory and other waterborne pathogens[J].J Biochem,2015,158(5):393-401.
[21]徐淑霞,靳赛,吴坤,等.小麦表面微生物多样性研究[J].谷物化学与品质分析,2004,32(6):41-43.
[22]Wang Lin,Mao Jiugeng,Zhao Hejuan,et al.Comparison of characterization and microbial communities in rice straw-and wheat straw-based compost for Agaricus bisporus production[J].J Ind Microbiol Biotechnol,2016.
[23]刘琳,刘洋,宋未.PCR-DGGE技术及其在植物微生态研究中的应用[J].生物技术通报,2009,(3):54-56.
[24]Lee G P,Min B E,Kim C S,et al.Plant virus c DNA chip hybridization for detection and differentiation of four cucurbit-infecting Tobamoviruses[J].Journal of Virological Methods,2003,110:19-24.
[25]Abdullahi I,Koerbler M.The 18S r DNA sequence of Synchytrium endobioticum and it's utility in microarrays for the simultaneous detection of fungal and viral pathogens of potato[J].Applied Microbiology Biotechnology,2005,68:368-375.
[26]廖晓兰,朱水芳,赵文军,等.水稻白叶枯病菌和水稻细菌性条斑病菌的实时荧光PCR快速检测鉴定[J].微生物学报,2003,43(5):626-634.
[27]黄冠军,殷幼平,张仑,等.柑桔溃疡病菌滚环扩增检测体系的建立[J].微生物学报,2008,48(3):375-379.
[28]龙海,李一农,李芳荣.四种黄单胞菌的基因芯片检测方法的建立[J].生物技术通报,2011,1(1):186-190.
[29]陆光涛,唐纪良,何勇强,等.野油菜黄单胞菌野油菜致病变种一个新的致病相关基因的克隆和鉴定[J].浙江大学学报,2003,29(6):591-598.
[30]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.
[31]雷丽萍,郭荣君,缪作清,等.微生物在烟草生产中应用研究进展[J].中国烟草学报,2006,12(4):47-51.
[32]王晓玲,杨冬,孙冲,等.微生物活菌剂对烤烟生长发育及烟叶品质的影响[J].中国农机化学报,2013,34(1):82-85.
[33]高冬冬,刘忠丽,孙希文,等.我国有机烟叶主要病虫害防治方法研究进展[J].《贵州农业科学》,2013,41(06):118-122.
[34]陈兴,张天栋,党立志,等.利用西姆芽孢杆菌改善烟叶品质的研究[J].云南农业大学学报:自然科学,2016(2):322-327.
[35]Zhao Min,Wang Changguo,Liu Jin,et al.Comparison of gene expression profiles in Bacillus megaterium treated tobacco leaves using microarray[J].African Journal of Biotechnology,2013,12(51):7017-7030..
[36]赵敏,汪长国,李宁,等.微生物制剂MP代谢产物的蛋白质组分析[J].中国烟草学报,2013,19(5):108-113.
[37]张万良,翟争光,谢扬军,等.烟草赤星病研究进展[J].《江西农业学报》,2011,23(01):118-120.
[38]王益平,刘森,夏木,等.烟草黑胫病研究进展[J].现代农业科技,2013(22):129-131.
[39]左娟,向金友,程智敏,等.不同药剂对烟草青枯病的防治研究[J].现代农业科技,2011(4):143-143.
[40]王振国,丁伟.烟草野火病发生与防治的研究进展[J].《中国烟草学报》,2012,18(02):101-106.
[41]王远山,王平,胡正嘉.绿针假单胞菌PL9菌株对烟草疫霉的拮抗作用研究[J].《华中农业大学学报》,2002,21(3):66-69.
[42]杨合同,王少杰,许勃.荧光假单胞菌与植物病害生物防治[J].山东科学,1993,6(3):50-56.
[43]翟熙伦.蒙氏假单胞菌(Pseudomonas monteilii)的活性小分子物质对TMV、PVY的抑制作用[D].《中国农业科学院》,2012.
[44]谭周进,肖罗,谢丙炎等.假单胞菌的微生态调节作用[J].核农学报,2004,18(1):72-76.
[45]左静,廖晓兰.应用假单胞菌防治植物真菌性病害研究进展[J].现代农业科技,2011,1(22):164-165.
[46]林海云.青枯雷尔氏菌(Ralstonia solanacearum)致病性差异及其相关基因的分析[D].《福建农林大学》,2012.
[47]Grenier AM,Duport G,Pages S,et al.The phytopathogen Dickeya dadantii(Erwinia chrysanthemi 3937)is a pathogen of the pea aphid[J].Appl Environ Microbiol,2006,72(3):1956-1965.
[48]Coutinho TA,Venter S N.Pantoea ananatis:an unconventional plant pathogen[J].Mol Plant Pathol,2009,10(3):325-335.
[49]Bereswill S,Pahl A,Bellemann P,et al.Sensitive and species-specific detection of Erwinia amylovora by polymerase chain reaction analysis[J].Appl Environ Microbiol,1992,58(11):3522-3526.
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