High genetic variation and recombination events in the vicinity of non-autonomous transposable elements from ‘Candidatus Liberibacter asiaticus’
WANG Xue-feng, CHEN Jiao-yue, TAN Jin , DUAN Suo, DENG Xiao-ling, CHEN Jian-chi, ZHOU Chang-yong
1、National Citrus Engineering Research Center, Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest
University, Chongqing 400712, P.R.China
2、College of Plant Protection, Southwest University, Chongqing 400715, P.R.China
3、Citrus Huanglongbing Research Center, South China Agricultural University, Guangzhou 510642, P.R.China
4、San Joaquin Valley Agricultural Sciences Center (SJVASC), USDA-ARS, Parlier, CA 93648, USA
摘要 Two miniature inverted-repeat transposable elements (MITEs), MCLas-A and MCLas-B, were recently identified from ‘Candidatus Liberibacter asiaticus’ known to be associated with citrus Huanglongbing (HLB, yellow shoot disease). MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus’ isolates from China, the United States and Brazil. Out of the 12 sequence types, three (T4, T5-2, T6) were reported for the first time. Recombination events were found in the two unique sequence types (T5-2 and T6) which were detected in all Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two well supported clades including five subclades were identified, clearly reflecting the geographical origins of isolates, especially that of Ruili isolates, São Paulo isolates and a few Florida isolates.
Abstract Two miniature inverted-repeat transposable elements (MITEs), MCLas-A and MCLas-B, were recently identified from ‘Candidatus Liberibacter asiaticus’ known to be associated with citrus Huanglongbing (HLB, yellow shoot disease). MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus’ isolates from China, the United States and Brazil. Out of the 12 sequence types, three (T4, T5-2, T6) were reported for the first time. Recombination events were found in the two unique sequence types (T5-2 and T6) which were detected in all Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two well supported clades including five subclades were identified, clearly reflecting the geographical origins of isolates, especially that of Ruili isolates, São Paulo isolates and a few Florida isolates.
Funding for this work was provided by the Special Fund for Agro-Scientific Research in the Public Interest, China (201003067-02), the Natural Science Foundation Project of CQ CSTC (cstc2012jjA80025) and the Fundamental Research Funds for the Central Universities, China (XDJK2014A001, XDJK2014D004).
About author: WANG Xue-feng, E-mail: wangxuefeng@cric.cn; CHEN Jiaoyue,E-mail: chenjiaoyueok@sina.com;* These authors contributed equally to this study.
WANG Xue-feng, CHEN Jiao-yue, TAN Jin , DUAN Suo, DENG Xiao-ling, CHEN Jian-chi, ZHOU Chang-yong.
2015.
High genetic variation and recombination events in the vicinity of non-autonomous transposable elements from ‘Candidatus Liberibacter asiaticus’. Journal of Integrative Agriculture, 14(10): 2002-2010.
Bové J M. 2006. Huanglongbing: A destructive, newly-emerging,century-old disease of citrus. Journal of Plant Pathology,88, 7-37
Chen J, Deng X, Sun X, Jones D, Irey M, Civerolo E. 2010.Guangdong and Florida populations of ‘CandidatusLiberibacter asiaticus’ distinguished by a genomic locuswith short tandem repeats. Phytopathology, 100, 567-572
Deng X, Lopes S, Wang X F, Sun X, Jones D, Irey M, Civerolo M,Chen J. 2014. Characterization of “Candidatus Liberibacterasiaticus” populations by double-locus analyses. CurrentMicrobiology, 69, 554-560
Dielot X C J, Maiden M. 2010. Impact of recombination onbacterial evolution. Trends in Microbiology, 18, 315-322
Duan Y, Zhou L, Hall D G, Li W, Doddapaneni H, Lin H, LiuL, Vahling C M, Gabriel D W, Williams K P, Dickerman A,Sun Y, Gottwald T. 2009. Complete genome sequence ofcitrus huanglongbing bacterium, ‘Candidatus Liberibacterasiaticus’ obtained through metagenomics. Molecular Plant-Microbe Interaction, 22, 1011-1020
Feschotte C, Zhang X, Wessler S R. 2002. Miniature invertedrepeattransposable elements and their relationship toestablished DNA transposons. In: Craig N L, Craigie R,Gellert M, Lambowitz A M, eds., Mobile DNA II. AmericanSociety of Microbiology, Washington, D.C.
Furuya N, Truc N, Iwanami T. 2011. Recombination-likesequences in the upstream of the phage-type DNApolymerase in ‘Candidatus Liberibacter asiaticus’. Journalof General Plant Patholology, 77, 295-298
Islam M S, Glynn J M, Bai Y, Duan Y P, Coletta-Filho HD, Kuruba G, Civerolo E L, Lin H. 2012. Multilocusmicrosatelliter analysis of ‘Candidatus Liberibacter asiaticus’associated with citrus Huanglongbing worldwide. BMCMicrobiology, 12, 39.
Jagoueix S, Bové J M. Garnier M. 1994. The phloem-limitedbacterium of greening disease of citrus is a member ofthe alpha subdivision of the Proteobacteria. International Journal of Systematic Bacteriology, 44, 379-386
Katoh H, Miyata S, Inoue H, Iwanami T. 2014. Unique featuresof a Japanese ‘Candidatus Liberibacter asiaticus’ strainrevealed by whole genome sequencing. PLoS ONE, 9,e106109.
Kumagai L, Levesque C, Blomquist C L, Madishetty K, GuoY Y, Woods P, Rooney-Latham S, Rascoe J, Gallindo T,Schnabel D, Polek M. 2013. First report of ‘CandidatusLiberibacter asiaticus’ associated with citrus Huanglongbing(HLB) in California. Plant Disease, 97, 283.
Lin H, Han C S, Liu B, Lou B, Bai X, Deng C, Civerolo E L,Gupta G. 2013. Complete genome sequence of a Chinesestrain of “Candidatus Liberibacter asiaticus”. GenomeAnnouncement, 1, e00184-13
Lin H, Lou B, Glynn J M, Doddapaneni H, Civerolo E, Chen C,Duan Y P, Zhou L J, Vahling C. 2011. The complete genomesequence of ‘Candidatus Liberibacter solanacearum’, thebacterium associated with potato zebra chip disease. PLoSONE, 6, e19135.
Liu R, Zhang P, Pu X, Xing X, Chen J, Deng X. 2011. Analysis ofa prophage gene frequency revealed population variation of‘Candidatus Liberibacter asiaticus’ from two citrus-growingprovinces in China. Plant Disease, 95, 431-435
Lopes S A, Frare G F. 2008. Graft transmission and cultivarreaction of citrus to ‘‘Candidatus Liberibacter americanus’’.Plant Disease, 92, 21-24
Mahillon J, Chandler M. 2002. Insertion sequences revisited. In:Craig N L, Craigie R, Gellert M, Lambowitz A M, eds., MobileDNA II. American Society of Microbiology, Washington,D.C. pp. 305-366
Martin D, Lerney P, Lott M, Moulton V, Posada D, LefeuvreP. 2010. RDP3: A flexible and fast computer program foranalyzing recombination. Bioinformatics, 26, 2462-2463
Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecularevolutionary genetics analysis (MEGA) software version 4.0.Molecular Biology and Evolution, 24, 1596-1599
Teixeira D C, Saillard C, Eveillard S, Danet J L, Ayres A J,Bové J M. 2005. ‘Candidatus Liberibacter americanus’,associated with citrus huanglongbing (greening disease) inSao Paulo State, Brazil. International Journal of Systematicand Evolutional Biology, 55, 1857-1862
Thompson J D, Higgins D G, Gibson T J. 1994. CLUSTAL W:Improving the sensitivity of progressive multiple sequencealignment through sequencing weighting, position-specificgap penalties and weight matrix choice. Nucleic AcidsResearch, 22, 4673-4680
Wang X F, Su H N, Huang L, Deng X, Chen J, Zhou C Y, Li ZA. 2015. Identification of a novel 1033-nucleotide deletionpolymorphism in the prophage region of ‘CandidatusLiberibacter asiaticus’: Potential applications for bacterialepidemiology. Journal of Phytopathology, 163, 681-685
Wang X F, Tan J, Bai Z Q, Su H N, Deng X, Li Z A, ZhouC Y, Chen J. 2013. Detection and characterization ofMiniature inverted-repeat transposable elements (MITEs) in“Candidatus Liberibacter asiaticus”. Journal of Bacteriology,195, 3979-3986
Wang X F, Zhou C Y, Deng X, Su H N, Chen J. 2012. Molecularcharacterization of a mosaic locus in the genome of‘Candidatus Liberibacter asiaticus’. BMC Microbiology,12, 18.
Zhang S, Flores-Cruz Z, Zhou L, Kang B H, Fleites L, GoochM D, Wulff N A, Davis M J, Duan Y, Gabriel D W. 2011.‘Ca. Liberibacter asiaticus’ carries an excision plasmidprophage and a chromosomally integrated prophage thatbecomes lytic in plant infections. Molecular Plant-MicrobeInteraction, 24, 458-468
Zheng Z, Deng X, Chen J. 2014. Whole genome sequence of“Candidatus Liberibacter asiaticus” from Guangdong, China.Genome Announcement, 2, e00273-14.
Zhou L, Powell C A, Li W, Irey M, Duan Y. 2013. Prophagemediateddynamics of ‘Candidatus Liberibacter asiaticus’populations, the destructive bacterial pathogens of citrusHuanglongbing. PLoS ONE, 8, e82248.
