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. 2015 Feb 5;3(1):e01528-14. doi: 10.1128/genomeA.01528-14

Draft Genome Sequences of Two Xanthomonas euvesicatoria Strains from the Balkan Peninsula

Taca Vancheva a,b, Pierre Lefeuvre c, Nevena Bogatzevska d, Penka Moncheva a, Ralf Koebnik b,✉
PMCID: PMC4319600  PMID: 25657284

Abstract

We report the draft genome sequences of two Xanthomonas euvesicatoria strains from the Balkan Peninsula, which were isolated from symptomatic pepper plants. The availability of these genome sequences will facilitate the development of modern genotyping assays for X. euvesicatoria strains and to define targets for resistance breeding.

GENOME ANNOUNCEMENT

First reported in the 20th century, bacterial spot has become an important disease affecting pepper and tomato production in the Balkan Peninsula (1–3). The causal agents of bacterial spot are included in the A2 list of pathogens of the European and Mediterranean Plant Protection Organization (http://www.eppo.int/QUARANTINE/quarantine.htm). Taxonomy and diversity of bacterial spot agents have been studied by phenotypic, biochemical, and DNA-based methods (4). When we applied these methods to Xanthomonas euvesicatoria strains isolated on the Balkan Peninsula (3, 5–9), we realized that these markers are not suitable to measure most population genetic parameters. A precise molecular typing tool for identification and differentiation is necessary for monitoring populations infecting pepper and tomato plants in order to develop strategies to control the disease in fields. To develop molecular markers of diversity, we decided to sequence the genomes of two X. euvesicatoria strains from the Balkan Peninsula.

Strain 66b, isolated from Capsicum annuum cv. Kambi in Bulgaria in 2012, and strain 83M, isolated from C. annuum cv. Kurtovska kapija in Macedonia in 2013, were chosen as representative X. euvesicatoria strains from the Balkan Peninsula based on their pathogenic, physiologic, and genetic characteristics (9). Their genomes were sequenced using the Illumina Hi-Seq2500 platform (Fasteris SA, Switzerland). The shotgun sequencing yielded 2,133,183 100-bp paired-end reads (533 Mb) for strain 66b and 1,605,465 paired-end reads (401 Mb) for strain 83M, with insert sizes ranging from of 250 bp to 1.5 kb. Draft genome sequences were assembled using the Edena algorithm v3.131028 (10), yielding 333 contigs larger than 500 bp (N50 = 28,793 bp) for strain 66b and 286 contigs (N50 = 31,385 bp) for strain 83M. Contigs were annotated with GeneMarkS+ release 2.9 (revision 452131) (11), as implemented in the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/), predicting a total of 4,726 genes for strain 66b and 4,495 genes for strain 83M.

These genomic resources will aid in the development of modern molecular markers to monitor epidemics and to study the dynamics of Xanthomonas populations (12–16). The genome sequence was mined for the type III effector repertoires of the two strains from the Balkan Peninsula, using the Xanthomonas resource (http://www.xanthomonas.org). Interestingly, comparison with the completely sequenced strain 85-10, which was isolated in Florida in 1985 (17), revealed some unique effectors that are present or absent in one or the other strain (e.g., AvrBs1, AvrBs3, XopE3, XopG, XopH, XopAF, and XopAQ). Knowledge about presence and allelic diversity of type III effectors will help to define targets for developing resistance strategies (18).

Nucleotide sequence accession numbers.

These whole-genome shotgun projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers JSZG00000000 (strain 66b) and JSZH00000000 (strain 83M). The versions described in this paper are the first versions, JSZG01000000 and JSZH01000000.

ACKNOWLEDGMENT

This work was supported by grant BG051PO001-3.3.05-000, financed by Operational Program “Human Resources Development” and co-financed by the European Social Fund of the European Union.

Footnotes

Citation Vancheva T, Lefeuvre P, Bogatzevska N, Moncheva P, Koebnik R. 2015. Draft genome sequences of two Xanthomonas euvesicatoria strains from the Balkan Peninsula. Genome Announc 3(1):e01528-14. doi:10.1128/genomeA.01528-14.

REFERENCES

  • 1.Karov S. 1965. Xanthomonas vesicatoria (Doidge) Dowson of pepper, p 245–250, vol 14 Scientific Publishing, High Agricultural Institute, Plovdiv, Bulgaria. [Google Scholar]
  • 2.Mitrev S, Pejcinovski F. 1999. Characterization of Xanthomonas campestris pv. vesicatoria, causal agent of bacterial spot of pepper, cv. Kurtovska kapija, p 151–163, vol X In Yearbook for plant protection. Society for Plant Protection of Republic of Macedonia, Skopje, Macedonia. [Google Scholar]
  • 3.Bogatzevska N, Stoimenova E, Mitrev S. 2007. Bacterial and virus diseases spread in Bulgaria and Macedonia on field and greenhouse pepper. Plant Protect Skopje 18:17–21. [Google Scholar]
  • 4.Jones JB, Stall RE, Bouzar H. 1998. Diversity among xanthomonads pathogenic on pepper and tomato. Annu Rev Phytopathol 36:41–58. [DOI] [PubMed] [Google Scholar]
  • 5.Mitrev S, Kovačevic B. 2006. Characterization of Xanthomonas axonopodis pv. vesicatoria isolated from peppers in Macedonia. J Plant Pathol 88:321–324. [Google Scholar]
  • 6.Kizheva Y, Vancheva T, Hristova P, Stoyanova M, Bogatzevska N, Moncheva P. 2011. Diversity of Xanthomonas spp. causal agents of bacterial spot on pepper and tomato plants in Bulgaria. Biotechnol Biotechnol Equip 25:98–104. doi: 10.5504/BBEQ.2011.0126. [DOI] [Google Scholar]
  • 7.Kizheva Y, Vancheva T, Hristova P, Stoyanova M, Stojanovska M, Moncheva P, Bogatzevska N. 2013. Identification of Xanthomonas strains from tomato and pepper and their sensitivity to antibiotics and copper. Bulgar J Agric Sci 19:80–82. [Google Scholar]
  • 8.Stoyanova M, Vancheva T, Moncheva P, Bogatzevska N. 2014. Differentiation of Xanthomonas spp. causing bacterial spot in Bulgaria based on Biolog system. Int J Microbiol 2014:495476. doi: 10.1155/2014/495476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Vancheva T, Stoyanova M, Tatyozova M, Bogatzevska N, Moncheva P. 2014. Sub-species diversity of Xanthomonas euvesicatoria Bulgarian and Macedonian strains from pepper. Biotechnol Biotechnol Equip 28:592–601. doi: 10.1080/13102818.2014.947722. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Hernandez D, Tewhey R, Veyrieras JB, Farinelli L, Østerås M, François P, Schrenzel J. 2014. De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. BioInformatics 30:40–49. doi: 10.1093/bioinformatics/btt590. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Borodovsky M, Lomsadze A. 2014. Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. Curr Protoc Microbiol 32:7. doi: 10.1002/9780471729259.mc01e07s32. [DOI] [PubMed] [Google Scholar]
  • 12.Ngoc LB, Verniere C, Vital K, Guerin F, Gagnevin L, Brisse S, Ah-You N, Pruvost O. 2009. Development of 14 minisatellite markers for the citrus canker bacterium, Xanthomonas citri pv. citri. Mol Ecol Resour 9:125–127. doi: 10.1111/j.1755-0998.2008.02242.x. [DOI] [PubMed] [Google Scholar]
  • 13.Zhao S, Poulin L, Rodriguez-R LM, Serna NF, Liu SY, Wonni I, Szurek B, Verdier V, Leach JE, He YQ, Feng JX, Koebnik R. 2012. Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola. Phytopathology 102:948–956. doi: 10.1094/PHYTO-04-12-0078-R. [DOI] [PubMed] [Google Scholar]
  • 14.Trujillo CA, Arias-Rojas N, Poulin L, Medina CA, Tapiero A, Restrepo S, Koebnik R, Bernal AJ. 2014. Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers. BMC Microbiol 14:161. doi: 10.1186/1471-2180-14-161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Cesbron S, Pothier J, Gironde S, Jacques MA, Manceau C. 2014. Development of multilocus variable-number tandem repeat analysis (MLVA) for Xanthomonas arboricola pathovars. J Microbiol Meth 100:84–90. doi: 10.1016/j.mimet.2014.02.017. [DOI] [PubMed] [Google Scholar]
  • 16.Poulin L, Grygiel P, Magne M, Gagnevin L, Rodriguez-R LM, Forero Serna N, Zhao S, El Rafii M, Dao S, Tekete C, Koita O, Pruvost O, Verdier V, Vernière C, Koebnik R. 14 2015. New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae. Appl Environ Microbiol 81:688–698. doi: 10.1128/AEM.02768-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O. 2005. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 187:7254–7266. doi: 10.1128/JB.187.21.7254-7266.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Bart R, Cohn M, Kassen A, McCallum EJ, Shybut M, Petriello A, Krasileva K, Dahlbeck D, Medina C, Alicai T, Kumar L, Moreira LM, Rodrigues Neto J, Verdier V, Santana MA, Kositcharoenkul N, Vanderschuren H, Gruissem W, Bernal A, Staskawicz BJ. 2012. High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance. Proc Natl Acad Sci USA 109:E1972–E1979. doi: 10.1073/pnas.1208003109. [DOI] [PMC free article] [PubMed] [Google Scholar]

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