Open access
12 February 2015

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


Xanthomonas vesicatoria causes bacterial spot disease of pepper and tomato plants. We report here the first genome sequences of X. vesicatoria strains that have been isolated from pepper plants. These data will be used for comparative genomics and will allow the development of new detection and typing tools for epidemiological surveillance.


Xanthomonas vesicatoria is one of the causal agents of bacterial spot disease on pepper and tomato plants (1). The disease symptoms include chlorotic and necrotic lesions on leaves, stems, petioles, fruits, and flowers, as well as defoliation. Bacterial spot disease is present worldwide where environmental conditions are suitable for the pathogen. The disease is one of the economically most important plant diseases on the Balkan Peninsula (2, 3), with annual losses reaching 10 to 20% (4). Bacterial spots of tomato were first recorded in Bulgaria in 1936 (5). Later, the disease was also reported on pepper plants in Bulgaria (6). The first report of bacterial spot disease in Macedonia dates back to 1999 (3). Current control of the disease is mainly based on agricultural practices and the use of copper compounds. In order to develop new molecular markers for epidemiological surveillance, such as variable-number tandem repeats (VNTR) (7), we sequenced the genomes of two strains from the Balkan Peninsula.
Strain 15b, isolated from Capsicum annuum in Sofia, Bulgaria, in 2005, and strain 53M, isolated from C. annuum in Strumitsa, Macedonia, in 2005, were chosen as representative X. vesicatoria strains from the Balkan Peninsula based on their pathogenic, physiologic, and genetic characteristics (8). Their genomes were sequenced using the Illumina HiSeq 2500 platform (Fasteris SA, Switzerland). The shotgun sequencing yielded 2,163,782 100-bp paired-end reads (541 Mb) for strain 15b and 2,007,779 paired-end reads (502 Mb) for strain 53M, with insert sizes ranging from 250 bp to 1.5 kb. The draft genome sequences were assembled using the Edena algorithm version 3.131028 (9), yielding 303 contigs of >500 bp (N50, 31,449 bp) for strain 15b and 320 contigs (N50, 29,340 bp) for strain 53M. The contigs were annotated with GeneMarkS+ release 2.9 (revision 452131) (10), as implemented in the NCBI Prokaryotic Genome Annotation Pipeline (, which predicted a total of 4,601 genes for strain 15b and 4,624 genes for strain 53M.
Combined with the draft genome sequence of the New Zealand strain X. vesicatoria ATCC 35937, which was isolated from Lycopersicon lycopersicum (11), these genomic resources will aid in the development of new diagnostic tools, such as multilocus VNTR analyses (MLVA), which have been proven to be powerful tools for studying bacterial phytopathogen populations (1215). In addition, these genome sequences may give new insight into the pathogen-host interaction. For instance, a comparison of the predicted repertoires of type III effectors with the effector repertoire of the tomato isolate X. vesicatoria ATCC 35937 revealed that both pepper isolates appear to lack xopD, xopE2, and xopJ2. Contrariwise, the pepper isolates possess homologs of avrBs1 and xopH, which were not found in strain ATCC 35937. Both genes are in tandem arrangement and might be located on a plasmid, as in Xanthomonas euvesicatoria strain 85-10 (16). More sequencing and pathotyping are required to assess the importance of these effectors with respect to the host plants.

Nucleotide sequence accession numbers.

These whole-genome shotgun projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers JSXZ00000000 (strain 15b) and JSYJ00000000 (strain 53M). The versions described in this paper are the first versions, JSXZ01000000 and JSYJ01000000.


This work was supported by grant BG051PO001-3.3.05-000, financed by Operational Program “Human resources development” and cofinanced by the European Social Fund of the European Union.
T.V. thanks the European Union Erasmus+ Program for support.


Jones JB, Lacy GH, Bouzar H, Stall RE, Schaad NW. 2004. Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper. Syst Appl Microbiol 27:755–762.
Bogatzevska N, Stoimenova E, Mitrev S. 2007. Bacterial and virus diseases spread in Bulgaria and Macedonia on field and greenhouse pepper. Plant Protect 18:17–21.
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 of Plant Protection of Republic of Macedonia, Skopje, Macedonia.
Mitrev S. 2001. Phytopathogenic bacteria of pepper in Macedonia. PSI Institute of Southern Crops Strumica, Strumica, Macedonia.
Kovachevski I. 1936. New parasitic fungi in Bulgaria. Trudove na Bulgarskoto prirodoizpitvatelno druzhestvo 7:13–24.
Karov S. 1965. Xanthomonas vesicatoria (Doidge) Dowson of pepper, p 245–250, vol 14. Scientific Publishing, High Agricultural Institute, Plovdiv, Bulgaria.
van Belkum A. 2007. Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA). FEMS Immunol Med Microbiol 49:22–27.
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.
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.
Borodovsky M, Lomsadze A. 2014. Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. Curr Protoc Microbiol 32:7.
Potnis N, Krasileva K, Chow V, Almeida NF, Patil PB, Ryan RP, Sharlach M, Behlau F, Dow, Potnis N, Krasileva K, Chow V, Almeida NF, Patil PB, Ryan RP, Sharlach M, Behlau F, Dow JM, Momol M, White FF, Preston JF, Vinatzer BA, Koebnik R, Setubal JC, Norman DJ, Staskawicz BJ, Jones JB. 2011. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. BMC Genomics 12:146.
Pruvost O, Magne M, Boyer K, Leduc A, Tourterel C, Drevet C, Ravigné V, Gagnevin L, Guérin F, Chiroleu F, Koebnik R, Verdier V, Vernière C. 2014. A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage. PLoS One 9:e98129.
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.
Bühlmann A, Dreo T, Rezzonico F, Pothier JF, Smits TH, Ravnikar M, Frey JE, Duffy B. 2014. Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites. Environ Microbiol 16:2112–2125.
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. 2014. 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.
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.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 126 February 2015
eLocator: e01558-14
PubMed: 25676765


Received: 29 December 2014
Accepted: 5 January 2015
Published online: 12 February 2015



Taca Vancheva
Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
UMR 186 IRD-Cirad-Université Montpellier 2 Résistance des Plantes aux Bioagresseurs, Montpellier, France
Nevena Bogatzevska
Institute of Soil Science, Agrotechnologies, and Plant Protection Nikola Poushkarov, Sofia, Bulgaria
Penka Moncheva
Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
Pierre Lefeuvre
CIRAD, UMR PVBMT, Pôle de Protection des Plantes, Saint-Pierre, Ile de la Réunion, France
UMR 186 IRD-Cirad-Université Montpellier 2 Résistance des Plantes aux Bioagresseurs, Montpellier, France


Address correspondence to Ralf Koebnik, [email protected].

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