Here, we report the complete genome sequence of the race 4 strain Xanthomonas campestris pv. campestris SB80, which was isolated from a symptomatic white head cabbage leaf in Samsun Province, Turkey, in 2019. The genome consists of a circular chromosome (5,129,762 bp) with a G+C content of 64.98%, for which 4,159 putative protein-coding genes, 2 rRNA operons, 54 tRNAs, and 86 noncoding RNAs (ncRNAs) were predicted.


Bacteria of the species Xanthomonas campestris cause black rot, which is the bacterial disease that causes the most devastation to Brassicaceae family plants worldwide. The pathovar X. campestris pv. campestris has been divided into 11 races based on interactions with a differential set of Brassica cultivars, with races 1 and 4 being the most prevalent and destructive (1, 2). Only one draft genome sequence of a race 4 strain, isolated in Chile in 2001, is available at NCBI GenBank (3).
X. campestris pv. campestris strain SB80 was isolated from a symptomatic leaf of white head cabbage (Brassica oleracea var. capitata) growing in a field in Samsun Province, Turkey, in 2019, as described (4). The race of strain SB80 was determined by evaluating the reactions of various Brassica sp. genotypes (compatible, Miracle F1, SxD1, Wirosa F1; incompatible, FBLM2, PIC1, Seven Top Turnip, COB60, Just Right Hybrid Turnip) (1). For DNA isolation, a single colony was grown at 28°C on PSA medium (0.5% peptone, 2% sucrose, 1.5% agar) for 24 h. Bacteria were then resuspended in 10 mM MgCl2 and diluted to an optical density at 600 nm of 1.0. Cells from 2 mL of this suspension were harvested by centrifugation, washed once with 10 mM MgCl2, and genomic DNA was isolated using the Genomic-tip 100/G protocol (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
For library construction and sequencing, performed by OhmX.bio (Ghent, Belgium), 1 μg DNA was mechanically fragmented using g-TUBE devices (Covaris, Woburn, MA) at approximately 13 kb. The sequencing library was prepared using the ligation sequencing kit (SQK-LSK110) and the native barcode expansion (PCR-free) pack (EXP-NBD114) based on the manufacturer’s protocol (ONT, Oxford, UK). The samples were sequenced on a GridION R9.4 flow cell for a total of 3 days. Bases were called using MinKNOW v21.10.8. The demultiplexed sequence reads (34,944; N50, 14,461 bp) were provided by OhmX.bio as FASTQ files.
Adapter sequences were trimmed from the reads using Porechop v0.2.1 (5). The raw reads were checked for quality using NanoFilt (6). The sequences were assembled using Flye v2.9 (7). Default parameters were used for all software unless otherwise specified. Closer inspection revealed issues with homopolymeric nucleotide runs, some of which were manually changed to match the high-quality reference genome sequences for strains ATCC 33913 and 8004 (8, 9). In addition to a large contig of 5.1 Mbp, corresponding to the circular chromosome, the Flye assembly resulted in a second contig of 23 kb, which was almost identical to a region in the large contig and did not encode typical plasmid-associated genes, suggesting an assembly artifact. Notably, this 23-kb region contained a perfect tandem duplication of 1,792 bp in the chromosome but not in the smaller contig. Again, comparison with the two reference genomes prompted us to delete the smaller contig from the assembly and to remove one copy of the duplication in the chromosome.
Assembly and polishing yielded one circular chromosome of 5,129,762 bp with a typical G+C content of 64.98%, corresponding to 136× sequence coverage. The chromosome was annotated using GeneMarkS-2+ (10), as implemented in the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/), which predicted a total of 4,520 genes, including 4,159 coding genes, 215 pseudogenes, 86 noncoding RNAs (ncRNAs), 54 tRNAs, and 2 rRNA operons (5S, 16S, 23S).
This genome sequence for X. campestris from Turkey will facilitate the identification of race-specific factors in X. campestris pv. campestris and thus contribute to the development and employment of resistant cabbage cultivars. Interestingly, this strain does not contain an endogenous plasmid, as the other sequenced race 4 strain does. Calculation of genome-wide average nucleotide identities demonstrates that both sequenced race 4 strains belong to two different clades of X. campestris pv. campestris (11, 12).

Data availability.

The genome sequence and raw sequencing reads for strain SB80 were deposited under GenBank accession number CP089952, BioProject accession number PRJNA785926, BioSample accession number SAMN23597367, and SRA accession number SRR17407536.


We thank the Institut de Recherche pour le Développement, France, for supporting the North-South-South Network on Xanthomonads (NSSN-X) within the International Scientific Coordination Network—South (GDRI-Sud). S.E.M., J.M., and R.K. thank the European Cooperation in Science and Technology (COST) program for support of the EuroXanth COST Action CA16107, which was key in initiating this collaborative genome project. J.M. was supported by the Ministry of Education, Science and Technological Development, Republic of Serbia, and Faculty of Agriculture contract number 451-03-9/2021-14/200116.
We thank Volkan Cevik (University of Bath, UK) for providing the seed material for race typing.


Vicente JG, Holub EB. 2013. Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops. Mol Plant Pathol 14:2–18.
Cruz J, Tenreiro R, Cruz L. 2017. Assessment of diversity of Xanthomonas campestris pathovars affecting cruciferous plants in Portugal and disclosure of two novel X. campestris pv. campestris races. J Plant Pathol 99:403–414.
Bolot S, Cerutti A, Carrère S, Arlat M, Fischer-Le Saux M, Portier P, Poussier S, Jacques MA, Noël LD. 2015. Genome sequences of the race 1 and race 4 Xanthomonas campestris pv. campestris strains CFBP 1869 and CFBP 5817. Genome Announc 3:e01023-15.
Schaad NW, Jones JB, Chun W. 2001. Laboratory guide for identification of plant pathogenic bacteria, 3rd ed. APS Press, St. Paul, MN.
Wick RR. 2018. Porechop: an adapter trimmer for Oxford Nanopore reads. https://github.com/rrwick/Porechop.
De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34:2666–2669.
Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, Kuhn K, Yuan J, Polevikov E, Smith TPL, Pevzner PA. 2020. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods 17:1103–1110.
da Silva AC, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorello CB, Van Sluys MA, Almeida NF, Alves LM, do Amaral AM, Bertolini MC, Camargo LE, Camarotte G, Cannavan F, Cardozo J, Chambergo F, Ciapina LP, Cicarelli RM, Coutinho LL, Cursino-Santos JR, El-Dorry H, Faria JB, Ferreira AJ, Ferreira RC, Ferro MI, Formighieri EF, Franco MC, Greggio CC, Gruber A, Katsuyama AM, Kishi LT, Leite RP, Lemos EG, Lemos MV, Locali EC, Machado MA, Madeira AM, Martinez-Rossi NM, Martins EC, Meidanis J, Menck CF, Miyaki CY, Moon DH, Moreira LM, Novo MT, Okura VK, Oliveira MC, Oliveira VR, Pereira HA, Rossi A, Sena JA, Silva C, de Souza RF, Spinola LA, Takita MA, Tamura RE, Teixeira EC, et al. 2002. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417:459–463.
Qian W, Jia Y, Ren SX, He YQ, Feng JX, Lu LF, Sun Q, Ying G, Tang DJ, Tang H, Wu W, Hao P, Wang L, Jiang BL, Zeng S, Gu WY, Lu G, Rong L, Tian Y, Yao Z, Fu G, Chen B, Fang R, Qiang B, Chen Z, Zhao GP, Tang JL, He C. 2005. Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris. Genome Res 15:757–767.
Lomsadze A, Gemayel K, Tang S, Borodovsky M. 2018. Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes. Genome Res 28:1079–1089.
Guy E, Genissel A, Hajri A, Chabannes M, David P, Carrere S, Lautier M, Roux B, Boureau T, Arlat M, Poussier S, Noël LD. 2013. Natural genetic variation of Xanthomonas campestris pv. campestris pathogenicity on Arabidopsis revealed by association and reverse genetics. mBio 4:e00538-12.
Erken MS, Bibi S, Díaz RC, Menković J, Bernal AJ, Koebnik R. 2022. ANI-based phylogenetic tree of Xanthomonas campestris pv. campestris. figshare.

Information & Contributors


Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 11Number 317 March 2022
eLocator: e00022-22
Editor: David A. Baltrus, University of Arizona
PubMed: 35191748


Received: 13 January 2022
Accepted: 7 February 2022
Published online: 22 February 2022



Department of Plant Health, Black Sea Agricultural Research Institute, Samsun, Turkey
Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, USA
Carlos Andrés Díaz Rodríguez https://orcid.org/0000-0001-7943-6920
Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France


David A. Baltrus
University of Arizona


The authors declare no conflict of interest.

Metrics & Citations


Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.


If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

View Options

Figures and Media






Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy