The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
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Genomic Analysis of the Carrot Bacterial Blight Pathogen Xanthomonas hortorum pv. carotae in Korea

  • Mi-Hyun Lee (Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Sung-Jun Hong (Organic Agricultural Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Dong Suk Park (Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Hyeonheui Ham (Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Hyun Gi Kong (Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration)
  • Received : 2022.11.16
  • Accepted : 2023.06.02
  • Published : 2023.08.01
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Abstract

Bacterial leaf blight of carrots caused by Xanthomonas hortorum pv. carotae (Xhc) is an important worldwide seed-borne disease. In 2012 and 2013, symptoms similar to bacterial leaf blight were found in carrot farms in Jeju Island, Korea. The phenotypic characteristics of the Korean isolation strains were similar to the type strain of Xhc. Pathogenicity showed symptoms on the 14th day after inoculation on carrot plants. Identification by genetic method was multi-position sequencing of the isolated strain JJ2001 was performed using four genes (danK, gyrB, fyuA, and rpoD). The isolated strain was confirmed to be most similar to Xhc M081. Furthermore, in order to analyze the genetic characteristics of the isolated strain, whole genome analysis was performed through the next-generation sequencing method. The draft genome size of JJ2001 is 5,443,372 bp, which contains 63.57% of G + C and has 4,547 open reading frames. Specifically, the classification of pathovar can be confirmed to be similar to that of the host lineage. Plant pathogenic factors and determinants of the majority of the secretion system are conserved in strain JJ2001. This genetic information enables detailed comparative analysis in the pathovar stage of pathogenic bacteria. Furthermore, these findings provide basic data for the distribution and diagnosis of Xanthomonas hortorum pv. carotae, a major plant pathogen that infects carrots in Korea.

Keywords

Acknowledgement

This work was carried out with the support of the Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ01624101), Rural Development Administration, Republic of Korea. This work was supported by the research grant of Chungbuk National University in 2022.

References

  1. Adriko, J., Mbega, E. R., Mortensen, C. N., Wulff, E. G., Tushemereirwe, W. K., Kubiriba, J. and Lund, O. S. 2014. Improved PCR for identification of members of the genus Xanthomonas. Eur. J. Plant Pathol. 138:293-306. https://doi.org/10.1007/s10658-013-0329-x
  2. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T. L. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421.
  3. Chin, C.-S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., Turner, S. W. and Korlach, J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563-569. https://doi.org/10.1038/nmeth.2474
  4. du Toit, L. J., Crowe, F. J., Derie, M. L., Simmons, R. B. and Pelter, G. Q. 2005. Bacterial blight in carrot seed crops in the Pacific Northwest. Plant Dis. 89:896-907. https://doi.org/10.1094/PD-89-0896
  5. du Toit, L. J., Derie, M. L., Christianson, C. E., Hoagland, L. and Simon, P. 2014. First report of bacterial blight of carrot in Indiana caused by Xanthomonas hortorum pv. carotae. Plant Dis. 98:685.
  6. Gilbertson, R. L. 2002. Bacterial leaf blight of carrot. In: Compendium of umbelliferous crop diseases, eds. by R. M. Davis and R. N. Raid, pp. 11-12. American Phytopathological Society, St Paul, MN, USA.
  7. Hauben, L., Vauterin, L., Swings, J. and Moore, E. R. 1997. Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int. J. Syst. Bacteriol. 47:328-335. https://doi.org/10.1099/00207713-47-2-328
  8. Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., Jensen, L. J., von Mering, C. and Bork, P. 2016. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44:D286-D293. https://doi.org/10.1093/nar/gkv1248
  9. Jones, P., Binns, D., Chang, H.-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A. F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S.-Y., Lopez, R. and Hunter, S. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236-1240. https://doi.org/10.1093/bioinformatics/btu031
  10. Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J. and Marra, M. A. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19:1639-1645. https://doi.org/10.1101/gr.092759.109
  11. Maes, M. 1993. Fast classification of plant-associated bacteria in the Xanthomonas genus. FEMS Microbiol Lett. 113:161-165. https://doi.org/10.1111/j.1574-6968.1993.tb06508.x
  12. Myung, I.-S., Yoon, M.-J., Lee, J.-Y., Kim, G -D., Lee, M.-H., Hwang, E.-Y. and Shim, H. S. 2014. First report of bacterial leaf blight of carrot caused by Xanthomonas hortorum pv. carotae in Korea. Plant Dis. 98:275.
  13. Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S. and Phillippy, A. M. 2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17:132.
  14. Parkinson, N., Aritua, V., Heeney, J., Cowie, C., Bew, J. and Stead, D. 2007. Phylogenetic analysis of Xanthomonas species by comparison of partial gyrase B gene sequences. Int. J. Syst. Evol. Microbiol. 57:2881-2887. https://doi.org/10.1099/ijs.0.65220-0
  15. Pruvost, O., Boyer, C., Robene-Soustrade, I., Jouen, E., Saison, A., Hostachy, B. and Benimadhu, S. 2010. First report of Xanthomonas hortorum pv. carotae causing bacterial leaf blight of carrot in Mauritius. Plant Dis. 94:1069.
  16. Seemann, T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068-2069. https://doi.org/10.1093/bioinformatics/btu153
  17. Tatusova, T., DiCuccio, M., Badretdin, A., Chetvernin, V., Nawrocki, E. P., Zaslavsky, L., Lomsadze, A., Pruitt, K. D., Borodovsky, M. and Ostell, J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44:6614-6624. https://doi.org/10.1093/nar/gkw569
  18. Vauterin, L., Hoste, B., Kersters, K. and Swings, J. 1995. Reclassification of Xanthomonas. Int. J. Syst. Evol. Microbiol. 45:472-489. https://doi.org/10.1099/00207713-45-3-472
  19. Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K. and Earl, A. M. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9:e112963.
  20. Young, J. M., Park, D.-C., Shearman, H. M. and Fargier, E. 2008. A multilocus sequence analysis of the genus Xanthomonas. Syst. Appl. Microbiol. 31:366-377. https://doi.org/10.1016/j.syapm.2008.06.004
  21. Zhang, Z., Schwartz, S., Wagner, L. and Miller, W. 2000. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7:203-214. https://doi.org/10.1089/10665270050081478