Genomic-associated Markers and comparative Genome Maps of Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola

Abstract

Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) cause two major seed quarantine diseases in rice, bacterial blight and bacterial leaf streak, respectively. Xoo and Xoc share high similarity in genomic sequence, which results in hard differentiation of the two pathogens. Genomic-associated Markers and comparative Genome Maps database (GMGM) is an integrated database providing comprehensive information including compared genome maps and full genomic-coverage molecular makers of Xoo and Xoc. This database was established based on bioinformatic analysis of complete sequenced genomes of several X. oryzae pathovars of which the similarity of the genomes was up to 91.39 %. The program was designed with a series of specific PCR primers, including 286 pairs of Xoo dominant markers, 288 pairs of Xoc dominant markers, and 288 pairs of Xoo and Xoc co-dominant markers, which were predicted to distinguish two pathovars. Test on a total of 40 donor pathogen strains using randomly selected 120 pairs of primers demonstrated that over 52.5 % of the primers were efficacious. The GMGM web portal (http://biodb.sdau.edu.cn/gmgm/) will be a powerful tool that can present highly specific diagnostic markers, and it also provides information about comparative genome maps of the two pathogens for future evolution study.

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Acknowledgments

This work was supported by National Natural Science Foundation of China (Grant Nos. 30900780, 30900050), Ph.D. Programs Foundation of Ministry of Education of China (Grant No. 20123702110014) and Foundation for the Author of National Excellent Doctoral Dissertation of PR China (Grant No. 201132).

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Correspondence to Xinhua Ding or Long Yang.

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Wenjie Feng and Yi Wang have contributed equally to this work.

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Feng, W., Wang, Y., Huang, L. et al. Genomic-associated Markers and comparative Genome Maps of Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola . World J Microbiol Biotechnol 31, 1353–1359 (2015). https://doi.org/10.1007/s11274-015-1883-5

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Keywords

  • Genomic-associated markers
  • Comparative genome maps
  • Rice pathogens
  • Database