bioRxiv preprint doi: https://doi.org/10.1101/2020.02.04.933507; this version posted February 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Deep phylo-taxono-genomics (DEEPT genomics) reveals misclassification of Xanthomonas species complexes into Xylella, Stenotrophomonas and Pseudoxanthomonas Kanika Bansal1,^, Sanjeet Kumar1,$,^, Amandeep Kaur1, Shikha Sharma1, Prashant Patil1,#, Prabhu B. Patil1,* 1Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh. $Present address: Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. #Present address: Department of Microbiology, School of Medicine, University of Washington, Seattle, WA, USA. ^Equal Contribution *Corresponding author Running Title: Comprehensive phylo-taxono-genomics of Xanthomonas and its relatives. Correspondence: Prabhu B. Patil Email:
[email protected] Principal Scientist CSIR- Institute of Microbial Technology Sector 39-A, Chandigarh, India- 160036 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.04.933507; this version posted February 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Genus Xanthomonas encompasses specialized group of phytopathogenic bacteria with genera Xylella, Stenotrophomonas and Pseudoxanthomonas being its closest relatives. While species of genera Xanthomonas and Xylella are known as serious phytopathogens, members of other two genera are found in diverse habitats with metabolic versatility of biotechnological importance. Few species of Stenotrophomonas are multidrug resistant opportunistic nosocomial pathogens. In the present study, we report genomic resource of genus Pseudoxanthomonas and further in-depth comparative studies with publically available genome resources of other three genera.