Comparative genomics using long-read sequencing identifies nearly identical TAL regions in two Xanthomonas oryzae pv. oryzae isolates, isolated from the Basmati rice growing region of Pakistan

Khansa Ejaz^1,2*Muhammad Zakria³Peiqi Zhang⁴Jose Carlos Huguet-Tapia⁴Muhammad Arif^1,2Frank White⁴Sumera Yasmin^1,2*

• ¹National Institute for Biotechnology and Genetic Engineering (Pakistan), Faisalabad, Pakistan
• ²Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Islamabad, Pakistan
• ³Crop Disease Research Institute, National Agricultural Research Center (Pakistan), Islamabad, Islamabad, Pakistan
• ⁴Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States

The emergence of hostile and novel plant pathogenic strains poses a serious threat to global food security that renders the strategies of disease management in modern agriculture ineffective. Preventing the consequences of these emerging phytopathogens requires accurate genetic information of the pathogen population to formulate effective management strategies. Bacterial Leaf Blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is the foremost reason for substantial yield losses of rice crops around the globe, especially in Asia. The genetic information of the Pakistani Xoo population is still unexplored. To bridge this gap, two of the representative Pakistani Xoo isolates namely PkXoo1 and PkXoo2 were sequenced using long-read Oxford Nanopore Sequencing Technology (ONT). Both isolates were isolated from the Basmati rice growing region of Pakistan, with substantially high virulence on certain susceptible rice varieties. The final assembly of both isolates PkXoo1 and PkXoo2 yields a circular chromosome of approximately 4.9 MBs with 64% G+C content. Genome annotation of both strains divulges the existence of the utmost genes involved in the hypersensitivity and virulence of Xoo. AnnoTALE analysis indicated that both strains contain eighteen TAL effectors, while three of them were predicted as pseudotals. A phylogenomic analysis grouped PkXoo1 and PkXoo2 with strains belonging to India and Thailand but far apart from the other major Asian Xoo strains. The present study revealed significant findings about the conservation of Repeat Variable Di-Residue (RVDs) of major TAL effectors and the utility of high throughput sequencing technologies in TAL effectors analysis and pathogen tracking. The complete genome sequence of Xoo isolates from Pakistan will enhance sequence resources for global comparison of Xoo diversity across the region. This information is also of great significance to launching effective and durable breeding programs.