Research Projects

The Xanthomonas group of phytopathogens causes severe diseases in ~400 plant species and presents a significant threat to the livelihood of farmers, particularly in tropical and subtropical regions like India. Despite having very similar genomes, Xanthomonas species show a high degree of host plant specificity. Transcription Activator-Like (TAL) effectors modulate host susceptibility (S) and resistance (R) genes through sequence-specific DNA binding thereby affecting their expression. The genomic diversity of TAL effectors plays a crucial role in determining the specificity between host plants and Xanthomonas pathogens. Our knowledge base about the diversity and evolution of the TAL effectors, especially among Indian Xanthomonas isolates, is largely limited. To better understand the Xanthomonas pathogenesis, we aim to delineate the genetic diversity and pathogenic evolution of the TAL effectors and identify their host targets. Hypothesis: Xanthomonas strains infecting Indian crops possess unique and diverse TAL effector repertoires that determine virulence and host specificity. Systematic characterization of these effectors and their host targets will uncover novel S/R genes and enable development of durable resistance strategies. Main objectives: 1. Isolation and characterization of Xanthomonas strains from diverse host plants. 2. Understanding genomic diversity and prevalence of TAL effectors 3. Functional characterization of TALEs with unique Repeat Variable Diresidues (RVDs). 4. Identification of host targets and validation of candidate susceptibility (S) or resistance (R) genes. Main experiments: Pathogen isolation: Field sampling and molecular identification of Xanthomonas species from multiple crops across different agroclimatic zones in India and predicting their phylogenetic relatedness. Genomic Characterization: Whole genome sequencing of representative strains using Oxford Nanopore/PacBio platforms to identify novel TAL effectors. Bioinformatic prediction of effector binding elements (EBEs) and TALE targets in host genomes. Mechanistic studies: Construction of TALE deletion mutants to assess their contribution towards pathogenesis. In planta RNA-seq to identify host transcriptional responses to wild type and mutant strains for effector target identification. GUS promoter reporter assays to validate TALE-dependent gene activation. Significance: This project will significantly advance our current understanding of the Xanthomonas pathogenesis in the Indian agricultural context by identifying key TALE-host gene interactions. It will uncover the molecular and evolutionary dynamics of TALEs across diverse Xanthomonas species offering critical insights into pathogen adaptation and host specificity. The findings will provide concepts for developing disease resistance strategies, including targets for marker assisted selection and genome editing of EBEs. Overall, the outcomes of this project will be a valuable resource for enhancing crop resilience and productivity.