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<p><i>Phytophthora melonis</i> is a broad host range pathogen causing devastating loss in Cucurbit crops. The rapid adaptation of this pathogen coupled with a surge in virulence factors makes designing management strategies of this organism difficult. Indian <i>Phytophthora melonis</i> isolate MCC 9865 WB from Pointed gourd, West Bengal, India was sequenced for the first time using short read technology and was assembled with multiple strategies including reference guided assembly resulting in a draft genome with reduced repeat contents. The genome of <i>Phytophthora melonis</i> has more than 53% repetitive contents. A comparison of genomes between the four available <i>P. melonis</i> isolates from different hosts suggest unique genomic regions present in MCC 9865 WB isolate are mostly confined to transposable elements. All the isolates exhibit bipartite genome architecture with effectors, secreted CAZymes and other virulent factors housed in the repeat rich gene sparse regions. Apart from housekeeping genes, the enriched genes in <i>P. melonis</i> encode proteins for carbohydrate metabolism and signal transduction, providing further insight into its pathogenic life cycle. Only 50% of the genes are co-orthologous with each other with singletons largely annotated as transposons indicating directed genome evolution. Effector repertoire of the four isolates have only 27% core RxLR effectors suggesting host mediated selection pressure acting upon the isolates. Higher number of telomeres and centromeres were detected from assemblies generated from long reads of the <i>P. melonis</i> isolates. The fully annotated genomes are hosted in a browsable database at <a href="http://www.eumicrobedb.org:3001">www.eumicrobedb.org:3001</a> for easy data access.</p>

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Comparative genome analysis of Phytophthora melonis MCC 9865 WB isolated from Eastern India with other isolates reveal host mediated adaptation

  • 期刊论文

  • 发表日期：

    2025年6月16日

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  • Subhajeet Dutta,
  • Kajal Mandal,
  • Aditya Upadhyay,
  • Soumen Das,
  • Tanmoy Dey,
  • Sanjoy Guha Roy,
  • Sucheta Tripathy

摘要

Phytophthora melonis is a broad host range pathogen causing devastating loss in Cucurbit crops. The rapid adaptation of this pathogen coupled with a surge in virulence factors makes designing management strategies of this organism difficult. Indian Phytophthora melonis isolate MCC 9865 WB from Pointed gourd, West Bengal, India was sequenced for the first time using short read technology and was assembled with multiple strategies including reference guided assembly resulting in a draft genome with reduced repeat contents. The genome of Phytophthora melonis has more than 53% repetitive contents. A comparison of genomes between the four available P. melonis isolates from different hosts suggest unique genomic regions present in MCC 9865 WB isolate are mostly confined to transposable elements. All the isolates exhibit bipartite genome architecture with effectors, secreted CAZymes and other virulent factors housed in the repeat rich gene sparse regions. Apart from housekeeping genes, the enriched genes in P. melonis encode proteins for carbohydrate metabolism and signal transduction, providing further insight into its pathogenic life cycle. Only 50% of the genes are co-orthologous with each other with singletons largely annotated as transposons indicating directed genome evolution. Effector repertoire of the four isolates have only 27% core RxLR effectors suggesting host mediated selection pressure acting upon the isolates. Higher number of telomeres and centromeres were detected from assemblies generated from long reads of the P. melonis isolates. The fully annotated genomes are hosted in a browsable database at www.eumicrobedb.org:3001 for easy data access.