title: Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing.
abstract: Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the important diseases of wheat. We used NGS technologies to generate a draft genome sequence of two highly virulent (46S 119 and 31) and a least virulent (K) pathotypes of P. striiformis from the Indian subcontinent. We generated ~24,000-32,000 sequence contigs (N50;7.4-9.2 kb), which accounted for ~86X-105X sequence depth coverage with an estimated genome size of these pathotypes ranging from 66.2-70.2 Mb. A genome-wide analysis revealed that pathotype 46S 119 might be highly evolved among the three pathotypes in terms of year of detection and prevalence. SNP analysis revealed that ~47% of the gene sets are affected by nonsynonymous mutations. The extracellular secreted (ES) proteins presumably are well conserved among the three pathotypes, and perhaps purifying selection has an important role in differentiating pathotype 46S 119 from pathotypes K and 31. In the present study, we decoded the genomes of three pathotypes, with 81% of the total annotated genes being successfully assigned functional roles. Besides the identification of secretory genes, genes essential for pathogen-host interactions shall prove this study as a huge genomic resource for the management of this disease using host resistance.
authors.affiliation: ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Kanti
authors.initials: K
authors.lastname: Kiran
authors.affiliation: ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Hukam C
authors.initials: HC
authors.lastname: Rawal
authors.affiliation: ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Himanshu
authors.initials: H
authors.lastname: Dubey
authors.affiliation: ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: R
authors.initials: R
authors.lastname: Jaswal
authors.affiliation: Indian Institute of Wheat and Barley Research, Regional Station Flowerdale, Shimla, H.P., India.
authors.forename: Subhash C
authors.initials: SC
authors.lastname: Bhardwaj
authors.affiliation: Indian Institute of Wheat and Barley Research, Regional Station Flowerdale, Shimla, H.P., India.
authors.forename: P
authors.initials: P
authors.lastname: Prasad
authors.affiliation: Indian Agricultural Research Institute, Regional Station, Shimla, H.P., India.
authors.forename: Dharam
authors.initials: D
authors.lastname: Pal
authors.affiliation: ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: B N
authors.initials: BN
authors.lastname: Devanna
authors.affiliation: ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Tilak R
authors.initials: TR
authors.lastname: Sharma
mesh_terms: D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D020543:Proteome; D040901:Proteomics / Q000379:methods; D011995:Recombination, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D014908:Triticum / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D000073336:Whole Genome Sequencing
chemical_list: D020543:Proteome