title: Draft Genome of the Wheat Rust Pathogen (Puccinia triticina) Unravels Genome-Wide Structural Variations during Evolution.
abstract: Leaf rust is one of the most important diseases of wheat and is caused by Puccinia triticina, a highly variable rust pathogen prevalent worldwide. Decoding the genome of this pathogen will help in unraveling the molecular basis of its evolution and in the identification of genes responsible for its various biological functions. We generated high quality draft genome sequences (approximately 100- 106 Mb) of two races of P. triticina; the variable and virulent Race77 and the old, avirulent Race106. The genomes of races 77 and 106 had 33X and 27X coverage, respectively. We predicted 27678 and 26384 genes, with average lengths of 1,129 and 1,086 bases in races 77 and 106, respectively and found that the genomes consisted of 37.49% and 39.99% repetitive sequences. Genome wide comparative analysis revealed that Race77 differs substantially from Race106 with regard to segmental duplication (SD), repeat element, and SNP/InDel characteristics. Comparative analyses showed that Race 77 is a recent, highly variable and adapted Race compared with Race106. Further sequence analyses of 13 additional pathotypes of Race77 clearly differentiated the recent, active and virulent, from the older pathotypes. Average densities of 2.4 SNPs and 0.32 InDels per kb were obtained for all P. triticina pathotypes. Secretome analysis demonstrated that Race77 has more virulence factors than Race 106, which may be responsible for the greater degree of adaptation of this pathogen. We also found that genes under greater selection pressure were conserved in the genomes of both races, and may affect functions crucial for the higher levels of virulence factors in Race77. This study provides insights into the genome structure, genome organization, molecular basis of variation, and pathogenicity of P. triticina The genome sequence data generated in this study have been submitted to public domain databases and will be an important resource for comparative genomics studies of the more than 4000 existing Puccinia species.
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: Kanti
authors: K
authors: Kiran
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: Hukam C
authors: HC
authors: Rawal
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: Himanshu
authors: H
authors: Dubey
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: Rajdeep
authors: R
authors: Jaswal
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: B N
authors: BN
authors: Devanna
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: Deepak Kumar
authors: DK
authors: Gupta
authors: ICAR - Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, India.
authors: Subhash C
authors: SC
authors: Bhardwaj
authors: ICAR - Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, India.
authors: P
authors: P
authors: Prasad
authors: ICAR - Indian Agricultural Research Institute, Regional Station Tutikandi Centre, Shimla, India.
authors: Dharam
authors: D
authors: Pal
authors: Punjab Agricultural University, Ludhiana, India.
authors: Parveen
authors: P
authors: Chhuneja
authors: Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
authors: P
authors: P
authors: Balasubramanian
authors: ICAR - National Institute of Biotic Stress Management, Raipur, Chhattisgarh, India.
authors: J
authors: J
authors: Kumar
authors: ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India.
authors: M
authors: M
authors: Swami
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: Amolkumar U
authors: AU
authors: Solanke
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: Kishor
authors: K
authors: Gaikwad
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
authors: Nagendra K
authors: NK
authors: Singh
authors: ICAR-National Research Centre on Plant Biotechnology, New Delhi, India trsharma1965@gmail.com trsharma@nrcpb.org.
authors: Tilak Raj
authors: TR
authors: Sharma
mesh_terms: D001487:Basidiomycota / Q000235:genetics* / Q000472:pathogenicity; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics; D016681:Genome, Fungal; D056914:Genomic Structural Variation; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D037521:Virulence Factors / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D037521:Virulence Factors
keywords: Puccinia triticina; comparative genomics; fungal pathogen; genome sequencing; genome variations; molecular evolution