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.

Population Differentiation of Wheat Leaf Rust Fungus <i>Puccinia triticina</i> in South Asia

“…Total genomic DNA from dried uredospores (~50 mg) was extracted with cetyltrimethylammonium bromide (CTAB) as described by Kiran et al 16 . The purity of genomic DNA and quantification of template DNA for PCR were measured in duplicate using NanoDrop 2000® UV-Vis Spectrophotometer (Thermo Scientific, Waltham, Massachusetts, USA) and stored at -20C till further use.…”

“…SSR analysis: Pt-specific SSR primers (Table 3) were designed from the genome sequences of Pt in our previous study 16 using Primer3 software and synthesized from Agile Life Science Technologies India Pvt Ltd, Sant Nagar, Garhi, New Delhi. All the PCR reactions were carried out in 20 l volume containing 25 ng of template DNA, 200 M each of the four dNTPs, 1 PCR buffer (10 mM Tris pH 9.0, 50 mM KCl), 1.5 mM MgCl 2 , 0.5 U Taq polymerase (Himedia Laboratory Pvt Ltd, India) and 10 pmol of both forward and reverse primers.…”

“…Virulence frequency of 48 South Asian Pt pathotypes varied from 0.00 (for Lr24) to 95.8% (for Agra Local; Figure 1) 9,10,15,17a,17b,19,21,23,24,25,26,27,28,29,32,36,39,42,43,45,47/Lr1,2a,2b,2c,11,12,13,14a,16,18,22a,22b,30,33,34,35,37,38,40,44,48,49 11 Lr1,2a,2b,2c,3,9,10,12,13,14a,14b,14ab,15,16,17a,…”

“…Lr1, 2a, 9,10,13,15,19,24,25,28,29,32,36,39,42,43,45,47/Lr2b,2c,3,11,12,14a,14b,14ab,16,17a,17b,18,20,21,22a,22b,23,26,27+31,30,33,34,35,37,38,40,44,46, 48,49…”

Mistura de cultivares de dois componentes no manejo de múltiplas doenças do trigo

“…O uso de cultivares resistentes é a medida preferencial, contudo, ainda não estão disponíveis cultivares resistentes para todas as doenças . Ademais, alguns patógenos, como os agentes causais do oídio e da ferrugem da folha, evoluem rapidamente sob pressão de seleção imposta pelos genes R presentes em cultivares resistentes superando a resistência (Wicker et al, 2013;Kiran et al, 2016).…”