Structured Framework and Genome Analysis of Magnaporthe grisea Inciting Pearl Millet Blast Disease Reveals Versatile Metabolic Pathways, Protein Families, and Virulence Factors

Abstract

Magnaporthe grisea (T.T. Herbert) M.E. Barr is a major fungal phytopathogen that causes blast disease in cereals, resulting in economic losses worldwide. An in-depth understanding of the basis of virulence and ecological adaptation of M. grisea is vital for devising effective disease management strategies. Here, we aimed to determine the genomic basis of the pathogenicity and underlying biochemical pathways in Magnaporthe using the genome sequence of a pearl millet-infecting M. grisea PMg_Dl generated by dual NGS techniques, Illumina NextSeq 500 and PacBio RS II. The short and long nucleotide reads could be draft assembled in 341 contigs and showed a genome size of 47.89 Mb with the N50 value of 765.4 Kb. Magnaporthe grisea PMg_Dl showed an average nucleotide identity (ANI) of 86% and 98% with M. oryzae and Pyricularia pennisetigena, respectively. The gene-calling method revealed a total of 10,218 genes and 10,184 protein-coding sequences in the genome of PMg_Dl. InterProScan of predicted protein showed a distinct 3637 protein families and 695 superfamilies in the PMg_Dl genome. In silico virulence analysis revealed the presence of 51VFs and 539 CAZymes in the genome. The genomic regions for the biosynthesis of cellulolytic endo-glucanase and beta-glucosidase, as well as pectinolytic endo-polygalacturonase, pectin-esterase, and pectate-lyases (pectinolytic) were detected. Signaling pathways modulated by MAPK, PI3K-Akt, AMPK, and mTOR were also deciphered. Multicopy sequences suggestive of transposable elements such as Type LTR, LTR/Copia, LTR/Gypsy, DNA/TcMar-Fot1, and Type LINE were recorded. The genomic resource presented here will be of use in the development of molecular marker and diagnosis, population genetics, disease management, and molecular taxonomy, and also provide a genomic reference for ascomycetous genome investigations in the future.

The First Telomere-to-Telomere Chromosome-Level Genome Assembly of Stagonospora tainanensis Causing Sugarcane Leaf Blight

“…In total, 12,206 high-confidence protein-coding genes were predicted by the BRAKER2 pipeline, which was more than the Magnaporthe grisea PMg_Dl (10,218) though its genome size (38.25 Mb) was less than the M. grisea (47.89 Mb) [ 69 ], and this phenomenon was also observed in the other necrotrophic fungal pathogen Pyrenophora teres f. teres (41.95 Mb size, 11,799 genes) [ 70 ] and L. maculans ‘brassicae’ WA74 (44.20 Mb size, 10,624 genes) [ 71 ]. However, the gene number and the genome size of S. tainanensis were comparable to M. oryzae (on average 12,684 genes, 40.12 Mb size) [ 72 ].…”

Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics

“…The genome of B. graminis f. sp. tritici Wtn1 also revealed peptidase families such as M28, carboxypeptidase Y, subtilisin, and signal peptidase I, important to various physiological processes and consequent fungal nutrition, development, and pathogenesis [87,88]. Additionally, chaperones, folding catalysts, and protein kinases suggest their involvement in stress adaptation, temperature resilience, and enzymatic regulation through phosphorylation for activation or deactivation [89].…”