Genomic insights into M. phaseolina: Multifactorial virulence via secreted effectors, carbohydrate enzymes and secondary metabolites.

Abstract

Macrophomina phaseolina, a soilborne necrotrophic pathogen causing charcoal rot across more than 500 host plant species, poses a significant and escalating threat to global food security under climate change-driven abiotic stresses. Despite its destructive importance, the molecular architecture underlying its broad host range and virulence versatility remains poorly characterized. De novo whole-genome sequencing, assembly, and multi-platform functional annotation were performed using BUSCO v6.0.0, eggNOG-mapper, Gene Ontology, KEGG, COG, PHI-base, SignalP 6.0, DeepTMHMM, EffectorP 3.0, CAZy, and antiSMASH. The draft genome assembly of M. phaseolina comprised 50.2 Mb across 1551 contigs (N50 = 125.1 kb, L50 = 118; GC = 51.9%) and showed 99.3% BUSCO completeness and 14,633 predicted protein-coding genes. Functional annotation revealed 10,954 genes classified across COG, GO, and KEGG databases, GO and KEGG over-representation analyses identified significant enrichment of extracellular, carbohydrate- and cell-wall-associated functions in the predicted secretome, including polysaccharide metabolism and degradation, together with selected metabolic and host-interaction pathways. PHI-base comparative screening identified 2000 pathogenicity-associated homologs showing strong conservation with virulence determinants from Fusarium graminearum and Magnaporthe oryzae. Secretome analysis yielded 1070 extracellular proteins, including 254 apoplastic effectors, 124 cytoplasmic effectors, and 135 cysteine-rich apoplastic effectors. CAZyme annotation identified 639 enzymes spanning six classes, with glycoside hydrolases (301) constituting the largest category. AntiSMASH analysis detected 73 secondary metabolite biosynthetic gene clusters enriched in terpene, NRPS, and polyketide synthase pathways. These findings reveal a highly diversified, multifactorial virulence arsenal in M. phaseolina, providing a comprehensive genomic framework for advancing host-pathogen interaction research and developing targeted disease management strategies.