Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees

Area of Science:

• Mycology and Plant Pathology
• Evolutionary Genomics
• Fungal Genetics

Background:

• The order Hymenochaetales includes aggressive white rot fungi responsible for significant tree mortality globally.
• Despite their ecological impact, the evolutionary history and transmission dynamics of these pathogens remain poorly understood.
• This study focuses on key species: Phellinus noxius, Phellinus lamaensis, Phellinus sulphurascens, and Porodaedalea pini.

Purpose of the Study:

• To conduct comparative genomic analyses of selected Hymenochaetales species to understand their evolution and pathogenicity.
• To investigate the population genomics and genetic diversity of the brown root rot fungus, Phellinus noxius, across the Asia Pacific region.
• To identify genetic factors contributing to the virulence and adaptation of these wood-decay fungi.

Main Methods:

• Whole-genome sequencing and comparative genomic analyses of four Hymenochaetales species.
• Identification and characterization of gene families, particularly those involved in lignin degradation and cell wall synthesis.
• Population genomic analysis of 60 Phellinus noxius isolates using whole-genome sequencing data.

Main Results:

• Abundant lignin-degrading enzyme gene families were identified, confirming their white rot capabilities.
• Phellinus noxius exhibits expanded 1,3-beta-glucan synthase gene families, potentially linked to its rapid growth.
• Analysis revealed conserved linkage groups, a bipolar heterothallic mating system in P. noxius with an expanded A locus, and two distinct, genetically diverse lineages of P. noxius with contrasting evolutionary trajectories across the Asia Pacific.

Conclusions:

• Comparative genomics provides a framework for understanding the evolution of white rot fungi.
• Phellinus noxius possesses unique genetic attributes, including an expanded mating locus and significant population genetic structure, influencing its spread and virulence.
• The study reveals complex population dynamics and high genetic diversity in P. noxius, offering insights into the adaptation and persistence of these important plant pathogens.