The Genetic Structure of Phellinus noxius and Dissemination Pattern of Brown Root Rot Disease in Taiwan

Abstract

Since the 1990s, brown root rot caused by Phellinus noxius (Corner) Cunningham has become a major tree disease in Taiwan. This fungal pathogen can infect more than 200 hardwood and softwood tree species, causing gradual to fast decline of the trees. For effective control, we must determine how the pathogen is disseminated and how the new infection center of brown root rot is established. We performed Illumina sequencing and de novo assembly of a single basidiospore isolate Daxi42 and obtained a draft genome of ~40 Mb. By comparing the 12,217 simple sequence repeat (SSR) regions in Daxi42 with the low-coverage Illumina sequencing data for four additional P. noxius isolates, we identified 154 SSR regions with potential polymorphisms. A set of 13 polymorphic SSR markers were then developed and used to analyze 329 P. noxius isolates collected from 73 tree species from urban/agricultural areas in 14 cities/counties all around Taiwan from 1989 to 2012. The results revealed a high proportion (~98%) of distinct multilocus genotypes (MLGs) and that none of the 329 isolates were genome-wide homozygous, which supports a possible predominant outcrossing reproductive mode in P. noxius. The diverse MLGs exist as discrete patches, so brown root rot was most likely caused by multiple clones rather than a single predominant strain. The isolates collected from diseased trees near each other tend to have similar genotype(s), which indicates that P. noxius may spread to adjacent trees via root-to-root contact. Analyses based on Bayesian clustering, F ST statistics, analysis of molecular variance, and isolation by distance all suggest a low degree of population differentiation and little to no barrier to gene flow throughout the P. noxius population in Taiwan. We discuss the involvement of basidiospore dispersal in disease dissemination.

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

“…However, some fungi are also one of the dominant groups of pathogens causing diseases in trees. There has been an emergence of tree disease outbreaks in different parts of the world such as ash dieback (Gross, Holdenrieder, Pautasso, Queloz, & Sieber, ), Dutch elm disease (Potter, Harwood, Knight, & Tomlinson, ), laminated root rot caused by Phellinus sulphurascens (Williams et al., ) and brown root rot caused by Phellinus noxius (Akiba et al., ; Ann, Chang, & Ko, ; Chung et al., ). Factors contributing to this phenomenon include climate change (Goberville et al., ) and human activity (Fisher et al., ).…”

“…Despite the recognized importance of P. noxius as an emerging pathogen, its genome, evolution and global population genetics are poorly understood. Previous reports based on simple sequence repeat (SSR) markers suggest the existence of highly diversified P. noxius populations (Akiba et al., ; Chung et al., ), but the isolates exhibited little to no host specificity (Ann et al., ; Nandris, Nicole, & Geiger, ; Sahashi, Akiba, Ishihara, Miyazaki, & Kanzaki, ). Currently, no gold standard genomes (Chain et al., ) are available for this group of wood decay fungi, which is a necessary step towards a better knowledge of their diversity, ecology and evolution.…”

Evidence of extensive intraspecific noncoding reshuffling in a 169-kb mitochondrial genome of a basidiomycetous fungus

“…In our previous study, we reported four Hymenochaetales genomes and revealed the nature of hyperdiversity of nuclear genomes in two lineages of P. noxium in Taiwan and Japan areas (Chung, et al 2015; Chung, et al 2017). To understand the mitochondrial genomics in Hymenochaetales, we analysed six mitogenomes in this order.…”

“…In particular, Pyrrhoderma noxium (syn. Phellinus noxius ) (Zhou, et al 2018) has a very wide host range, spanning more than 200 broadleaved and coniferous tree species (at least 59 families), and are the causative agents responsible for brown root rot disease in parts of Asia (Akiba, et al 2015; Chung, et al 2015). A recent comparative and population genomics study of six genomes from this order and 60 P. noxium strains from Taiwan and Japan revealed that P. noxium possesses extraordinarily high diversity in its nuclear genomes (Chung, et al 2017).…”

Draft genomes of the fungal pathogen Phellinus noxius in Hong Kong

“…This fungal pathogen has become a growing concern in many countries in recent years as it would lead to swift deterioration of the health of the plant host within a year if left untreated. The pathogen is extremely infectious, and can be spread easily over short distances through root-to-root contact or contact with infected soil or wood pieces [2,3], or through air-borne basidiospores for long distance dispersal [4]. It targets the roots and water transport system of the host plants, causing root mortality and compromising tree stability.…”