Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees
Journal
Molecular Ecology
Journal Volume
26
Journal Issue
22
Start Page
6301
End Page
6316
ISSN
0962-1083
1365-294X
Date Issued
2017-10-10
Author(s)
Lee, Tracy J.
Akiba, Mitsuteru
Lee, Hsin‐Han
Kuo, Tzu‐Hao
Liu, Dang
Ke, Huei‐Mien
Yokoi, Toshiro
Roa, Marylette B.
Lu, Mei‐Yeh J.
Chang, Ya‐Yun
Ann, Pao‐Jen
Tsai, Jyh‐Nong
Tzean, Shean‐Shong
Ota, Yuko
Hattori, Tsutomu
Sahashi, Norio
Kikuchi, Taisei
Tsai, Isheng J.
Abstract
The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomic analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens and trunk pathogen Porodaedalea pini. Many gene families of lignin-degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3-beta-glucan synthases in P. noxius, which may account for its fast-growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P. noxius has a bipolar heterothallic mating system, with unusual highly expanded ~60 kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P. noxius isolates across multiple islands of the Asia Pacific region. Whole-genome sequencing showed this multinucleate species contains abundant poly-allelic single nucleotide polymorphisms with atypical allele frequencies. Different patterns of intra-isolate polymorphism reflect mono-/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.
Subjects
comparative genomics
fungi
microbial biology
population genomics
SDGs
Publisher
Wiley
Type
journal article