Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, Phellinus noxius, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates

Creator

Jorge R. Ibarra Caballero, Colorado State University
Jessa P. Ata, Colorado State University
K. A. Leddy, Colorado State University
Travis C. Glenn, University of Georgia
Troy J. Kieran, University of Georgia
Ned B. Klopfenstein, USDA ARS Moscow Forestry Sciences Lab
Mee Sook Kim, USDA ARS Corvallis Forestry Sciences Laboratory
Jane E. Stewart, Colorado State University

Issue Date

2-2020

Abstract

Phellinus noxius is a root-decay pathogen with a pan-tropical/subtropical distribution that attacks a wide range of tree hosts. For this study, genomic sequencing was conducted on P. noxius isolate P919-02W.7 from Federated States of Micronesia (Pohnpei), and its gene expression profile was analyzed using different host wood (Acer, Pinus, Prunus, and Salix) substrates. The assembled genome was 33.92 Mbp with 2954 contigs and 9389 predicted genes. Only small differences were observed in size and gene content in comparison with two other P. noxius genome assemblies (isolates OVT-YTM/97 from Hong Kong, China and FFPRI411160 from Japan, respectively). Genome analysis of P. noxius isolate P919-02W.7 revealed 488 genes encoding proteins related to carbohydrate and lignin metabolism, many of these enzymes are associated with degradation of plant cell wall components. Most of the transcripts expressed by P. noxius isolate P919-02W.7 were similar regardless of wood substrates. This study highlights the vast suite of decomposing enzymes produced by P. noxius, which suggests potential for degrading diverse wood substrates, even from temperate host trees. This information contributes to our understanding of pathogen ecology, mechanisms of wood decomposition, and pathogenic/saprophytic lifestyle.

Source or Periodical Title

Fungal Biology

ISSN

1878-6146

Volume

124

Issue

2

Page

144-154

Document Type

Article

Physical Description

figure, graphs, tables, references

Language

English

Subject

Illumina, Invasive forest pathogen, Plant cell wall degrading enzymes, Root decay pathogen, White-rot fungus

Recommended Citation

Ibarra Caballero, J.R., Ata, J.P., Leddy, K.A., Glenn, T.C., Kieran, T.J., Klopfenstein, N.B., Kim, M-S., & Stewart, J.E. (2020). Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, Phellinus noxius, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates. Fungal Biology, 124 (2), 144-154. 10.1016/j.funbio.2019.12.007.

Identifier

10.1016/j.funbio.2019.12.007.

Digital Copy

yes

En – AGROVOC descriptors

ILLUMINA; INVASIVE FOREST PATHOGEN; PLANT CELL WALL DEGRADING ENZYMES; ROOT DECAY PATHOGEN; WHITE-ROT FUNGUS