Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi

Baojun Wu, Jill Gaskell, Jiwei Zhang, Christina Toapanta, Steven Ahrendt, Igor V. Grigoriev, Robert A Blanchette, Jonathan S Schilling, Emma Master, Daniel Cullen, David S. Hibbett

Research output: Contribution to journalArticle

Abstract

Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the ‘Antrodia clade’ (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. This work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts.

Original languageEnglish (US)
Pages (from-to)1391-1403
Number of pages13
JournalISME Journal
Volume13
Issue number6
DOIs
StatePublished - Jun 1 2019

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RNA Editing
RNA editing
decay fungi
gene expression
RNA
Fungi
fungus
Gene Expression
substrate
gene
Antrodia
Genes
genes
decayed wood
Polyporales
Agaricomycetes
Ascomycota
fungi
Host Specificity
Gene Editing

Cite this

Wu, B., Gaskell, J., Zhang, J., Toapanta, C., Ahrendt, S., Grigoriev, I. V., ... Hibbett, D. S. (2019). Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi. ISME Journal, 13(6), 1391-1403. https://doi.org/10.1038/s41396-019-0359-2

Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi. / Wu, Baojun; Gaskell, Jill; Zhang, Jiwei; Toapanta, Christina; Ahrendt, Steven; Grigoriev, Igor V.; Blanchette, Robert A; Schilling, Jonathan S; Master, Emma; Cullen, Daniel; Hibbett, David S.

In: ISME Journal, Vol. 13, No. 6, 01.06.2019, p. 1391-1403.

Research output: Contribution to journalArticle

Wu, B, Gaskell, J, Zhang, J, Toapanta, C, Ahrendt, S, Grigoriev, IV, Blanchette, RA, Schilling, JS, Master, E, Cullen, D & Hibbett, DS 2019, 'Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi', ISME Journal, vol. 13, no. 6, pp. 1391-1403. https://doi.org/10.1038/s41396-019-0359-2
Wu, Baojun ; Gaskell, Jill ; Zhang, Jiwei ; Toapanta, Christina ; Ahrendt, Steven ; Grigoriev, Igor V. ; Blanchette, Robert A ; Schilling, Jonathan S ; Master, Emma ; Cullen, Daniel ; Hibbett, David S. / Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi. In: ISME Journal. 2019 ; Vol. 13, No. 6. pp. 1391-1403.
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