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.

doi:10.1038/s41396-019-0359-2

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

Journal Article · 04 February 2019 · The ISME Journal

DOI: https://doi.org/10.1038/s41396-019-0359-2 · OSTI ID:1619121

Wu, Baojun ^[1]; Gaskell, Jill ^[2]; Zhang, Jiwei ^[3]; Toapanta, Christina ^[3]; Ahrendt, Steven ^[4];

^[5]; Blanchette, Robert A. ^[3]; Schilling, Jonathan S. ^[3]; Master, Emma ^[6]; Cullen, Daniel ^[2]; Hibbett, David S. ^[1]

Clark Univ., Worcester, MA (United States)
US Dept. of Agriculture (USDA), Madison, WI (United States)
Univ. of Minnesota, St. Paul, MN (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
Univ. of Toronto, ON (Canada)

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. Finally, 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1619121

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 6 Vol. 13; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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