RETRACTED ARTICLE: Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi

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 wooddecaying 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.

Fungal RNA editing: who, when, and why?

“…In these fungi, editing has been reported to diversify transcripts coding for enzymes that are required for the degradation of wood (Zhu et al 2014;Wu et al 2018). A comparative study using the wood-decaying fungi Antrodia sinuosa, Daedalea quercina, Fomitopsis pinicola, Laetiporus sulphureus, and Wolfiporia cocos found an effect of different substrates on editing positions and frequency (Wu et al 2019).…”

Carbon metabolism, transcriptome and RNA editome in developmental paths differentiation ofCoprinopsis cinerea

“…Our results show that RNA editing not only occurs in fruiting, but also other developmental paths. Similar to the stage-specific and substrate-specific RNA editing studies on basidiomycetes, editing events in C. cinerea regulate the genes in carbohydrate metabolism and cell structure formation (37, 38). All these results emphasize the functional similarity of RNA editing in regulating carbohydrate metabolism, and further, the essential role of carbon metabolism in fungal development.…”

“…Vegetative mycelium grows in changeable environment and it is in charge of primary occupation of new habitat. The Agaricales-specific and species unique genes are very likely to benefit the fungus on niche segmentation and adapting to the complex and changing environment during vegetative growth (38, 67, 68). High expression on species-specific genes and relative lower selective pressure of purifying selection enable mycelium to minimize the interspecific competition and improve fitness (69).…”

“…As a special kind of transcriptional modification, RNA editing has been widely found in all domains of life and showed significant impacts on diverging the transcriptome and proteome (73–76). In fungi, developmentally regulated for sexual reproduction and evolutionarily conserved across genus are two main patterns of RNA editing events (35, 37, 38). Our results show that RNA editing not only occurs in fruiting, but also other developmental paths.…”

Insights into the cellulose degradation mechanism of the thermophilic fungus Chaetomium thermophilum based on integrated functional omics

“…Plant biomass is recognized as a sustainable source of mixed sugars for fermentation to second generation biofuels and high-value molecules. Fungi have evolved different strategies to degrade lignocellulose [53][54][55][56][57][58]. The genome of the thermophilic fungus C. thermophilum suggested that this fungus should prefer to degrade monocots that are rich in cellulose, xylan and β-glucan.…”