Genome-wide gene expression patterns in dikaryon of the basidiomycete fungus Pleurotus ostreatus

Abstract

Dikarya is a subkingdom of fungi that includes Ascomycota and Basidiomycota. The gene expression patterns of dikaryon are poorly understood. In this study, we bred a dikaryon DK13 × 3 by mating monokaryons MK13 and MK3, which were from the basidiospores of Pleurotus ostreatus TD300. Using RNA-Seq, we obtained the transcriptomes of the three strains. We found that the total transcript numbers in the transcriptomes of the three strains were all more than ten thousand, and the expression profile in DK13 × 3 was more similar to MK13 than MK3. However, the genes involved in macromolecule utilization, cellular material synthesis, stress-resistance and signal transduction were much more up-regulated in the dikaryon than its constituent monokaryons. All possible modes of differential gene expression, when compared to constituent monokaryons, including the presence/absence variation, and additivity/nonadditivity gene expression in the dikaryon may contribute to heterosis. By sequencing the urease gene poure sequences and mRNA sequences, we identified the monoallelic expression of the poure gene in the dikaryon, and its transcript was from the parental monokaryon MK13. Furthermore, we discovered RNA editing in the poure gene mRNA of the three strains. These results suggest that the gene expression patterns in dikaryons should be similar to that of diploids during vegetative growth.

RETRACTED ARTICLE: Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi

“…In ascomycetes, A-to-G editing appeared to be the dominant form, with >95% of the identified editing sites belonging to this category. In the basidiomycetes [28,72], including G. lucidum, Pleurotus ostreatus and the species in our study, A-to-G is not the only dominant transition and four of twelve possible editing types (A-to-G, C-to-T, G-to-A, and T-to-C) can account for up to 50% or more of total editing events. Given that A-to-G editing is dominant in animals and Ascomycetes, the expansion of editing types in basidiomycetes may suggest the occurrence of novel mechanisms of RNA editing.…”

Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum

“…A recent theoretical model shows that haploid-diploid life cycles can occur only under a restricted set of conditions (Scott and Rescan 2017): (i) Haploid-diploid life cycles are stable only when diploids have higher intrinsic fitness compared to haploids (hereafter, ploidy effects on fitness). Such fitness differences between haploids and diploids can be due to the fixation of mutations with different fitness effects in haploids vs. diploids due to differences in physiology (Simchen and Jinks 1964;Szafraniec et al 2003;McBride et al 2008;Gerstein 2013;Zörgö et al 2013), in physical characteristics (e.g., cell morphology, Mable 2001), in gene expression (Coelho et al 2007;von Dassow et al 2009;Rokitta et al 2011;Meng et al 2013;Liu et al 2017), or in ecology (Thornber 2006;Rescan et al 2016). (ii) Haploid-diploid life cycles can be stable only when the effect of intrinsic fitness differences, which favors the diploid phase, balances the effect of selection against deleterious mutations, which favors the haploid phase ( Figure 1).…”

Adenosine to inosine mRNA editing in fungi and how it may relate to fungal pathogenesis

“…verticillioides , Neurospora crassa , N . tetrasperma , Pyronema confluens , and Sordaria macrospora [ 11 , 12 , 13 , 14 , 15 ]. In the basidiomycete G .…”

“…Fungal nuclear genes whose transcripts are affected by editing tend to have a role in late sexual development, i.e., meiotic spore (ascospore) formation and/or ascospore discharge [ 11 , 15 , 30 ; Fig 1 ]. This observation is of interest because ascospores are the primary inoculum of several phytopathogenic ascomycetes, including the wheat and barley pathogen F .…”