Genomic and transcriptomic profiles associated to fast and slow-growing phenotypes in Pleurotus ostreatus

Pleurotus ostreatus is an important edible mushroom with biotechnological properties. The parental monokaryotic strains mkPC9 and mkPC15, obtained by de-dikaryotization of the dikaryotic strain dkN001 and whose genomes sequences are available, are Fast and Slow growing strains (FG/SG) respectively. In this work, we analyzed the growth rate of a dkN001 meiotic progeny consisting of 60 monokaryons, and selected two groups of nine individuals each one showing the largest differences in this trait (FG vs SG, p < 0.05). These monokaryons were mated with the compatible tester mkPC23 to form a collection of 18 half-sib dikaryotic strains. We found that monokaryotic and dikaryotic growth rates were not correlated (p < 0.05). RNAseq experiments were carried out using FG and SG monokaryotic populations as well as the dikaryons derived from them, to identify the transcriptomic and genotypic profiles associated with growth rate phenotype. Using the RNAseq mapped reads and the whole set of Single-Nucleotide Polymorphisms between mkPC15 and mkPC9, we determined the entire genotype (PC15-type or PC9-type) of each monokaryon at a very high resolution. Using this approach, we identified regions in chromosomes III and VIII of the genetic linkage map with a strong association between parental origin and growth rate phenotype. Additionally, transcriptional analysis of 9 fast-growing (FG) and 9 slow-growing (SG) monokaryotic populations yielded 114 differentially expressed (DEG) genes showing positive correlation with growth rate and 70 DEG genes showing negative correlation (p < 0.05). Functions of positively correlated genes were mainly enriched in translation, whereas negatively correlated genes were enriched in regulation of oxidoreductase activity and respiratory gaseous exchange. Intriguingly, none of this monokaryotic DEG genes was found to be differentially expressed between the FG and SG dikaryons analyzed, which showed interesting transcription factors involved in multicellular developmental processes in eukaryotes.