Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce

The basidiomycete Phanerochaete carnosa is a white-rot species that has been almost exclusively isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides) species. P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder at each time point was also analyzed for total sugar and lignin composition.Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, the highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with AA3 and AA5 oxidases. In addition, a lytic polysaccharide monooxygenase (AA9) was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi. The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of particular glycoside hydrolase GH5 and GH16 subfamilies, and permitted co-expression analyses that identified new targets for study, including loosenins, hydrophobins, and proteins with unknown function.