Transcriptome Analysis of Podoscypha petalodes Strain GGF6 Reveals the Diversity of Proteins Involved in Lignocellulose Degradation and Ligninolytic Function

Abstract

The present study reports transcriptomic profiling of a Basidiomycota fungus, Podoscypha petalodes strain GGF6 belonging to the family Podoscyphaceae, isolated from the North-Western Himalayan ranges in Himachal Pradesh, India. Podoscypha petalodes strain GGF6 possesses significant biotechnological potential as it has been reported for endocellulase, laccase, and other lignocellulolytic enzymes under submerged fermentation conditions. The present study attempts to enhance our knowledge of its lignocellulolytic potential as no previous omics-based analysis is available for this white-rot fungus. The transcriptomic analysis of P. petalodes GGF6 reveals the presence of 280 CAZy proteins. Furthermore, bioprospecting transcriptome signatures in the fungi revealed a diverse array of proteins associated with cellulose, hemicellulose, pectin, and lignin degradation. Interestingly, two copper-dependent lytic polysaccharide monooxygenases (AA14) and one pyrroloquinolinequinone-dependent oxidoreductase (AA12) were also identified, which are known to help in the lignocellulosic plant biomass degradation. Overall, this transcriptome profiling-based study provides deeper molecular-level insights into this Basidiomycota fungi, P. petalodes, for its potential application in diverse biotechnological applications, not only in the biofuel industry but also in the environmental biodegradation of recalcitrant molecules.

Supplementary information: The online version contains supplementary material available at 10.1007/s12088-022-01037-6.

Keywords: CAZyme; Fungal diversity; Laccase; Ligninolytic; Lignocellulose; Transcriptome.

Fig. 1

A Morphological characteristics of P. petalodes strain GGF6: (I) Fungal mycelial growth on PDA plate, (II) Microscopic observation of hyphae at 10x, (II) Microscopic observation of hyphae at 40x. B ITS sequence-based phylogenetic tree shows the position of P. petalodes strain GGF6 amongst its close relatives within the family Podoscyphaceae. Colour codes are according to the order-level fungus taxonomy shown on the left. Red-colored clade depicts the ITS sequences of those selected organisms from which we have identified the percent identity as in Table S1. C RPB1-protein-based maximum likelihood phylogenetic tree confirms the taxonomy of P. petalodes strain GGF6 amongst its close relatives within the family Podoscyphaceae. Colour codes are according to the order-level fungus taxonomy shown on the left. Both trees are drawn to scale, as shown on the top of the phylogenetic tree

Fig. 2

Homology information for the unigenes identified from P. petalodes strain GGF6 transcriptome: A Distribution of unigene length. B Sequence identity-based distribution of the top BLAST hits for each unigene-encoded protein against the NR database. C E‑value-based distribution as identified using the best BLASTp hit for each unigene-encoded protein against the non-redundant (NR) database. D Taxonomy classification (at order, family, and genus level) of best BLASTp homolog per each unigene-encoded protein against the non-redundant (NR) database and their relative distribution

Fig. 3

Functional characterization of identified unigenes identified from P. petalodes strain GGF6 transcriptome: A The distribution of top 25 Pfam families B Distribution of CAZy families C Distribution of KEGG pathways