Transcriptomic analysis ofLentinus squarrosulusprovide insights into its biodegradation ability

Abstract

Basidiomycetes are of special interest in biotechnological research for their versatile potential in degradation of lignocellulosic biomass. This study accordingly reports analysis of transcriptome of a white-rot Basidiomycete L.squarrosulus grown in simple potato dextrose broth supplemented with aromatic compound, reactive black dye to gain an insight into the degradation ability of the fungus. RNA was sequenced using Illumina NextSeq 500 to obtain 6,679,162 high quality paired end reads that were assembled de novo using CLC assembly cell to generate 25,244 contigs.Putative functions were assigned for the 10,494 transcripts based on sequence similarities through BLAST2GO 5.2 and Function annotator. Functional assignments revealed enhanced oxidoreductase activity through the expression of diverse biomass degrading enzymes and their corresponding co-regulators. CAZyme analysis through dbCAN and CUPP revealed the presence of 6 families of polysaccharide lyases, 51 families of glycoside hydrolases, 23 families of glycoside transferases, 7 families of carbohydrate esterases and 10 families of Auxiliary activities.Genes encoding the ligninolytic enzymes and auxiliary activities among the transcript sequences were identified through gene prediction by AUGUSTUS and FGENESH. Biochemical analysis of a couple of biomass degrading enzymes substantiated the functional predictions. In essence, L.squarrosulus grown in a simple medium devoid of lignocellulosic substrate demonstrated presence of a repertoire of lignocellulose degrading enzymesimplying that source of lignocellulose is not required for expression of these biomass degrading enzymes. The study hereby underlines the significance of L.squarrosulus in biomass degradation and its future functional exploitation in biomass conversion applications.

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi

“…Different authors have reviewed and compared these platforms for various applications [ 107 , 108 , 109 , 110 ]. Ravichandran et al [ 111 ] used RNA-seq on an Illumina platform to obtain insight on the degradative ability of a white-rot fungus based on the expression of genes for these degrading enzymes. Henske et al [ 112 ] used RNA-seq to investigate the differential expression of LMEs in the presence of different substrates.…”