De novo transcriptome assembly and protein profiling of copper-induced lignocellulolytic fungus Ganoderma lucidum MDU-7 reveals genes involved in lignocellulose degradation and terpenoid biosynthetic pathways

Ganoderma lucidum is an important medicinal fungus that possesses exceedingly high lignocellulose degrading ability. Evidently, Cu2+ has decisive roles on the mycelial growth and enzyme production. To reveal the effect of Cu2+ on G. lucidum transcriptome, predominantly associated with lignocelluloly...

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Published in:Genomics (San Diego, Calif.) Calif.), 2020-01, Vol.112 (1), p.184-198
Main Authors: Jain, Kavish Kumar, Kumar, Amit, Shankar, Akshay, Pandey, Dhananjay, Chaudhary, Bhupendra, Sharma, Krishna Kant
Format: Article
Language:English
Subjects:
Copper
Ganoderma lucidum
Laccase
Next-generation sequencing
Proteome
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Summary:Ganoderma lucidum is an important medicinal fungus that possesses exceedingly high lignocellulose degrading ability. Evidently, Cu2+ has decisive roles on the mycelial growth and enzyme production. To reveal the effect of Cu2+ on G. lucidum transcriptome, predominantly associated with lignocellulolytic progression, we conducted comparative NGS based de novo transcriptome assembly using Illumina Hi SeqTM sequencing platform. We obtained 26,083,372 and 35,713,076 high-quality reads from induced and uninduced cultures. For wood degrading activity, 194 transcript coding for oxidoreductases and 402 transcripts for CAZymes were predicted. Further, secretome studies revealed high score GO terms related to oxidoreductases, glycosyl hydrolases, and chitinases from Cu-induced mycelia. The increased Cu2+ concentrations showed higher secretion of lignocellulases such as laccases, cellulases, and xylanases along with increased production of phenolics and antioxidants. Several differences in the transcriptomic and proteomic signatures for lignocellulolytic enzymes provide vital clues about Cu2+ mediated gene regulation and metabolic pathways in basidiomycetous fungi. •Copper supplementation increases laccase production Ganoderma•Transcriptome reveals copper mediated gene regulation in Ganoderma•Upregulation of genes for lignin degradation, secondary metabolites and autophaghy•LCMS/MS analysis also suggests increase in glycosyl hydrolase and oxidoreductase
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2019.01.012