Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Abstract

We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.

Systematic review of publicly available non-Dikarya fungal proteomes for understanding their plant biomass-degrading and bioremediation potentials

“…Recent genome sequencing studies have also reported about the evolutionary loss of CAZymeencoding genes in few fungal divisions (Skamnioti et al 2008). Comparative metadata analysis of fungal genomewide annotations especially CAZymes has been studied and reported Sista Kameshwar and Qin 2017;Zhao et al 2013). However, previous Page 10 of 19 Sista Kameshwar and Qin Bioresour.…”

“…The fungal genomic repositories such as joint genome institute MycoCosm (Grigoriev et al 2011;Nordberg et al 2013), 1000 fungal genome project and Hungate collection residing in the rumen microbial genomics network are continuously enhancing the genomic details of various fungi. Studies being conducted to understand the genomic potentials of different fungi belonging to different phyla were compared for their plant cell wall-degrading potentials to explore their applications in biofuel and bioremediation industries King et al 2011;Rytioja et al 2014;Sista Kameshwar and Qin 2017;Zhao et al 2013). Till date, there are 1054 wholegenome sequences of fungi belonging to different phyla in JGI-MycoCosm repository, out of which 444 wholegenome sequences of fungi have been published and publicly available and the remaining 610 whole-genome sequences of fungi were under study and unpublished (Grigoriev et al 2011;Nordberg et al 2013).…”

Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production ofTrametes

“…Carbohydrate-active enzymes (CAZymes) are involved in the polysaccharide degradation of plant cell wall [11], lignin, cellulose, hemicellulose, and pectin [12]. In particular, CAZyme classes (glycoside hydrolases [GH], carbohydrate esterases [CEs], and polysaccharide lyases) play central roles in plant biomass decomposition by bacteria and fungi [13].…”

Comparative genomics uncovers genetic diversity and synthetic biology of secondary metabolite production of the genus Trametes

“…Carbohydrate-active enzymes (known as CAZymes) are involved in the degradation processes of polysaccharides of plant cell wall [ 11], lignin, cellulose, hemicellulose and pectin [ 12]. Especially, the CAZyme classes (glycoside hydrolases, carbohydrate eaterases, and polysaccharide lyases) play central roles in plant biomass decomposition by bacteria and fungi [ 13].…”