Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

Show full item record



Permalink

http://hdl.handle.net/10138/303119

Citation

Mäkinen , M , Kuuskeri , J , Laine , P , Smolander , O-P , Kovalchuk , A , Zeng , Z , Asiegbu , F , Paulin , L , Auvinen , P & Lundell , T 2019 , ' Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi ' , BMC Genomics , vol. 20 , 430 . https://doi.org/10.1186/s12864-019-5817-8

Title: Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi
Author: Mäkinen, Mari; Kuuskeri, Jaana; Laine, Pia; Smolander, Olli-Pekka; Kovalchuk, Andriy; Zeng, Zhen; Asiegbu, Fred; Paulin, Lars; Auvinen, Petri; Lundell, Taina
Contributor: University of Helsinki, Fungal Co-life, Omics and Ecophysiology Research Group
University of Helsinki, Fungal Genetics and Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Forest Sciences
University of Helsinki, Department of Forest Sciences
University of Helsinki, Helsinki Institute of Sustainability Science (HELSUS)
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Microbiology
Date: 2019-05-28
Language: eng
Number of pages: 22
Belongs to series: BMC Genomics
ISSN: 1471-2164
URI: http://hdl.handle.net/10138/303119
Abstract: Background The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol from various waste lignocellulose substrates. Thus, P. radiata is a promising organism for biotechnological applications aiming at sustainable utilization of plant biomass. Here we report the genome sequence of P. radiata isolate 79 originally isolated from decayed alder wood in South Finland. To better understand the evolution of wood decay mechanisms in this fungus and the Polyporales phlebioid clade, gene content and clustering of genes encoding specific carbohydrate-active enzymes (CAZymes) in seven closely related fungal species was investigated. In addition, other genes encoding proteins reflecting the fungal lifestyle including peptidases, transporters, small secreted proteins and genes involved in secondary metabolism were identified in the genome assembly of P. radiata. Results The PACBio sequenced nuclear genome of P. radiata was assembled to 93 contigs with 72X sequencing coverage and annotated, revealing a dense genome of 40.4 Mbp with approximately 14 082 predicted protein-coding genes. According to functional annotation, the genome harbors 209 glycoside hydrolase, 27 carbohydrate esterase, 8 polysaccharide lyase, and over 70 auxiliary redox enzyme-encoding genes. Comparisons with the genomes of other phlebioid fungi revealed shared and specific properties among the species with seemingly similar saprobic wood-decay lifestyles. Clustering of especially GH10 and AA9 enzyme-encoding genes according to genomic localization was discovered to be conserved among the phlebioid species. In P. radiata genome, a rich repertoire of genes involved in the production of secondary metabolites was recognized. In addition, 49 genes encoding predicted ABC proteins were identified in P. radiata genome together with 336 genes encoding peptidases, and 430 genes encoding small secreted proteins. Conclusions The genome assembly of P. radiata contains wide array of carbohydrate polymer attacking CAZyme and oxidoreductase genes in a composition identifiable for phlebioid white rot lifestyle in wood decomposition, and may thus serve as reference for further studies. Comparative genomics also contributed to enlightening fungal decay mechanisms in conversion and cycling of recalcitrant organic carbon in the forest ecosystems.
Subject: 1184 Genetics, developmental biology, physiology
Genomics
Comparative genomics
Enzyme encoding genes
Gene clusters
Wood decay metabolism
1183 Plant biology, microbiology, virology
Filamentous fungi
Basidiomycota
Polyporales
Phlebioid clade
Wood decay fungi
Lignin biodegradation
Phlebia radiata
comparative genomics
wood decay
carbohydrate-active enzyme genes
lignin biodegradation
co-regulation
peptidases
secondary metabolism
ABC transporters
small secreted proteins
LIGNIN-MODIFYING ENZYMES
WOOD-DECAY
PHANEROCHAETE-CHRYSOSPORIUM
DEGRADING ENZYMES
HYDROPHOBIN GENE
ABC PROTEINS
BASIDIOMYCETE
POLYPORALES
ANNOTATION
EXPRESSION
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
s12864_019_5817_8.pdf 1.918Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record