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

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-encodingmore » 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.« less

Authors:
 [1];  [1];  [2];  [2];  [2];  [3];  [3];  [2];  [2]; ORCiD logo [1]
  1. Univ. of Helsinki (Finland). Faculty of Agriculture and Forestry. Viikki Campus. Dept. of Microbiology
  2. Univ. of Helsinki (Finland). Viikki Campus. Inst. of Biotechnology. DNA Sequencing and Genomics Lab.
  3. Univ. of Helsinki (Finland). Viikki Campus. Faculty of Agriculture and Forestry. Dept. of Forest Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1626824
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity; Phlebia radiata; comparative genomics; wood decay; carbohydrate-active enzyme genes; lignin biodegradation; co-regulation; peptidases; secondary metabolism; ABC transporters; small secreted proteins

Citation Formats

Mäkinen, Mari, Kuuskeri, Jaana, Laine, Pia, Smolander, Olli-Pekka, Kovalchuk, Andriy, Zeng, Zhen, Asiegbu, Fred O., Paulin, Lars, Auvinen, Petri, and Lundell, Taina. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. United States: N. p., 2019. Web. doi:10.1186/s12864-019-5817-8.
Mäkinen, Mari, Kuuskeri, Jaana, Laine, Pia, Smolander, Olli-Pekka, Kovalchuk, Andriy, Zeng, Zhen, Asiegbu, Fred O., Paulin, Lars, Auvinen, Petri, & Lundell, Taina. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. United States. https://doi.org/10.1186/s12864-019-5817-8
Mäkinen, Mari, Kuuskeri, Jaana, Laine, Pia, Smolander, Olli-Pekka, Kovalchuk, Andriy, Zeng, Zhen, Asiegbu, Fred O., Paulin, Lars, Auvinen, Petri, and Lundell, Taina. Tue . "Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi". United States. https://doi.org/10.1186/s12864-019-5817-8. https://www.osti.gov/servlets/purl/1626824.
@article{osti_1626824,
title = {Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi},
author = {Mäkinen, Mari and Kuuskeri, Jaana and Laine, Pia and Smolander, Olli-Pekka and Kovalchuk, Andriy and Zeng, Zhen and Asiegbu, Fred O. and Paulin, Lars and Auvinen, Petri and Lundell, Taina},
abstractNote = {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.},
doi = {10.1186/s12864-019-5817-8},
url = {https://www.osti.gov/biblio/1626824}, journal = {BMC Genomics},
issn = {1471-2164},
number = 1,
volume = 20,
place = {United States},
year = {2019},
month = {5}
}

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    Works referencing / citing this record:

    Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus
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