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

Mäkinen, Mari; Kuuskeri, Jaana; Laine, Pia; Smolander, Olli-Pekka; Kovalchuk, Andriy; Zeng, Zhen; Asiegbu, Fred O.; Paulin, Lars; Auvinen, Petri; Lundell, Taina

doi:10.1186/s12864-019-5817-8

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

Journal Article · Tue May 28 00:00:00 EDT 2019 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-019-5817-8· OSTI ID:1626824

Mäkinen, Mari ^[1]; Kuuskeri, Jaana ^[1]; Laine, Pia ^[2]; Smolander, Olli-Pekka ^[2]; Kovalchuk, Andriy ^[2]; Zeng, Zhen ^[3]; Asiegbu, Fred O. ^[3]; Paulin, Lars ^[2]; Auvinen, Petri ^[2];

^[1]

Univ. of Helsinki (Finland). Faculty of Agriculture and Forestry. Viikki Campus. Dept. of Microbiology
Univ. of Helsinki (Finland). Viikki Campus. Inst. of Biotechnology. DNA Sequencing and Genomics Lab.
Univ. of Helsinki (Finland). Viikki Campus. Faculty of Agriculture and Forestry. Dept. of Forest Sciences

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626824

Journal Information:: BMC Genomics, Vol. 20, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Emiliania huxleyi endures N-limitation with an efficient metabolic budgeting and effective ATP synthesis Rokitta, Sebastian D.; Von Dassow, Peter; Rost, Björn BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-1051	journal	January 2014

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Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus Mattila, Hans Kristian; Mäkinen, Mari; Lundell, Taina Biotechnology for Biofuels, Vol. 13, Issue 1 https://doi.org/10.1186/s13068-020-01677-0	journal	February 2020
Seeking the Roles for Fungal Small-Secreted Proteins in Affecting Saprophytic Lifestyles Feldman, Daria; Yarden, Oded; Hadar, Yitzhak Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00455	journal	March 2020

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Related Subjects

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

Additional file 1: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi Mäkinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196539 The current record is supplemented by this dataset	dataset	January 2019
Additional file 1: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi Mäkinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196539.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 2: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196548.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 3: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196557 The current record is supplemented by this dataset	dataset	January 2019
Additional file 3: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196557.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 4: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196566 The current record is supplemented by this dataset	dataset	January 2019
Additional file 4: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196566.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 5: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196575 The current record is supplemented by this dataset	dataset	January 2019
Additional file 5: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196575.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 6: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196578 The current record is supplemented by this text	text	January 2019
Additional file 6: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196578.v1 The current record is supplemented by this text	text	January 2019
Additional file 7: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196590.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 8: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196593 The current record is supplemented by this dataset	dataset	January 2019
Additional file 8: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196593.v1 The current record is supplemented by this dataset	dataset	January 2019
Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.c.4521080 The current record is supplemented by this collection	collection	January 2019
Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.c.4521080.v1 The current record is supplemented by this collection	collection	January 2019
Additional file 2: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196548 The current record is supplemented by this dataset	dataset	January 2019
Additional file 7: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi MĂ¤Kinen, Mari; Kuuskeri, Jaana; Laine, Pia https://doi.org/10.6084/m9.figshare.8196590 The current record is supplemented by this dataset	dataset	January 2019