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

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

doi:10.1186/s12864-019-5817-8

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

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

Tutkimustuotos: Artikkelijulkaisu › Artikkeli › Tieteellinen › vertaisarvioitu

Kuvaus

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.

Alkuperäiskieli	englanti
Artikkeli	430
Lehti	BMC Genomics
Vuosikerta	20
Sivumäärä	22
ISSN	1471-2164
DOI - pysyväislinkit	https://doi.org/10.1186/s12864-019-5817-8
Tila	Julkaistu - 28 toukokuuta 2019
OKM-julkaisutyyppi	A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä, vertaisarvioitu

Tieteenalat

1184 Genetiikka, kehitysbiologia, fysiologia
1183 Kasvibiologia, mikrobiologia, virologia

Lainaa tätä

Mäkinen, M., Kuuskeri, J., Laine, P., Smolander, O-P., Kovalchuk, A., Zeng, Z., ... Lundell, T. (2019). Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics, 20, [430]. https://doi.org/10.1186/s12864-019-5817-8

Mäkinen, Mari ; Kuuskeri, Jaana ; Laine, Pia ; Smolander, Olli-Pekka ; Kovalchuk, Andriy ; Zeng, Zhen ; Asiegbu, Fred ; Paulin, Lars ; Auvinen, Petri ; Lundell, Taina. / Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. Julkaisussa: BMC Genomics. 2019 ; Vuosikerta 20.

@article{08956435795e44eaa7ab5e08181a64da,

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

abstract = "BackgroundThe 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.ResultsThe 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.ConclusionsThe 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.",

keywords = "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",

author = "Mari M{\"a}kinen and Jaana Kuuskeri and Pia Laine and Olli-Pekka Smolander and Andriy Kovalchuk and Zhen Zeng and Fred Asiegbu and Lars Paulin and Petri Auvinen and Taina Lundell",

year = "2019",

month = "5",

day = "28",

doi = "10.1186/s12864-019-5817-8",

language = "English",

volume = "20",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BMC",

}

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, Vuosikerta 20, 430. https://doi.org/10.1186/s12864-019-5817-8

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 ; Paulin, Lars ; Auvinen, Petri ; Lundell, Taina.

julkaisussa: BMC Genomics, Vuosikerta 20, 430, 28.05.2019.

Tutkimustuotos: Artikkelijulkaisu › Artikkeli › Tieteellinen › vertaisarvioitu

TY - JOUR

T1 - Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

AU - Mäkinen, Mari

AU - Kuuskeri, Jaana

AU - Laine, Pia

AU - Smolander, Olli-Pekka

AU - Kovalchuk, Andriy

AU - Zeng, Zhen

AU - Asiegbu, Fred

AU - Paulin, Lars

AU - Auvinen, Petri

AU - Lundell, Taina

PY - 2019/5/28

Y1 - 2019/5/28

N2 - BackgroundThe 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.ResultsThe 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.ConclusionsThe 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.

AB - BackgroundThe 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.ResultsThe 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.ConclusionsThe 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.

KW - 1184 Genetics, developmental biology, physiology

KW - Genomics

KW - Comparative genomics

KW - Enzyme encoding genes

KW - Gene clusters

KW - Wood decay metabolism

KW - 1183 Plant biology, microbiology, virology

KW - Filamentous fungi

KW - Basidiomycota

KW - Polyporales

KW - Phlebioid clade

KW - Wood decay fungi