DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions

Abstract

Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.

Authors:
ORCiD logo [1];  [2];  [2];  [3];  [4]; ORCiD logo [5];  [6];  [2];  [3];  [7];  [6];  [6];  [2];  [6]; ORCiD logo [3];  [3]; ORCiD logo [8];  [2];  [2];  [6] more »; ORCiD logo [9];  [10];  [2] « less
  1. Univ. of Manitoba, Winnipeg, MB (Canada); Univ. of Benin, Benin City (Nigeria); Univ. of Helsinki (Finalnd)
  2. Univ. of Helsinki (Finalnd)
  3. Consejo Superior de Invesitgaciones Cientificas, Madrid (Spain)
  4. Friedrich Sciller Univ., Jena (Germany)
  5. Aix-Marseille Univ., Marseille (France); Inst. National de la Recherche Agronomique, Marseille (France); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  6. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
  7. Univ. of California, Berkeley, CA (United States)
  8. Chinese Academy of Forestry, Beijing (China)
  9. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Univ. de Salamanca, Villamayor (Spain)
  10. Inst. National de la Recherche Agronomique (INRA), Champenoux (France); Univ. of Lorraine, Champenoux (France)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Academy of Finland
OSTI Identifier:
1619169
Grant/Contract Number:  
AC02-05CH11231; 307580
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; comparative genomics; ecological genetics

Citation Formats

Oghenekaro, Abbot O., Kovalchuk, Andriy, Raffaello, Tommaso, Camarero, Susana, Gressler, Markus, Henrissat, Bernard, Lee, Juna, Liu, Mengxia, Martínez, Angel T., Miettinen, Otto, Mihaltcheva, Sirma, Pangilinan, Jasmyn, Ren, Fei, Riley, Robert, Ruiz-Dueñas, Francisco Javier, Serrano, Ana, Thon, Michael R., Wen, Zilan, Zeng, Zhen, Barry, Kerrie, Grigoriev, Igor V., Martin, Francis, and Asiegbu, Fred O. Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions. United States: N. p., 2020. Web. doi:10.1038/s41598-020-62150-4.
Oghenekaro, Abbot O., Kovalchuk, Andriy, Raffaello, Tommaso, Camarero, Susana, Gressler, Markus, Henrissat, Bernard, Lee, Juna, Liu, Mengxia, Martínez, Angel T., Miettinen, Otto, Mihaltcheva, Sirma, Pangilinan, Jasmyn, Ren, Fei, Riley, Robert, Ruiz-Dueñas, Francisco Javier, Serrano, Ana, Thon, Michael R., Wen, Zilan, Zeng, Zhen, Barry, Kerrie, Grigoriev, Igor V., Martin, Francis, & Asiegbu, Fred O. Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions. United States. https://doi.org/10.1038/s41598-020-62150-4
Oghenekaro, Abbot O., Kovalchuk, Andriy, Raffaello, Tommaso, Camarero, Susana, Gressler, Markus, Henrissat, Bernard, Lee, Juna, Liu, Mengxia, Martínez, Angel T., Miettinen, Otto, Mihaltcheva, Sirma, Pangilinan, Jasmyn, Ren, Fei, Riley, Robert, Ruiz-Dueñas, Francisco Javier, Serrano, Ana, Thon, Michael R., Wen, Zilan, Zeng, Zhen, Barry, Kerrie, Grigoriev, Igor V., Martin, Francis, and Asiegbu, Fred O. Mon . "Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions". United States. https://doi.org/10.1038/s41598-020-62150-4. https://www.osti.gov/servlets/purl/1619169.
@article{osti_1619169,
title = {Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions},
author = {Oghenekaro, Abbot O. and Kovalchuk, Andriy and Raffaello, Tommaso and Camarero, Susana and Gressler, Markus and Henrissat, Bernard and Lee, Juna and Liu, Mengxia and Martínez, Angel T. and Miettinen, Otto and Mihaltcheva, Sirma and Pangilinan, Jasmyn and Ren, Fei and Riley, Robert and Ruiz-Dueñas, Francisco Javier and Serrano, Ana and Thon, Michael R. and Wen, Zilan and Zeng, Zhen and Barry, Kerrie and Grigoriev, Igor V. and Martin, Francis and Asiegbu, Fred O.},
abstractNote = {Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.},
doi = {10.1038/s41598-020-62150-4},
journal = {Scientific Reports},
number = 1,
volume = 10,
place = {United States},
year = {2020},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Figures / Tables:

Figure 1 Figure 1: (A) Fruiting bodies of Rigidoporus microporus developing in the lower part of Hevea brasiliensis trunk heavily colonized by the pathogen (plantation of the Rubber Research Institute Nigeria, July 2017). (B) Longitudinal section of H. brasiliensis wood colonized by R. microporus (stained by aniline blue).

Save / Share:

Works referenced in this record:

A Fungal Family of Transcriptional Regulators: the Zinc Cluster Proteins
journal, September 2006

  • MacPherson, S.; Larochelle, M.; Turcotte, B.
  • Microbiology and Molecular Biology Reviews, Vol. 70, Issue 3
  • DOI: 10.1128/MMBR.00015-06

Plant Cell Wall–Degrading Enzymes and Their Secretion in Plant-Pathogenic Fungi
journal, August 2014


Sidera, a new genus in Hymenochaetales with poroid and hydnoid species
journal, June 2010


Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans
journal, March 2007

  • Bergmann, Sebastian; Schümann, Julia; Scherlach, Kirstin
  • Nature Chemical Biology, Vol. 3, Issue 4
  • DOI: 10.1038/nchembio869

Interspecific combative interactions between wood-decaying basidiomycetes
journal, March 2000


Three Redundant Synthetases Secure Redox-Active Pigment Production in the Basidiomycete Paxillus involutus
journal, October 2015


STAR: ultrafast universal RNA-seq aligner
journal, October 2012


New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
journal, March 2010

  • Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent
  • Systematic Biology, Vol. 59, Issue 3
  • DOI: 10.1093/sysbio/syq010

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000


Further analysts of the data by akaike' s information criterion and the finite corrections: Further analysts of the data by akaike' s
journal, January 1978


The importance of inoculum size for the competitive ability of wood decomposing fungi
journal, July 1993


Horizontal gene transfer in eukaryotic evolution
journal, August 2008

  • Keeling, Patrick J.; Palmer, Jeffrey D.
  • Nature Reviews Genetics, Vol. 9, Issue 8
  • DOI: 10.1038/nrg2386

Fungal Effectors and Plant Susceptibility
journal, April 2015


Locating proteins in the cell using TargetP, SignalP and related tools
journal, April 2007

  • Emanuelsson, Olof; Brunak, Søren; von Heijne, Gunnar
  • Nature Protocols, Vol. 2, Issue 4
  • DOI: 10.1038/nprot.2007.131

Molecular phylogeny of Rigidoporus microporus isolates associated with white rot disease of rubber trees (Hevea brasiliensis)
journal, May 2014


Differential expression analysis for sequence count data
journal, October 2010


The α-Aminoadipate Pathway for Lysine Biosynthesis in Fungi
journal, January 2006

  • Xu, Hengyu; Andi, Babak; Qian, Jinghua
  • Cell Biochemistry and Biophysics, Vol. 46, Issue 1
  • DOI: 10.1385/CBB:46:1:43

Comparative and population genomic landscape of Phellinus noxius : A hypervariable fungus causing root rot in trees
journal, October 2017

  • Chung, Chia-Lin; Lee, Tracy J.; Akiba, Mitsuteru
  • Molecular Ecology, Vol. 26, Issue 22
  • DOI: 10.1111/mec.14359

Root Rot Diseases of Rubber Trees.
journal, January 1987


SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade
journal, November 2006


The saprotrophic wood-degrading abilities of Rigidoporus microporus
journal, January 2015

  • Oghenekaro, Abbot; Daniel, Geoffrey; Asiegbu, Fred
  • Silva Fennica, Vol. 49, Issue 4
  • DOI: 10.14214/sf.1320

Draft genome sequence of the rubber tree Hevea brasiliensis
journal, January 2013

  • Rahman, Ahmad Yamin Abdul; Usharraj, Abhilash O.; Misra, Biswapriya B.
  • BMC Genomics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2164-14-75

The separate roles of plant cis and trans prenyl transferases in cis-1,4-polyisoprene biosynthesis
journal, November 1993


FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer
journal, January 2015

  • Jaramillo, Vinicio D. Armijos; Sukno, Serenella A.; Thon, Michael R.
  • BMC Genomics, Vol. 16, Issue 1
  • DOI: 10.1186/1471-2164-16-2

Fungal Transporters Involved in Efflux of Natural Toxic Compounds and Fungicides
journal, June 2000

  • Del Sorbo, Giovanni; Schoonbeek, Henk-jan; De Waard, Maarten A.
  • Fungal Genetics and Biology, Vol. 30, Issue 1
  • DOI: 10.1006/fgbi.2000.1206

The Biodegradation of Latex Rubber: A Minireview
journal, June 2013


Heme-Dependent Rubber Oxygenase RoxA of Xanthomonas sp. Cleaves the Carbon Backbone of Poly(cis-1,4-Isoprene) by a Dioxygenase Mechanism
journal, May 2005


A Highly Conserved Basidiomycete Peptide Synthetase Produces a Trimeric Hydroxamate Siderophore
journal, August 2017

  • Brandenburger, Eileen; Gressler, Markus; Leonhardt, Robin
  • Applied and Environmental Microbiology, Vol. 83, Issue 21
  • DOI: 10.1128/AEM.01478-17

A revised family-level classification of the Polyporales (Basidiomycota)
journal, September 2017


MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013

  • Katoh, K.; Standley, D. M.
  • Molecular Biology and Evolution, Vol. 30, Issue 4
  • DOI: 10.1093/molbev/mst010

Host-specific toxins: effectors of necrotrophic pathogenicity
journal, July 2008


Concluding remarks: Methods for studying microbial interactions
journal, May 1978


Selective replacement between species of wood-rotting basidiomycetes, a laboratory study
journal, June 1997


Selectivity of Fungal Sesquiterpene Synthases: Role of the Active Site's H-1α Loop in Catalysis
journal, October 2010

  • L�pez-Gallego, Fernando; Wawrzyn, GraysonT.; Schmidt-Dannert, Claudia
  • Applied and Environmental Microbiology, Vol. 76, Issue 23
  • DOI: 10.1128/AEM.01811-10

Linear fusigen as the major hydroxamate siderophore of the ectomycorrhizal Basidiomycota Laccaria laccata and Laccaria bicolor
journal, September 2013


The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
journal, June 2012


Genome sequence of a white rot fungus Schizopora paradoxa KUC8140 for wood decay and mycoremediation
journal, October 2015


A survey of genes encoding H2O2-producing GMC oxidoreductases in 10 Polyporales genomes
journal, August 2015

  • Ferreira, P.; Carro, J.; Serrano, A.
  • Mycologia, Vol. 107, Issue 6
  • DOI: 10.3852/15-027

Management of basidiomycete root- and stem-rot diseases in oil palm, rubber and tropical hardwood plantation crops
journal, December 2014

  • Mohammed, C. L.; Rimbawanto, A.; Page, D. E.
  • Forest Pathology, Vol. 44, Issue 6
  • DOI: 10.1111/efp.12140

HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014


A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus
journal, November 2017


SMS: Smart Model Selection in PhyML
journal, May 2017

  • Lefort, Vincent; Longueville, Jean-Emmanuel; Gascuel, Olivier
  • Molecular Biology and Evolution, Vol. 34, Issue 9
  • DOI: 10.1093/molbev/msx149

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001

  • Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
  • Journal of Molecular Biology, Vol. 305, Issue 3
  • DOI: 10.1006/jmbi.2000.4315

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016

  • Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
  • Molecular Biology and Evolution, Vol. 33, Issue 7
  • DOI: 10.1093/molbev/msw054

FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
journal, June 2015


Transformation of the mycorrhizal fungus Laccaria bicolor using Agrobacterium tumefaciens
journal, January 2011


OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs
journal, November 2016

  • Zdobnov, Evgeny M.; Tegenfeldt, Fredrik; Kuznetsov, Dmitry
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1119

De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood
journal, March 2016


Effect of water activity, temperature and substrate on interactions between field and storage fungi
journal, February 1984


PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database
journal, December 2016

  • Urban, Martin; Cuzick, Alayne; Rutherford, Kim
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1089

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
journal, April 2014

  • Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew
  • Nucleic Acids Research, Vol. 42, Issue W1
  • DOI: 10.1093/nar/gku340

Fungal metabolic gene clusters—caravans traveling across genomes and environments
journal, March 2015


Differential Gene Expression in Pycnoporus coccineus during Interspecific Mycelial Interactions with Different Competitors
journal, August 2013

  • Arfi, Yonathan; Levasseur, Anthony; Record, Eric
  • Applied and Environmental Microbiology, Vol. 79, Issue 21
  • DOI: 10.1128/AEM.02316-13

Horizontal gene transfer in fungi
journal, December 2011


An efficient algorithm for large-scale detection of protein families
journal, April 2002


Fungal communities in decaying hardwood branches
journal, April 1979


Fungal Genomics
book, May 2014


Evaluation of potential reference genes for use in gene expression studies in the conifer pathogen (Heterobasidion annosum)
journal, May 2013


Root-rot diseases of the rubber tree in the Ivory Coast. 1. Severity, dynamics, and characterization of epidemics
journal, October 1988

  • Nandris, Daniel; Nicole, Michel; Geiger, Jean Paul
  • Canadian Journal of Forest Research, Vol. 18, Issue 10
  • DOI: 10.1139/x88-192

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
journal, November 2013

  • Nordberg, Henrik; Cantor, Michael; Dusheyko, Serge
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1069

Activity of α-Aminoadipate Reductase Depends on the N-Terminally Extending Domain
journal, June 2015


Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities
journal, December 2015

  • Nagy, László G.; Riley, Robert; Tritt, Andrew
  • Molecular Biology and Evolution, Vol. 33, Issue 4
  • DOI: 10.1093/molbev/msv337

Nonribosomal peptide synthesis in Aspergillus fumigatus and other fungi
journal, May 2007


MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013

  • Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1183

Isolation of good quality RNA from a medicinal plant seabuckthorn, rich in secondary metabolites
journal, November 2009

  • Ghangal, Rajesh; Raghuvanshi, Saurabh; Chand Sharma, Prakash
  • Plant Physiology and Biochemistry, Vol. 47, Issue 11-12
  • DOI: 10.1016/j.plaphy.2009.09.004

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
journal, June 2014

  • Riley, Robert; Salamov, Asaf A.; Brown, Daren W.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 27
  • DOI: 10.1073/pnas.1400592111

Horizontal Gene Transfer in Eukaryotic Plant Pathogens
journal, August 2014


Distinct Roles for Intra- and Extracellular Siderophores during Aspergillus fumigatus Infection
journal, September 2007


Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.