Research Articles

First fungal genome sequence from Africa: A preliminary analysis

Brenda D. Wingfield, Emma T. Steenkamp, Quentin C. Santana, Martin P.A. Coetzee, Stefan Bam, Irene Barnes, Chrizelle W. Beukes, Wai Yin Chan, Lieschen de Vos, Gerda Fourie, Melanie Friend, Thomas R. Gordon, Darryl A. Herron, Carson Holt, Ian Korf, Marija Kvas, Simon H. Martin, X. Osmond Mlonyeni, Kershney Naidoo, Mmatshepho M. Phasha, Alisa Postma, Oleg Reva, Heidi Roos, Melissa Simpson, Stephanie Slinski, Bernard Slippers, Rene Sutherland, Nicolaas A. van der Merwe, Magriet A. van der Nest, Stephanus N. Venter, Pieter M. Wilken, Mark Yandell, Renate Zipfel, Mike J. Wingfield
South African Journal of Science | Vol 108, No 1/2 | a537 | DOI: https://doi.org/10.4102/sajs.v108i1/2.537 | © 2012 Brenda D. Wingfield, Emma T. Steenkamp, Quentin C. Santana, Martin P.A. Coetzee, Stefan Bam, Irene Barnes, Chrizelle W. Beukes, Wai Yin Chan, Lieschen de Vos, Gerda Fourie, Melanie Friend, Thomas R. Gordon, Darryl A. Herron, Carson Holt, Ian Korf, Marija Kvas, Simon H. Martin, X. Osmond Mlonyeni, Kershney Naidoo, Mmatshepho M. Phasha, Alisa Postma, Oleg Reva, Heidi Roos, Melissa Simpson, Stephanie Slinski, Bernard Slippers, Rene Sutherland, Nicolaas A. van der Merwe, Magriet A. van der Nest, Stephanus N. Venter, Pieter M. Wilken, Mark Yandell, Renate Zipfel, Mike J. Wingfield | This work is licensed under CC Attribution 4.0
Submitted: 29 November 2010 | Published: 25 January 2012

About the author(s)

Brenda D. Wingfield, University of Pretoria, South Africa
Emma T. Steenkamp, University of Pretoria, South Africa
Quentin C. Santana, University of Pretoria, South Africa
Martin P.A. Coetzee, University of Pretoria, South Africa
Stefan Bam, University of Pretoria, South Africa
Irene Barnes, University of Pretoria, South Africa
Chrizelle W. Beukes, University of Pretoria, South Africa
Wai Yin Chan, University of Pretoria, South Africa
Lieschen de Vos, University of Pretoria, South Africa
Gerda Fourie, University of Pretoria, South Africa
Melanie Friend, University of Pretoria, South Africa
Thomas R. Gordon, University of California, United States
Darryl A. Herron, University of Pretoria, South Africa
Carson Holt, University of Utah, United States
Ian Korf, University of California, United States
Marija Kvas, University of Pretoria, South Africa
Simon H. Martin, University of Pretoria, South Africa
X. Osmond Mlonyeni, University of Pretoria, South Africa
Kershney Naidoo, University of Pretoria, South Africa
Mmatshepho M. Phasha, University of Pretoria, South Africa
Alisa Postma, University of Pretoria, South Africa
Oleg Reva, University of Pretoria, South Africa
Heidi Roos, University of Pretoria, South Africa
Melissa Simpson, University of Pretoria, South Africa
Stephanie Slinski, University of California, United States
Bernard Slippers, University of Pretoria, South Africa
Rene Sutherland, University of Pretoria, South Africa
Nicolaas A. van der Merwe, University of Pretoria, South Africa
Magriet A. van der Nest, University of Pretoria, South Africa
Stephanus N. Venter, University of Pretoria, South Africa
Pieter M. Wilken, University of Pretoria, South Africa
Mark Yandell, University of Utah, United States
Renate Zipfel, University of Pretoria, South Africa
Mike J. Wingfield, University of Pretoria, South Africa

Abstract

Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the ’tsunami‘ of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists including students in a significant genome project that is certain to provide a platform for growth in this important area of research in the future.

Keywords

genome; Fusarium circinatum; annotation; MAT genes; fusarin; mycotoxin

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25. Intra-Species Genomic Variation in the Pine Pathogen Fusarium circinatum
Mkhululi N. Maphosa, Emma T. Steenkamp, Aquillah M. Kanzi, Stephanie van Wyk, Lieschen De Vos, Quentin C. Santana, Tuan A. Duong, Brenda D. Wingfield
Journal of Fungi  vol: 8  issue: 7  first page: 657  year: 2022  
doi: 10.3390/jof8070657

26. Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex
Claudette Dewing, Magrieta A. Van der Nest, Quentin C. Santana, Robert H. Proctor, Brenda D. Wingfield, Emma T. Steenkamp, Lieschen De Vos
Pathogens  vol: 11  issue: 8  first page: 858  year: 2022  
doi: 10.3390/pathogens11080858

27. Genome-Wide Macrosynteny among Fusarium Species in the Gibberella fujikuroi Complex Revealed by Amplified Fragment Length Polymorphisms
Lieschen De Vos, Emma T. Steenkamp, Simon H. Martin, Quentin C. Santana, Gerda Fourie, Nicolaas A. van der Merwe, Michael J. Wingfield, Brenda D. Wingfield, Ines Teichert
PLoS ONE  vol: 9  issue: 12  first page: e114682  year: 2014  
doi: 10.1371/journal.pone.0114682

28. Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts
Erik A. Visser, Jill L. Wegrzyn, Emma T. Steenkamp, Alexander A. Myburg, Sanushka Naidoo
Microorganisms  vol: 7  issue: 9  first page: 315  year: 2019  
doi: 10.3390/microorganisms7090315

29. Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum
Lieschen De Vos, Magriet A. van der Nest, Quentin C. Santana, Stephanie van Wyk, Kyle S. Leeuwendaal, Brenda D. Wingfield, Emma T. Steenkamp
Pathogens  vol: 13  issue: 1  first page: 70  year: 2024  
doi: 10.3390/pathogens13010070

30. Zearalenone contamination in maize, its associated producing fungi, control strategies, and legislation in Sub‐Saharan Africa
Abdul Rashid Hudu, Francis Addy, Gustav Komla Mahunu, Abdul‐Halim Abubakari, Nelson Opoku
Food Science & Nutrition  vol: 12  issue: 7  first page: 4489  year: 2024  
doi: 10.1002/fsn3.4125

31. IMA genome - F14
Magriet A. van der Nest, Renato Chávez, Lieschen De Vos, Tuan A. Duong, Carlos Gil-Durán, Maria Alves Ferreira, Frances A. Lane, Gloria Levicán, Quentin C. Santana, Emma T. Steenkamp, Hiroyuki Suzuki, Mario Tello, Jostina R. Rakoma, Inmaculada Vaca, Natalia Valdés, P. Markus Wilken, Michael J. Wingfield, Brenda D. Wingfield
IMA Fungus  vol: 12  issue: 1  year: 2021  
doi: 10.1186/s43008-021-00055-1

32. Comparative Genomics of Fusarium circinatum Isolates Used to Screen Southern Pines for Pitch Canker Resistance
James C. Fulton, Pei-Ling Yu, Katherine E. Smith, Jose C. Huguet-Tapia, Owen Hudson, April Meeks, Tania Quesada, Kathleen McKeever, Jeremy T. Brawner
Molecular Plant-Microbe Interactions®  vol: 35  issue: 6  first page: 477  year: 2022  
doi: 10.1094/MPMI-10-21-0247-R

33. The Fusarium Circinatum Gene Fcrho1, Encoding a Putative Rho1 GTPase, Is Involved in Vegetative Growth but Dispensable for Pathogenic Development
E. Jordán Muñoz-Adalia, M. Carmen Cañizares, Mercedes Fernández, Julio J. Diez, M. Dolores García-Pedrajas
Forests  vol: 9  issue: 11  first page: 684  year: 2018  
doi: 10.3390/f9110684

34. Genetic Background of Variable Gibberellin Production in the Fusarium Fujikuroi Species Complex
WanXue Bao, Haruhisa Suga
Reviews in Agricultural Science  vol: 9  first page: 32  year: 2021  
doi: 10.7831/ras.9.0_32

35. FusariumPathogenomics
Li-Jun Ma, David M. Geiser, Robert H. Proctor, Alejandro P. Rooney, Kerry O'Donnell, Frances Trail, Donald M. Gardiner, John M. Manners, Kemal Kazan
Annual Review of Microbiology  vol: 67  issue: 1  first page: 399  year: 2013  
doi: 10.1146/annurev-micro-092412-155650