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


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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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