First fungal genome sequence from Africa: A preliminary analysis

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


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.


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