First fungal genome sequence from Africa : a preliminary analysis
Wingfield, Brenda D.; Steenkamp, Emma Theodora; Santana, Quentin C.; Coetzee, Martin Petrus Albertus; Bam, Stefan; Barnes, Irene; Beukes, Chrizelle Winsie; Chan, Wai Yin; De Vos, Lieschen; Fourie, Gerda; Friend, Melanie; Gordon, Thomas R. (Tom); Herron, Darryl A.; Holt, Carson; Korf, Ian; Kvas, Marija; Martin, Simon H.; Mlonyeni, X.O.M. (Xolile Osmond Mnyamezeli); Naidoo, Kershney; Phasha, Mmatshepho Malekgale; Postma, Alisa; Reva, Oleg N.; Roos, Heidi; Simpson, M.C. (Melissa Claire); Slinski, Stephanie; Slippers, Bernard; Sutherland, Rene; Van der Merwe, Nicolaas Albertus (Albie); Van der Nest, Magrieta Aletta; Venter, S.N. (Stephanus Nicolaas); Wilken, Pieter Markus; Yandell, Mark; Zipfel, Renate; Wingfield, Michael J.
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.