First fungal genome sequence from Africa: A preliminary analysis
South African Journal of Science
Field | Value | |
Title | First fungal genome sequence from Africa: A preliminary analysis | |
Creator | Wingfield, Brenda D. Steenkamp, Emma T. Santana, Quentin C. Coetzee, Martin P.A. Bam, Stefan Barnes, Irene Beukes, Chrizelle W. Chan, Wai Yin de Vos, Lieschen Fourie, Gerda Friend, Melanie Gordon, Thomas R. Herron, Darryl A. Holt, Carson Korf, Ian Kvas, Marija Martin, Simon H. Mlonyeni, X. Osmond Naidoo, Kershney Phasha, Mmatshepho M. Postma, Alisa Reva, Oleg Roos, Heidi Simpson, Melissa Slinski, Stephanie Slippers, Bernard Sutherland, Rene van der Merwe, Nicolaas A. van der Nest, Magriet A. Venter, Stephanus N. Wilken, Pieter M. Yandell, Mark Zipfel, Renate Wingfield, Mike J. | |
Description | 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. | |
Publisher | AOSIS | |
Date | 2012-01-25 | |
Identifier | 10.4102/sajs.v108i1/2.537 | |
Source | South African Journal of Science; Vol 108, No 1/2 (2012); 9 pages 1996-7489 0038-2353 | |
Language | eng | |
Relation |
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https://journals.sajs.aosis.co.za/index.php/sajs/article/view/537/1026
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https://journals.sajs.aosis.co.za/index.php/sajs/article/view/537/991
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https://journals.sajs.aosis.co.za/index.php/sajs/article/downloadSuppFile/537/3211
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