First fungal genome sequence from Africa: A preliminary analysis
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...
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Academy of Science of South Africa
2012-01-01
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doaj-1725f279a07c48c5b500a14388fdb73e2021-02-20T06:04:09ZengAcademy of Science of South AfricaSouth African Journal of Science1996-74892012-01-011081/2First fungal genome sequence from Africa: A preliminary analysisBrenda Wingfield0Emma Steenkamp1Quentin Santana2Martin Coetzee3Stefan Bam4Irene Barnes5Chrizelle Beukes6Wai Yin Chan7Lieschen de Vos8Gerda Fourie9Melanie Friend10Thomas Gordon11Darryl Herron12Carson Holt13Ian Korf14Marija Kvas15Simon Martin16X. Mlonyeni17Kershney Naidoo18Mmatshepho Phasha19Alisa Postma20Oleg Reva21Heidi Roos22Melissa Simpson23Stephanie Slinski24Bernard Slippers25Rene Sutherland26Nicolaas van der Merwe27Magriet van der Nest28Stephanus Venter29Pieter Wilken30Mark Yandell31Renate Zipfel32Mike Wingfield33University of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of CaliforniaUniversity of PretoriaUniversity of UtahUniversity of CaliforniaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of CaliforniaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of UtahUniversity of PretoriaUniversity of PretoriaSome 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.https://www.sajs.co.za/article/view/9718genomeFusarium circinatumannotationMAT genesfusarinmycotoxin |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Brenda Wingfield Emma Steenkamp Quentin Santana Martin Coetzee Stefan Bam Irene Barnes Chrizelle Beukes Wai Yin Chan Lieschen de Vos Gerda Fourie Melanie Friend Thomas Gordon Darryl Herron Carson Holt Ian Korf Marija Kvas Simon Martin X. Mlonyeni Kershney Naidoo Mmatshepho Phasha Alisa Postma Oleg Reva Heidi Roos Melissa Simpson Stephanie Slinski Bernard Slippers Rene Sutherland Nicolaas van der Merwe Magriet van der Nest Stephanus Venter Pieter Wilken Mark Yandell Renate Zipfel Mike Wingfield |
spellingShingle |
Brenda Wingfield Emma Steenkamp Quentin Santana Martin Coetzee Stefan Bam Irene Barnes Chrizelle Beukes Wai Yin Chan Lieschen de Vos Gerda Fourie Melanie Friend Thomas Gordon Darryl Herron Carson Holt Ian Korf Marija Kvas Simon Martin X. Mlonyeni Kershney Naidoo Mmatshepho Phasha Alisa Postma Oleg Reva Heidi Roos Melissa Simpson Stephanie Slinski Bernard Slippers Rene Sutherland Nicolaas van der Merwe Magriet van der Nest Stephanus Venter Pieter Wilken Mark Yandell Renate Zipfel Mike Wingfield First fungal genome sequence from Africa: A preliminary analysis South African Journal of Science genome Fusarium circinatum annotation MAT genes fusarin mycotoxin |
author_facet |
Brenda Wingfield Emma Steenkamp Quentin Santana Martin Coetzee Stefan Bam Irene Barnes Chrizelle Beukes Wai Yin Chan Lieschen de Vos Gerda Fourie Melanie Friend Thomas Gordon Darryl Herron Carson Holt Ian Korf Marija Kvas Simon Martin X. Mlonyeni Kershney Naidoo Mmatshepho Phasha Alisa Postma Oleg Reva Heidi Roos Melissa Simpson Stephanie Slinski Bernard Slippers Rene Sutherland Nicolaas van der Merwe Magriet van der Nest Stephanus Venter Pieter Wilken Mark Yandell Renate Zipfel Mike Wingfield |
author_sort |
Brenda Wingfield |
title |
First fungal genome sequence from Africa: A preliminary analysis |
title_short |
First fungal genome sequence from Africa: A preliminary analysis |
title_full |
First fungal genome sequence from Africa: A preliminary analysis |
title_fullStr |
First fungal genome sequence from Africa: A preliminary analysis |
title_full_unstemmed |
First fungal genome sequence from Africa: A preliminary analysis |
title_sort |
first fungal genome sequence from africa: a preliminary analysis |
publisher |
Academy of Science of South Africa |
series |
South African Journal of Science |
issn |
1996-7489 |
publishDate |
2012-01-01 |
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. |
topic |
genome Fusarium circinatum annotation MAT genes fusarin mycotoxin |
url |
https://www.sajs.co.za/article/view/9718 |
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