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...
Ausführliche Beschreibung
Autor*in: |
Brenda Wingfield [verfasserIn] Emma Steenkamp [verfasserIn] Quentin Santana [verfasserIn] Martin Coetzee [verfasserIn] Stefan Bam [verfasserIn] Irene Barnes [verfasserIn] Chrizelle Beukes [verfasserIn] Wai Yin Chan [verfasserIn] Lieschen de Vos [verfasserIn] Gerda Fourie [verfasserIn] Melanie Friend [verfasserIn] Thomas Gordon [verfasserIn] Darryl Herron [verfasserIn] Carson Holt [verfasserIn] Ian Korf [verfasserIn] Marija Kvas [verfasserIn] Simon Martin [verfasserIn] X. Mlonyeni [verfasserIn] Kershney Naidoo [verfasserIn] Mmatshepho Phasha [verfasserIn] Alisa Postma [verfasserIn] Oleg Reva [verfasserIn] Heidi Roos [verfasserIn] Melissa Simpson [verfasserIn] Stephanie Slinski [verfasserIn] Bernard Slippers [verfasserIn] Rene Sutherland [verfasserIn] Nicolaas van der Merwe [verfasserIn] Magriet van der Nest [verfasserIn] Stephanus Venter [verfasserIn] Pieter Wilken [verfasserIn] Mark Yandell [verfasserIn] Renate Zipfel [verfasserIn] Mike Wingfield [verfasserIn] |
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E-Artikel |
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Sprache: |
Englisch |
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2012 |
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In: South African Journal of Science - Academy of Science of South Africa, 2010, 108(2012), 1/2 |
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Übergeordnetes Werk: |
volume:108 ; year:2012 ; number:1/2 |
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DOAJ055072054 |
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(DE-627)DOAJ055072054 (DE-599)DOAJbeee7e4644984751b9dd3456eea10bfa DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Brenda Wingfield verfasserin aut First fungal genome sequence from Africa: A preliminary analysis 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. genome Fusarium circinatum annotation MAT genes fusarin mycotoxin Science Q Science (General) Social Sciences H Social sciences (General) Emma Steenkamp verfasserin aut Quentin Santana verfasserin aut Martin Coetzee verfasserin aut Stefan Bam verfasserin aut Irene Barnes verfasserin aut Chrizelle Beukes verfasserin aut Wai Yin Chan verfasserin aut Lieschen de Vos verfasserin aut Gerda Fourie verfasserin aut Melanie Friend verfasserin aut Thomas Gordon verfasserin aut Darryl Herron verfasserin aut Carson Holt verfasserin aut Ian Korf verfasserin aut Marija Kvas verfasserin aut Simon Martin verfasserin aut X. Mlonyeni verfasserin aut Kershney Naidoo verfasserin aut Mmatshepho Phasha verfasserin aut Alisa Postma verfasserin aut Oleg Reva verfasserin aut Heidi Roos verfasserin aut Melissa Simpson verfasserin aut Stephanie Slinski verfasserin aut Bernard Slippers verfasserin aut Rene Sutherland verfasserin aut Nicolaas van der Merwe verfasserin aut Magriet van der Nest verfasserin aut Stephanus Venter verfasserin aut Pieter Wilken verfasserin aut Mark Yandell verfasserin aut Renate Zipfel verfasserin aut Mike Wingfield verfasserin aut In South African Journal of Science Academy of Science of South Africa, 2010 108(2012), 1/2 (DE-627)593556860 (DE-600)2482725-3 19967489 nnns volume:108 year:2012 number:1/2 https://doaj.org/article/beee7e4644984751b9dd3456eea10bfa kostenfrei http://192.168.0.117/index.php/sajs/article/view/9780 kostenfrei https://doaj.org/toc/1996-7489 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 108 2012 1/2 |
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(DE-627)DOAJ055072054 (DE-599)DOAJbeee7e4644984751b9dd3456eea10bfa DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Brenda Wingfield verfasserin aut First fungal genome sequence from Africa: A preliminary analysis 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. genome Fusarium circinatum annotation MAT genes fusarin mycotoxin Science Q Science (General) Social Sciences H Social sciences (General) Emma Steenkamp verfasserin aut Quentin Santana verfasserin aut Martin Coetzee verfasserin aut Stefan Bam verfasserin aut Irene Barnes verfasserin aut Chrizelle Beukes verfasserin aut Wai Yin Chan verfasserin aut Lieschen de Vos verfasserin aut Gerda Fourie verfasserin aut Melanie Friend verfasserin aut Thomas Gordon verfasserin aut Darryl Herron verfasserin aut Carson Holt verfasserin aut Ian Korf verfasserin aut Marija Kvas verfasserin aut Simon Martin verfasserin aut X. Mlonyeni verfasserin aut Kershney Naidoo verfasserin aut Mmatshepho Phasha verfasserin aut Alisa Postma verfasserin aut Oleg Reva verfasserin aut Heidi Roos verfasserin aut Melissa Simpson verfasserin aut Stephanie Slinski verfasserin aut Bernard Slippers verfasserin aut Rene Sutherland verfasserin aut Nicolaas van der Merwe verfasserin aut Magriet van der Nest verfasserin aut Stephanus Venter verfasserin aut Pieter Wilken verfasserin aut Mark Yandell verfasserin aut Renate Zipfel verfasserin aut Mike Wingfield verfasserin aut In South African Journal of Science Academy of Science of South Africa, 2010 108(2012), 1/2 (DE-627)593556860 (DE-600)2482725-3 19967489 nnns volume:108 year:2012 number:1/2 https://doaj.org/article/beee7e4644984751b9dd3456eea10bfa kostenfrei http://192.168.0.117/index.php/sajs/article/view/9780 kostenfrei https://doaj.org/toc/1996-7489 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 108 2012 1/2 |
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(DE-627)DOAJ055072054 (DE-599)DOAJbeee7e4644984751b9dd3456eea10bfa DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Brenda Wingfield verfasserin aut First fungal genome sequence from Africa: A preliminary analysis 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. genome Fusarium circinatum annotation MAT genes fusarin mycotoxin Science Q Science (General) Social Sciences H Social sciences (General) Emma Steenkamp verfasserin aut Quentin Santana verfasserin aut Martin Coetzee verfasserin aut Stefan Bam verfasserin aut Irene Barnes verfasserin aut Chrizelle Beukes verfasserin aut Wai Yin Chan verfasserin aut Lieschen de Vos verfasserin aut Gerda Fourie verfasserin aut Melanie Friend verfasserin aut Thomas Gordon verfasserin aut Darryl Herron verfasserin aut Carson Holt verfasserin aut Ian Korf verfasserin aut Marija Kvas verfasserin aut Simon Martin verfasserin aut X. Mlonyeni verfasserin aut Kershney Naidoo verfasserin aut Mmatshepho Phasha verfasserin aut Alisa Postma verfasserin aut Oleg Reva verfasserin aut Heidi Roos verfasserin aut Melissa Simpson verfasserin aut Stephanie Slinski verfasserin aut Bernard Slippers verfasserin aut Rene Sutherland verfasserin aut Nicolaas van der Merwe verfasserin aut Magriet van der Nest verfasserin aut Stephanus Venter verfasserin aut Pieter Wilken verfasserin aut Mark Yandell verfasserin aut Renate Zipfel verfasserin aut Mike Wingfield verfasserin aut In South African Journal of Science Academy of Science of South Africa, 2010 108(2012), 1/2 (DE-627)593556860 (DE-600)2482725-3 19967489 nnns volume:108 year:2012 number:1/2 https://doaj.org/article/beee7e4644984751b9dd3456eea10bfa kostenfrei http://192.168.0.117/index.php/sajs/article/view/9780 kostenfrei https://doaj.org/toc/1996-7489 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 108 2012 1/2 |
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(DE-627)DOAJ055072054 (DE-599)DOAJbeee7e4644984751b9dd3456eea10bfa DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Brenda Wingfield verfasserin aut First fungal genome sequence from Africa: A preliminary analysis 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. genome Fusarium circinatum annotation MAT genes fusarin mycotoxin Science Q Science (General) Social Sciences H Social sciences (General) Emma Steenkamp verfasserin aut Quentin Santana verfasserin aut Martin Coetzee verfasserin aut Stefan Bam verfasserin aut Irene Barnes verfasserin aut Chrizelle Beukes verfasserin aut Wai Yin Chan verfasserin aut Lieschen de Vos verfasserin aut Gerda Fourie verfasserin aut Melanie Friend verfasserin aut Thomas Gordon verfasserin aut Darryl Herron verfasserin aut Carson Holt verfasserin aut Ian Korf verfasserin aut Marija Kvas verfasserin aut Simon Martin verfasserin aut X. Mlonyeni verfasserin aut Kershney Naidoo verfasserin aut Mmatshepho Phasha verfasserin aut Alisa Postma verfasserin aut Oleg Reva verfasserin aut Heidi Roos verfasserin aut Melissa Simpson verfasserin aut Stephanie Slinski verfasserin aut Bernard Slippers verfasserin aut Rene Sutherland verfasserin aut Nicolaas van der Merwe verfasserin aut Magriet van der Nest verfasserin aut Stephanus Venter verfasserin aut Pieter Wilken verfasserin aut Mark Yandell verfasserin aut Renate Zipfel verfasserin aut Mike Wingfield verfasserin aut In South African Journal of Science Academy of Science of South Africa, 2010 108(2012), 1/2 (DE-627)593556860 (DE-600)2482725-3 19967489 nnns volume:108 year:2012 number:1/2 https://doaj.org/article/beee7e4644984751b9dd3456eea10bfa kostenfrei http://192.168.0.117/index.php/sajs/article/view/9780 kostenfrei https://doaj.org/toc/1996-7489 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 108 2012 1/2 |
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(DE-627)DOAJ055072054 (DE-599)DOAJbeee7e4644984751b9dd3456eea10bfa DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Brenda Wingfield verfasserin aut First fungal genome sequence from Africa: A preliminary analysis 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. genome Fusarium circinatum annotation MAT genes fusarin mycotoxin Science Q Science (General) Social Sciences H Social sciences (General) Emma Steenkamp verfasserin aut Quentin Santana verfasserin aut Martin Coetzee verfasserin aut Stefan Bam verfasserin aut Irene Barnes verfasserin aut Chrizelle Beukes verfasserin aut Wai Yin Chan verfasserin aut Lieschen de Vos verfasserin aut Gerda Fourie verfasserin aut Melanie Friend verfasserin aut Thomas Gordon verfasserin aut Darryl Herron verfasserin aut Carson Holt verfasserin aut Ian Korf verfasserin aut Marija Kvas verfasserin aut Simon Martin verfasserin aut X. Mlonyeni verfasserin aut Kershney Naidoo verfasserin aut Mmatshepho Phasha verfasserin aut Alisa Postma verfasserin aut Oleg Reva verfasserin aut Heidi Roos verfasserin aut Melissa Simpson verfasserin aut Stephanie Slinski verfasserin aut Bernard Slippers verfasserin aut Rene Sutherland verfasserin aut Nicolaas van der Merwe verfasserin aut Magriet van der Nest verfasserin aut Stephanus Venter verfasserin aut Pieter Wilken verfasserin aut Mark Yandell verfasserin aut Renate Zipfel verfasserin aut Mike Wingfield verfasserin aut In South African Journal of Science Academy of Science of South Africa, 2010 108(2012), 1/2 (DE-627)593556860 (DE-600)2482725-3 19967489 nnns volume:108 year:2012 number:1/2 https://doaj.org/article/beee7e4644984751b9dd3456eea10bfa kostenfrei http://192.168.0.117/index.php/sajs/article/view/9780 kostenfrei https://doaj.org/toc/1996-7489 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR 108 2012 1/2 |
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Brenda Wingfield @@aut@@ Emma Steenkamp @@aut@@ Quentin Santana @@aut@@ Martin Coetzee @@aut@@ Stefan Bam @@aut@@ Irene Barnes @@aut@@ Chrizelle Beukes @@aut@@ Wai Yin Chan @@aut@@ Lieschen de Vos @@aut@@ Gerda Fourie @@aut@@ Melanie Friend @@aut@@ Thomas Gordon @@aut@@ Darryl Herron @@aut@@ Carson Holt @@aut@@ Ian Korf @@aut@@ Marija Kvas @@aut@@ Simon Martin @@aut@@ X. Mlonyeni @@aut@@ Kershney Naidoo @@aut@@ Mmatshepho Phasha @@aut@@ Alisa Postma @@aut@@ Oleg Reva @@aut@@ Heidi Roos @@aut@@ Melissa Simpson @@aut@@ Stephanie Slinski @@aut@@ Bernard Slippers @@aut@@ Rene Sutherland @@aut@@ Nicolaas van der Merwe @@aut@@ Magriet van der Nest @@aut@@ Stephanus Venter @@aut@@ Pieter Wilken @@aut@@ Mark Yandell @@aut@@ Renate Zipfel @@aut@@ Mike Wingfield @@aut@@ |
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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. |
abstractGer |
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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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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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. 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