Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics
Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published ge...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Journal Article |
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Public Library of Science
2016
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| Online Access: | http://hdl.handle.net/20.500.11937/7114 |
| _version_ | 1848745273198641152 |
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| author | Syme, Robert Tan, Kar-Chun Hane, James Dodhia, Kejal Stoll, T. Hastie, M. Furuki, Eiko Ellwood, Simon Williams, A. Tan, Y. Renwick, Alison Gorman, J. Oliver, Richard |
| author_facet | Syme, Robert Tan, Kar-Chun Hane, James Dodhia, Kejal Stoll, T. Hastie, M. Furuki, Eiko Ellwood, Simon Williams, A. Tan, Y. Renwick, Alison Gorman, J. Oliver, Richard |
| author_sort | Syme, Robert |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (<a href="https://github.com/robsyme/Parastagonospora_nodorum_SN15">https://github.com/robsyme/Parastagonospora_nodorum_SN15</a>). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models. |
| first_indexed | 2025-11-14T06:14:44Z |
| format | Journal Article |
| id | curtin-20.500.11937-7114 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T06:14:44Z |
| publishDate | 2016 |
| publisher | Public Library of Science |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-71142017-09-13T14:42:16Z Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics Syme, Robert Tan, Kar-Chun Hane, James Dodhia, Kejal Stoll, T. Hastie, M. Furuki, Eiko Ellwood, Simon Williams, A. Tan, Y. Renwick, Alison Gorman, J. Oliver, Richard Fungal genomics gene annotation Parastagonospora nodorum Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (<a href="https://github.com/robsyme/Parastagonospora_nodorum_SN15">https://github.com/robsyme/Parastagonospora_nodorum_SN15</a>). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models. 2016 Journal Article http://hdl.handle.net/20.500.11937/7114 10.1371/journal.pone.0147221 Public Library of Science fulltext |
| spellingShingle | Fungal genomics gene annotation Parastagonospora nodorum Syme, Robert Tan, Kar-Chun Hane, James Dodhia, Kejal Stoll, T. Hastie, M. Furuki, Eiko Ellwood, Simon Williams, A. Tan, Y. Renwick, Alison Gorman, J. Oliver, Richard Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics |
| title | Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics |
| title_full | Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics |
| title_fullStr | Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics |
| title_full_unstemmed | Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics |
| title_short | Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics |
| title_sort | comprehensive annotation of the parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics |
| topic | Fungal genomics gene annotation Parastagonospora nodorum |
| url | http://hdl.handle.net/20.500.11937/7114 |