Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery
Stagonospora nodorum is an important wheat (Triticum aestivum) pathogen in many parts of the world, causing major yield losses. It was the first species in the large fungal Dothideomycete class to be genome sequenced. The reference genome sequence (SN15) has been instrumental in the discovery of gen...
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| Format: | Journal Article |
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Genetics Society of America
2013
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| Online Access: | http://hdl.handle.net/20.500.11937/14733 |
| _version_ | 1848748702194204672 |
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| author | Syme, Robert Hane, James Friesen, T. Oliver, Richard |
| author_facet | Syme, Robert Hane, James Friesen, T. Oliver, Richard |
| author_sort | Syme, Robert |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Stagonospora nodorum is an important wheat (Triticum aestivum) pathogen in many parts of the world, causing major yield losses. It was the first species in the large fungal Dothideomycete class to be genome sequenced. The reference genome sequence (SN15) has been instrumental in the discovery of genes encoding necrotrophic effectors that induce disease symptoms in specific host genotypes. Here we present the genome sequence of two further S. nodorum strains (Sn4 and Sn79) that differ in their effector repertoire from the reference. Sn79 is avirulent on wheat and produces no apparent effectors when infiltrated onto many cultivars and mapping population parents. Sn4 is pathogenic on wheat and has virulences not found in SN15. The new strains, sequenced with short-read Illumina chemistry, are compared with SN15 by a combination of mapping and de novo assembly approaches.Each of the genomes contains a large number of strain-specific genes, many of which have no meaningful similarity to any known gene. Large contiguous sections of the reference genome are absent in the two newly sequenced strains. We refer to these differences as “sectional gene absences.” The presence of genes in pathogenic strains and absence in Sn79 is added to computationally predicted properties of known proteins to produce a list of likely effector candidates. Transposon insertion was observed in the mitochondrial genomes of virulent strains where the avirulent strain retained the likely ancestral sequence. The study suggests that short-read enabled comparative genomics is an effective way to both identify new S. nodorum effector candidates and to illuminate evolutionary processes in this species. |
| first_indexed | 2025-11-14T07:09:14Z |
| format | Journal Article |
| id | curtin-20.500.11937-14733 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T07:09:14Z |
| publishDate | 2013 |
| publisher | Genetics Society of America |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-147332018-07-11T03:12:50Z Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery Syme, Robert Hane, James Friesen, T. Oliver, Richard Phytopathogen Fungal comparative genomics Fungal effectors Stagonospora nodorum is an important wheat (Triticum aestivum) pathogen in many parts of the world, causing major yield losses. It was the first species in the large fungal Dothideomycete class to be genome sequenced. The reference genome sequence (SN15) has been instrumental in the discovery of genes encoding necrotrophic effectors that induce disease symptoms in specific host genotypes. Here we present the genome sequence of two further S. nodorum strains (Sn4 and Sn79) that differ in their effector repertoire from the reference. Sn79 is avirulent on wheat and produces no apparent effectors when infiltrated onto many cultivars and mapping population parents. Sn4 is pathogenic on wheat and has virulences not found in SN15. The new strains, sequenced with short-read Illumina chemistry, are compared with SN15 by a combination of mapping and de novo assembly approaches.Each of the genomes contains a large number of strain-specific genes, many of which have no meaningful similarity to any known gene. Large contiguous sections of the reference genome are absent in the two newly sequenced strains. We refer to these differences as “sectional gene absences.” The presence of genes in pathogenic strains and absence in Sn79 is added to computationally predicted properties of known proteins to produce a list of likely effector candidates. Transposon insertion was observed in the mitochondrial genomes of virulent strains where the avirulent strain retained the likely ancestral sequence. The study suggests that short-read enabled comparative genomics is an effective way to both identify new S. nodorum effector candidates and to illuminate evolutionary processes in this species. 2013 Journal Article http://hdl.handle.net/20.500.11937/14733 10.1534/g3.112.004994 Genetics Society of America fulltext |
| spellingShingle | Phytopathogen Fungal comparative genomics Fungal effectors Syme, Robert Hane, James Friesen, T. Oliver, Richard Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery |
| title | Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery |
| title_full | Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery |
| title_fullStr | Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery |
| title_full_unstemmed | Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery |
| title_short | Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery |
| title_sort | resequencing and comparative genomics of stagonospora nodorum: sectional gene absence and effector discovery |
| topic | Phytopathogen Fungal comparative genomics Fungal effectors |
| url | http://hdl.handle.net/20.500.11937/14733 |