A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres
Background: Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the cause of one of barley’s most important diseases, net form of net blotch. Here we report the first genome assembly for this species based solely on short Solexa sequencing reads of isolate 0-1. The assembly was validate...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
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BioMed Central
2010
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| Online Access: | http://hdl.handle.net/20.500.11937/12256 |
| _version_ | 1848748027163967488 |
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| author | Ellwood, Simon Liu, Zhaohui Syme, Robert Lai, Zhibing Hane, James Keiper, Felicity Moffat, Caroline Oliver, Richard Friesen, Timonthy |
| author_facet | Ellwood, Simon Liu, Zhaohui Syme, Robert Lai, Zhibing Hane, James Keiper, Felicity Moffat, Caroline Oliver, Richard Friesen, Timonthy |
| author_sort | Ellwood, Simon |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Background: Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the cause of one of barley’s most important diseases, net form of net blotch. Here we report the first genome assembly for this species based solely on short Solexa sequencing reads of isolate 0-1. The assembly was validated by comparison to BAC sequences, ESTs, orthologous genes and by PCR, and complemented by cytogenetic karyotyping and the first genome-wide genetic map for P. teres f. teres. Results: The total assembly was 41.95 Mbp and contains 11,799 gene models of 50 amino acids or more. Comparison against two sequenced BACs showed that complex regions with a high GC content assembled effectively. Electrophoretic karyotyping showed distinct chromosomal polymorphisms between isolates 0-1 and 15A, and cytological karyotyping confirmed the presence of at least nine chromosomes. The genetic map spans 2477.7 cM and is composed of 243 markers in 25 linkage groups, and incorporates SSR markers developed from the assembly. Among predicted genes, non-ribosomal peptide synthetases and efflux pumps in particular appear to have undergone a P. teres f. teres-specific expansion of non-orthologous gene families. Conclusions: This study demonstrates that paired-end Solexa sequencing can successfully capture coding regions of a filamentous fungal genome. The assembly contains a plethora of predicted genes that have been implicated in a necrotrophic lifestyle and pathogenicity and presents a significant resource for examining the bases for P. teres f. teres pathogenicity. |
| first_indexed | 2025-11-14T06:58:30Z |
| format | Journal Article |
| id | curtin-20.500.11937-12256 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T06:58:30Z |
| publishDate | 2010 |
| publisher | BioMed Central |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-122562017-09-13T14:59:18Z A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Ellwood, Simon Liu, Zhaohui Syme, Robert Lai, Zhibing Hane, James Keiper, Felicity Moffat, Caroline Oliver, Richard Friesen, Timonthy Background: Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the cause of one of barley’s most important diseases, net form of net blotch. Here we report the first genome assembly for this species based solely on short Solexa sequencing reads of isolate 0-1. The assembly was validated by comparison to BAC sequences, ESTs, orthologous genes and by PCR, and complemented by cytogenetic karyotyping and the first genome-wide genetic map for P. teres f. teres. Results: The total assembly was 41.95 Mbp and contains 11,799 gene models of 50 amino acids or more. Comparison against two sequenced BACs showed that complex regions with a high GC content assembled effectively. Electrophoretic karyotyping showed distinct chromosomal polymorphisms between isolates 0-1 and 15A, and cytological karyotyping confirmed the presence of at least nine chromosomes. The genetic map spans 2477.7 cM and is composed of 243 markers in 25 linkage groups, and incorporates SSR markers developed from the assembly. Among predicted genes, non-ribosomal peptide synthetases and efflux pumps in particular appear to have undergone a P. teres f. teres-specific expansion of non-orthologous gene families. Conclusions: This study demonstrates that paired-end Solexa sequencing can successfully capture coding regions of a filamentous fungal genome. The assembly contains a plethora of predicted genes that have been implicated in a necrotrophic lifestyle and pathogenicity and presents a significant resource for examining the bases for P. teres f. teres pathogenicity. 2010 Journal Article http://hdl.handle.net/20.500.11937/12256 10.1186/gb-2010-11-11-r109 BioMed Central fulltext |
| spellingShingle | Ellwood, Simon Liu, Zhaohui Syme, Robert Lai, Zhibing Hane, James Keiper, Felicity Moffat, Caroline Oliver, Richard Friesen, Timonthy A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres |
| title | A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres |
| title_full | A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres |
| title_fullStr | A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres |
| title_full_unstemmed | A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres |
| title_short | A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres |
| title_sort | first genome assembly of the barley fungal pathogen pyrenophora teres f. teres |
| url | http://hdl.handle.net/20.500.11937/12256 |