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A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres

Simon R Ellwood1*, Zhaohui Liu2, Rob A Syme1, Zhibing Lai2, James K Hane3, Felicity Keiper4, Caroline S Moffat5, Richard P Oliver1 and Timothy L Friesen26

Author Affiliations

1 Department of Environment and Agriculture, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia

2 Department of Plant Pathology, North Dakota State University, Fargo, North Dakota 58105, USA

3 CSIRO Plant Industry, Centre for Environment and Life Sciences, Private Bag 5, Wembley, Western Australia 6913, Australia

4 South Australian Research and Development Institute, Waite Institute, Adelaide, South Australia 5064, Australia

5 Division of Health Sciences, Murdoch University, Murdoch Drive, Perth, Western Australia 6150, Australia

6 USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, 1307 18th Street North, Fargo, North Dakota 58105, USA

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Genome Biology 2010, 11:R109  doi:10.1186/gb-2010-11-11-r109

Published: 10 November 2010

Abstract

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 simple sequence repeat 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.