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United States Department of Agriculture

Agricultural Research Service

Research Project: CHARACTERIZATION OF HOST-PATHOGEN INTERACTIONS IN BARLEY AND WHEAT

Location: Cereal Crops Research

Title: A first genome sequence survey of the barley fungal pathogen Pyrenophora teres f. teres

Authors
item Ellwood, Simon -
item Liu, Zhaohui -
item Syme, Rob -
item Lai, Zhibing -
item Hane, James -
item Keiper, Felicity -
item Moffat, Caroline -
item Oliver, Richard -
item Friesen, Timothy

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 15, 2010
Publication Date: November 11, 2010
Citation: Ellwood, S.R., Liu, Z., Syme, R., Lai, Z., Hane, J., Keiper, F., Moffat, C.S., Oliver, R.P., Friesen, T.L. 2010. A first genome sequence survey of the barley fungal pathogen Pyrenophora teres f. teres. Genome Biology. 11:R109.

Interpretive Summary: Net form net blotch is caused by the fungal pathogen Pyrenophora teres f. teres. Here we report the first genome assembly for this species based on short sequencing reads of isolate 0-1. The total assembly was 41.95 Mbp and contains 11,799 gene models. Complex gene rich regions assembled effectively however, repetitive regions did not assemble as efficiently. Cytological karyotyping confirmed the presence of at least nine chromosomes. This study demonstrates that paired-end short read sequencing can successfully capture coding regions of a 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.

Technical Abstract: 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. 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. 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.

Last Modified: 8/1/2014
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