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United States Department of Agriculture

Agricultural Research Service

Research Project: HOST-PATHOGEN INTERACTIONS IN BARLEY AND WHEAT

Location: Cereal Crops Research

Title: Resequencing and comparative genomics of Stagonospora nodorum: Sectional gene absence and effector discovery

Authors
item Syme, Rob -
item Hane, James -
item Friesen, Timothy
item Oliver, Richard -

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 1, 2013
Publication Date: June 1, 2013
Repository URL: http://handle.nal.usda.gov/10113/57865
Citation: Syme, R.A., Hane, J.K., Friesen, T.L., Oliver, R.P. 2013. Resequencing and comparative genomics of Stagonospora nodorum: Sectional gene absence and effector discovery. Genes, Genomes, Genetics. 3:959-969.

Interpretive Summary: Stagonospora nodorum blotch is a destructive disease of wheat worldwide and the control of this disease has been difficult due in part to the lack of understanding of how Stagonospora nodorum is causing disease. The sequencing of a reference genome (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 ability to induce disease. Sn79 is avirulent on wheat and produces no apparent necrotrophic 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 were compared to SN15 and each of the genomes contains a large number of strain-specific genes. Large contiguous sections of the reference genome are absent in the two newly sequenced strains. Information about genes in the virulent but not in the avirulent strains is being used to generate necrotrophic effector candidate gene lists.

Technical Abstract: S. 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 which 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 to 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.

Last Modified: 10/25/2014
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