Resequencing and Comparative Genomics of Stagonospora nodorum: Sectional Gene Absence and Effector Discovery

Author:

Syme Robert Andrew1,Hane James K2,Friesen Timothy L3,Oliver Richard P11

Affiliation:

1. Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Department of Environment and Agriculture, Bentley WA 6845, Australia

2. Molecular Pathology and Plant Pathology Laboratory, Centre for Environment and Life Sciences, CSIRO, Floreat WA 6014, Australia

3. U.S. Department of Agriculture, Agricultural Research Service, Cereal Crops Research Unit, Fargo, North Dakota 58102-2765

Abstract

Abstract 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.

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology

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