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

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.

Sensitivity to three Parastagonospora nodorum necrotrophic effectors in current Australian wheat cultivars and the presence of further fungal effectors

“…This is consistent with studies in the US and Australia showing that many further effectors remain to be discovered (Abeysekara et al 2012;Crook et al 2012;Francki et al 2011;Friesen et al 2012;Oliver et al 2012;Syme et al 2013). In this study, we show that crude culture filtrates of a strain lacking expression of ToxA, SnTox1 and SnTox3 contain effector activity that induced reactions in 23 of the tested cultivars ( Table 2).…”

Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

“…To this end, several general criteria based on existing knowledge about protein effectors from other fungal pathogens were established that ought to be fulfilled by candidate effector proteins ( cf. [116, 117]). Effectors are secreted, i.e.…”

Understanding the structure and variation within the genome of the pathogenic ascomycete fungus Leptosphaeria maculans

“…This suggests that this region is undergoing selective pressure which is significantly higher than other areas of the genome, particularly considering that the variations are not merely SNPs but larger variations of several hundred bases. A study conducted in Parastagonospora nodurum found a similar pattern, which was termed sectional gene absence (Syme et al, 2013).…”

“…It appears that both LmUVI-1h and LmHDX are single-copy genes in L. maculans, which could have a deleterious effect on growth and infection success if absent. Interestingly, a cluster of genes, including a polyketide synthase, was also found to be lost in a comparison of isolates in Parastagonospora nodurum (Syme et al, 2013).…”