Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

Abstract

Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (https://github.com/robsyme/Parastagonospora_nodorum_SN15). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models.

The global regulator of pathogenesis PnCon7 positively regulates Tox3 effector gene expression through direct interaction in the wheat pathogen Parastagonospora nodorum

“…Previous studies on Con7 have reported the gene to have different splicing variants (Odenbach et al ., ; Ruiz‐Roldán et al ., ). By analysing previously published RNA‐seq data from P. nodorum (Syme et al ., ), four alternative splicing variants of PnCon7 were identified. The 1553bp PnCon7 pre‐mRNA was processed to 4 variants, which differ only at the boxed 5′ regions (alternative splicing region) (Fig.…”

“…An analysis of previously published RNAseq data revealed four alternative splicing variants of PnCon7 (Syme et al ., ). These analyses were subsequently verified through experimental approaches as described above.…”

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

“…In contrast, broad host‐range necrotrophic fungal pathogens such as S. sclerotiorum and B. cinerea exhibit relatively repeat‐poor genomes (Derbyshire et al , ; Van Kan et al , ). Nevertheless, effector genes may also be associated with repeat sequences in necrotrophic fungi and fungi with a broad host range (Dallery et al , ; Laurent et al , ; Syme et al , ; Wang et al , ). Secretome analyses highlighted a number of candidate effector‐like proteins in the genome of S. sclerotiorum (Badet et al , ; Derbyshire et al , ; Guyon et al , ; Heard et al , ).…”

The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana

“…To examine the homology on the ToxA ‐containing scaffolds alone, an initial Mauve alignment was conducted with the full‐length scaffold from P. tritici‐repentis (http://fungi.ensembl.org/Pyrenophora_triticirepentis/Info/Index) and P. nodorum (http://fungi.ensembl.org/Pyrenophora_triticirepentis/Info/Index) (Manning et al ., ; Syme et al ., ) and the de novo scaffold from B. sorokiniana . The Mauve alignment was conducted with the setting to automatically calculate the seed weight and the minimum Locally Collinear Block (LCB) score.…”