PRJNA686477
Reference quality resequencing of Parastagonospora nodorum SN15
A chromosome-scale genome assembly of Parastagonospora nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data and fungal specific gene prediction techniques were combined with manual curation, to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2,534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to apanel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction.Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mb length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions. Overall, we present an updated series of genomic resources for P. nodorum Sn15 - an important reference isolate and model necrotroph - with a comprehensive survey of its predicted pathogenicity content.