Reference quality genome assemblies of three Parastagonospora nodorum isolates differing in virulence on wheat

Authors: RICHARDS, JONATHAN - North Dakota State University; WYATT, NATHAN - North Dakota State University; LIU, ZHAOHUI - North Dakota State University; Faris, Justin; Friesen, Timothy

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/8/2017
Publication Date: 2/1/2018
Citation: Richards, J.K., Wyatt, N.A., Liu, Z., Faris, J.D., Friesen, T.L. 2018. Reference quality genome assemblies of three Parastagonospora nodorum isolates differing in virulence on wheat. G3, Genes/Genomes/Genetics. 8:393-399. https://doi.org/10.1534/g3.117.300462.
DOI: https://doi.org/10.1534/g3.117.300462

Interpretive Summary: Septoria nodorum blotch (SNB) of wheat is caused by the fungal pathogen Parastagonospora nodorum, and results in annual yield losses of 5 to 20%. Although several studies have reported on the genetics of resistance in wheat, breeders have had difficulty developing wheat with resistance due to the lack of understanding of the quantitative nature of this disease. P. nodorum is somewhat unique in that it uses secreted proteins called necrotrophic effectors to induce the host (wheat) to kill itself and then feeds on the nutrients from the dying cells. A single P. nodorum reference quality genome sequence is publicly available for an isolate collected in Western Australia. Because different isolates of P. nodorum collected from around the world produce different necrotrophic effectors, it is critical that we have access to multiple genome sequences to allow for comparative studies in this pathogen, especially for those collected in the wheat growing regions of the United States. Therefore, we determined the genome sequences for three P. nodorum isolates collected in North Dakota, including a virulent isolate collected several decades ago, a virulent isolate collected recently, and an isolate collected from wild grasses that is avirulent on all local wheat lines tested. Making these sequences publicly available will provide a foundation for advancing our knowledge of this important wheat disease.

Technical Abstract: Parastagonospora nodorum, the causal agent of Septoria nodorum blotch of wheat, has emerged as a model necrotrophic fungal organism for the study of host-microbe interactions. To date, three necrotrophic effectors have been identified and characterized from this pathogen, including SnToxA, SnTox1, and SnTox3. Necrotrophic effector identification was greatly aided by the development of a draft genome of Australian isolate SN15 via Sanger sequencing, yet remained largely fragmented. This research presents the development of near-finished genomes of P. nodorum isolates Sn4, Sn2000, and Sn79-1087 using long-read sequencing technology. RNAseq analysis of isolate Sn4 consisting of eight time-points covering various developmental and infection stages mediated the annotation of 13,379 genes. Analysis of these genomes revealed large-scale polymorphism between the three isolates, including the complete absence of contig 23 from isolate Sn79-1087 and a region of genome expansion on contig 10 in isolates Sn4 and Sn2000. Additionally, these genomes exhibit the hallmark characteristics of a ‘two-speed’ genome, being partitioned into two distinct GC-equilibrated and AT-rich compartments. Interestingly, isolate Sn79-1087 contains a lower proportion of AT-rich segments, indicating a potential lack of evolutionary hot spots. These newly sequenced genomes, consisting of telomere to telomere assemblies of nearly all 23 P. nodorum chromosomes provides a robust foundation for the further examination of effector biology and genome evolution.