GENOME ASSEMBLIES FOR 28 PHAEOSPHAERIACEAE ISOLATES FROM CANADA
- 1Canadian Grain Commission
Abstract
Glume blotch and Septoria Tritici Blotch (STB) are destructive crop diseases caused by fungal pathogens formerly classified under the genus Septoria. Recent taxonomical revisions have led to the reclassification and renaming of these fungi, some of which are now under the genus Parastagonospora, family Phaeosphaeriaceae, order Pleosporales, and class Dothideomycetes. In this study, we performed whole genome sequencing and assembly for 28 Phaeosphaeriaceae isolates from Canada. Sequencing was performed using a combination of Oxford Nanopore Technologies (ONT) long-read and Illumina short-read sequencing platforms. Most of the genomes were very complete, BUSCO >99%, with the genomes assemblies derived from ONT sequencing having very few contigs that likely encompass entire chromosomes or chromosome arms. To determine the relationship between these isolates and similar fungi that have been previously characterized, we performed whole genome alignments to 2,668 other Dothidiomycete genomes obtained from NCBI using NUCmer. Comparative genomic analysis revealed that 27 of the isolates clustered discretely with either Parastagonospora nodorum, or Parastagonospora pseudonodorum (Parastagonospora avenae f. sp. tritici), with one genome having no other similar genome in NCBI which we hypothesize to be the first genome assembly of Phaeosphaeria pontiformis. Both P. nodorum and P. pseudonodorum species were isolated from wheat and barley and only the latter was isolated from durum, while the P. pontiformis was isolated from wheat. In summary, we sequenced and assembled the genomes of 28 isolates of Phaeosphaeriaceae spp. from Canada and the genomes add to our foundational knowledge of these plant pathogens and efforts to better understand their diversity.
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BibTeX
@misc{bamforth2026genome,
title = {{GENOME ASSEMBLIES FOR 28 PHAEOSPHAERIACEAE ISOLATES FROM CANADA}},
author = {J. Bamforth and R. Gourlie and M. Abdel-Fattah and R. Aboukhaddour and S. Walkowiak},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.02.763635},
url = {https://www.biorxiv.org/content/10.64898/2026.11.02.763635v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - GENOME ASSEMBLIES FOR 28 PHAEOSPHAERIACEAE ISOLATES FROM CANADA
AU - J. Bamforth
AU - R. Gourlie
AU - M. Abdel-Fattah
AU - R. Aboukhaddour
AU - S. Walkowiak
PY - 2026
DA - 2026/11/02
PB - bioRxiv
DO - 10.64898/2026.11.02.763635
UR - https://www.biorxiv.org/content/10.64898/2026.11.02.763635v1
AB - Glume blotch and Septoria Tritici Blotch (STB) are destructive crop diseases caused by fungal pathogens formerly classified under the genus Septoria. Recent taxonomical revisions have led to the reclassification and renaming of these fungi, some of which are now under the genus Parastagonospora, family Phaeosphaeriaceae, order Pleosporales, and class Dothideomycetes. In this study, we performed whole genome sequencing and assembly for 28 Phaeosphaeriaceae isolates from Canada. Sequencing was performed using a combination of Oxford Nanopore Technologies (ONT) long-read and Illumina short-read sequencing platforms. Most of the genomes were very complete, BUSCO >99%, with the genomes assemblies derived from ONT sequencing having very few contigs that likely encompass entire chromosomes or chromosome arms. To determine the relationship between these isolates and similar fungi that have been previously characterized, we performed whole genome alignments to 2,668 other Dothidiomycete genomes obtained from NCBI using NUCmer. Comparative genomic analysis revealed that 27 of the isolates clustered discretely with either Parastagonospora nodorum, or Parastagonospora pseudonodorum (Parastagonospora avenae f. sp. tritici), with one genome having no other similar genome in NCBI which we hypothesize to be the first genome assembly of Phaeosphaeria pontiformis. Both P. nodorum and P. pseudonodorum species were isolated from wheat and barley and only the latter was isolated from durum, while the P. pontiformis was isolated from wheat. In summary, we sequenced and assembled the genomes of 28 isolates of Phaeosphaeriaceae spp. from Canada and the genomes add to our foundational knowledge of these plant pathogens and efforts to better understand their diversity.
ER -