|ZACCARON, ALEX - University Of California, Davis|
|Mahaffee, Walter - Walt|
|STERGIOPOULOS, IOANNIS - University Of California, Davis|
Submitted to: mBio
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2023
Publication Date: 6/25/2023
Citation: Zaccaron, A.Z., Neill, T.M., Corcoran, J., Mahaffee, W.F., Stergiopoulos, I. 2023. A chromosome-scale genome assembly of the grape powdery mildew pathogen Erysiphe necator reveals its genomic architecture and previously unknown features of its biology. mBio. Article e00645-23. https://doi.org/10.1128/mbio.00645-23.
Interpretive Summary: The complete genome of Erysiphe necator isolate EnFRAME01 was sequenced and assembled to 98% completion (34 organized into 11 chromosomes). The genome consists of 62.7% repeats and transposable elements that indicate a highly flexible genetic organization that could affect function and gene expression. There were also a large number of duplicated genes that indicate adaptive variation could play a role in response to environmental stress (e.g. development of fungicide resistance). This resource will now facilitate genetic investigations into understanding the development of fungicide resistance and potential novel bio-synthetic pathways to target with new fungicides or emerging technology such as RNA silencing.
Technical Abstract: Erysiphe necator is an obligate fungal pathogen that causes grape powdery mildew (GPM), globally the most important disease on grapevines. Previous attempts to obtain a quality genome assembly for this pathogen were hindered by its high content in repetitive DNA. Here, we combined chromatin conformation capture (Hi-C) with long-read PacBio sequencing to obtain a chromosome-scale assembly and a high-quality annotation for E. necator isolate EnFRAME01. The resulting 81.1 Mb genome assembly is 98% complete and consists of 34 scaffolds assembled into 11 complete chromosomes. All chromosomes contain large centromeric-like regions and lack synteny to the 11 chromosomes of the cereal PM pathogen Blumeria graminis. Further analysis of their composition showed that repeats and transposable elements (TEs) occupy 62.7% of their content. TEs were almost evenly interspersed outside centromeric and telomeric regions, and massively overlapped with regions of annotated genes, suggesting that they could have a significant functional impact. Abundant gene duplicates were observed too, particularly in genes encoding candidate secreted effector proteins (CSEPs). Moreover, younger in age gene duplicates exhibited more relaxed selection pressure and were more likely to be located physically close in the genome than older duplicates. A total of 122 genes with copy number variations among six isolates of E. necator were also identified and were enriched in genes that were duplicated in EnFRAME01, indicating they may reflect an adaptive variation. Taken together, our study illuminates higher-order genomic architectural features of E. necator and provides a valuable resource for studying genomic structural variations in this plant pathogen.