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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #394988

Research Project: Disease Management and Improved Detection Systems for Control of Pathogens of Vegetables and Strawberries

Location: Crop Improvement and Protection Research

Title: The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes

Author
item FLETCHER, KYLE - University Of California
item Martin, Frank
item ISAKEIT, THOMAS - Texas A&M University
item CAVANAUGH, KERI - University Of California
item MAGILL, CLINT - Texas A&M University
item MICHELMORE, RICHARD - University Of California

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2022
Publication Date: 1/2/2023
Citation: Fletcher, K., Martin, F.N., Isakeit, T., Cavanaugh, K., Magill, C., Michelmore, R. 2023. The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes. G3. 13(3). Article jkac340. https://doi.org/10.1093/g3journal/jkac340.
DOI: https://doi.org/10.1093/g3journal/jkac340

Interpretive Summary: This manuscript describes an assembly of the genome of the oomycete pathogen Pseudoperonospora sorghi, the downy mildew pathogen of sorghum. Given the worldwide importance of this pathogen the reported results will provide background information that will be useful for better understanding the genetics of this pathogen. Given that Peronosclerospora species in general are important pathogens of grass hosts worldwide (in particular Peronosclerospora philippinensis, a pathogen of corn that is on the select agent list) this genomic resource is invaluable for molecular research on other species.

Technical Abstract: Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Biosurveillance of these pathogens is a high priority to prevent epidemics on maize in the US and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitochondrial genome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10x Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 319.6 Mb—larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.