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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #394986
Research Project: Disease Management and Improved Detection Systems for Control of Pathogens of Vegetables and Strawberries

Location: Crop Improvement and Protection Research

Title: A reference genome sequence resource for the sugar beet root rot pathogen Aphanomyces cochlioides

Author
item BOTKIN, JACOB - University Of Minnesota
item CHANDA, ASHOK - University Of Minnesota
item Martin, Frank
item HIRSCH, CORY - University Of Minnesota

Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2022
Publication Date: 8/31/2022
Citation: Botkin, J.R., Chanda, A.K., Martin, F.N., Hirsch, C.D. 2022. A reference genome sequence resource for the sugar beet root rot pathogen Aphanomyces cochlioides. Molecular Plant-Microbe Interactions. 35(8):706-710. https://doi.org/10.1094/MPMI-11-21-0277-A.
DOI: https://doi.org/10.1094/MPMI-11-21-0277-A

Interpretive Summary: This manuscript describes an assembly of the genome of the oomycete pathogen Aphanomyces cochlioides responsible for causing sugar beet damping off and root rot. Having a genome assembly is useful for making comparisons with related plant pathogens and assist in the development of diagnostic assays.

Technical Abstract: Aphanomyces cochlioides, the causal agent of damping-off and root rot of sugar beet (Beta vulgaris L.), is a soil dwelling oomycete responsible for yield losses in all major sugar beet growing regions. Currently, genomic resources for A. cochlioides are limited. Here we report a de novo genome assembly using a combination of long-read MinION (Oxford Nanopore Technologies) and short-read Illumina sequence data for A. cochlioides isolate 103-1, from Breckenridge, MN. The assembled genome was 76.3 Mb, with a contig N50 of 2.6 Mb. The reference assembly was annotated and was composed of 32.1% repetitive elements and 20,274 gene models. This high-quality genome assembly of A. cochlioides will be a valuable resource for understanding genetic variation, virulence factors, and comparative genomics of this important sugar beet pathogen.