Rapid genomics approaches for downy mildews on high-value crops

A novel isothermal LAMP assay has been designed for detecting P. matthiolae on column stocks based on newly sequenced ITS regions. This has been compared to closely related downy mildew and related species in an effort to design a highly specific diagnostic and will now be tested against a panel of related organisms to ensure efficacy, in conjunction with new LAMP assays for P. effusa and P. farinosa. New isothermal diagnostics will provide growers and seed producers with enhanced tools for limiting the impact of disease in production environments.

Draft long-read assemblies have been generated for two key downy mildew pathogens on brassica and sweet basil hosts; genome sequencing of spinach and sugarbeet downy mildews is currently being finalised. Additional Illumina short reads shall be utilised for polishing the respective genomes and generating hybrid assemblies. The de novo sequencing of P. matthiolae has enabled us to identify high-levels of homology with H. arabidopsidis, positioning the pathogen alongside the other Brassiciolous downy mildews, and providing essential resources for conducting comparative genomics studies in closely- related downy mildew

This work was funded by the Biotechnology and Biological Sciences Research Council, a part of UK Research and Innovation, through a joint initiative with the Agriculture and Horticulture Development Board “AHDB/BBSRC Pilot Initiative: Rapid response to high priority pests and diseases in UK Horticulture”

The aim of the project was to generate de novo hybrid genome assemblies to provide new, novel genomics resources for a range of downy mildew species on high value crops.  Subsequently we proposed to conduct a preliminary phylogenetic investigation to establish relatedness between the four downy mildew (DM) species, design new isothermal amplification (LAMP) assays to provide diagnostic support for growers, and finally to ensure the new sequence data was made available through public repositories (Genbank).

The work program was organised to address the following objectives:

1. Obtain pure cultures of target DMs and extract DNA for sequencing
2. Produce de novo draft genome assemblies of four target DM species
3. Conduct comparative genomics and phylogenetic analyses to compare gene content, genome structure/organization
4. Design three new isothermal assays for detecting target species
5. Sequence data and assay sequences deposited in public repository so the information can be accessed and utilized effectively