Telomere-to-telomere genome assembly of the clubroot pathogen Plasmodiophora brassicae
Plasmodiophora brassicae is the causal agent of clubroot disease of cruciferous plants and one of the biggest threats to the rapeseed (Brassica napus) and brassica vegetable industry worldwide. The clubroot pathogen P. brassicae belongs to the class Phytomyxea in the eukaryotic supergroup Rhizaria (Bi et al., 2019; Neuhauser et al., 2014; Sierra et al., 2015). The Phytomyxea consists of obligate biotrophic parasites into the order Plasmodiophorids, brown algae and oomycetes (Phagomyxids), and the newly described Marinomyxa (Hittorf et al., 2020; Kolatkova et al., 2021; Neuhauser et al., 2014). P. brassicae remains impossible to grow in axenic culture due to intracellular growth in the host cells and obligate biotrophy, preventing the production of high-quality and contamination-free DNA for genome sequencing. The first genome of the pathogen (e3) was published in 2015 (Schwelm et al., 2015), which was relatively late compared to other plant-pathogenic organisms with similar agricultural and economic impacts. The draft genome was generated utilizing 454 sequencing and Illumina short-read sequencing technologies (Schwelm et al., 2015). However, the existing reference genome of the clubroot pathogen available in the NCBI database is not at the chromosome level, as it was sequenced with Illumina short-read approach. With the advent of third-generation sequencing technologies, it is now possible to achieve a high-quality telomere-to-telomere reference genome. Utilizing an improved protocol of high-quality DNA extraction, we sequenced the whole genome of Canadian pathotype Pb3A, using PacBio-HiFi and Oxford Nanopore Sequencing technologies, in addition to Illumina sequencing and achieved a complete telomere-to-telomere chromosome level genome of P. brassicae. The availability of this high-quality genome for the clubroot pathogen (Pb3A), and its identification as the reference genome, will greatly benefit future genome assemblies of P. brassicae isolates, population genomics studies, and comparative genomics analyses among Plasmodiophorids.