Chromosome level assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae

We generate a chromosome-scale assembly for each of the two nuclear genomes of the oat crown rust pathogen Puccinia coronata f. sp. avenae (Pca). To create a complementary resource to the two previous Pca references that would allow the discovery of rust effectors and further our understanding of virulence evolution, a high-quality genome reference of an isolate of the historic race 203 \nLineage: High molecular weight DNA was extracted from the rust isolate Pca203 for library construction using the PacBio SMRTbell 1.0 kit and sequencing using five PacBio Sequel System SMRT cells with v3 chemistry. DNA was also extracted of isolate Pca203 spores using the OmniprepTM DNA isolation kit from G-Biosciences for library preparation with the Illumina TruSeq Nano DNA protocol and Illumina NovaSeq sequencing in the S2 flow cell to produce 150 bp paired-end reads. DNA-crosslinking and Hi-C analysis was completed by Phase Genomics (Seattle, WA, U.S.A) for Hi-C library preparation with the Proximo Fungal 4.0 protocol and libraries were sequenced to 100 million 150 bp paired-end reads at Genewiz (South Plainfield, NJ, U.S.A.). RNA was extracted from infected oat cv. Marvelous at 2 and 5 days post-inoculation (dpi) for library preparation with the Illumina TruSeq Stranded mRNA protocol and sequencing using Illumina NextSeq in mid-output mode, producing 75 bp paired-end reads and assist with gene annotation protocols. An initial genome assembly was constructed from 2,260,466 PacBio subreads using Canu version 2.1 (Koren et al. 2017). For polishing with the PacBio read data, half of the subreads were mapped back to the assembly using PacBio software pbmm2 version 1.4.0 (https://github.com/PacificBiosciences/pbmm2/releases/tag/v1.4.0) and a new consensus generated with PacBio software GenomicConsensus version 2.3.3 (https://github.com/PacificBiosciences/GenomicConsensus/releases/tag/2.3.3). This process was repeated using the new consensus as the reference. Next, the updated consensus was polished twice in Pilon version 1.22 using Illumina short reads trimmed with trimmomatic version 0.33 (Bolger et al. 2014; Walker et al. 2014). Assembly statistics were calculated using Quast (Gurevich et al. 2013).  The NuclearPhaser pipeline was used to correct phase swaps and assign haplotypes as described by Duan et al. (2021), except that two rounds of phase swap correction instead of one round were conducted. \n\nFor scaffolding, the Hi-C reads were first mapped to each haplotype using BWA-MEM 0.7.17 (Li and Duribn, 2009). Alignments were then processed with the Arima Genomics pipeline (https://github.com/ArimaGenomics/mapping_pipeline/blob/master/01_mapping_arima.sh). Scaffolding was performed using SALSA 2.2 (Ghurye et al., 2017). \n\nAnnotation was performed with funannote v1.7.4 (Palmer and Stajich 2020).\n\n