De novo assembly of the signal processed data was performed using Hybrid assembly method. Genome assembly was done using the PacBio and Illumina DNA-seq data separately (using Canu for the PacBio and Masurca for the Illumina data), and then the two sets of contigs were assembled using CLC Genomics Workbench.
The assemblied genomic sequences were annotated using MAKER (Campbell et al. 2014; Cantarel et al. 2008). The input resource of MAKER comprised an in-house database consisting of six Illumina RNA-seq samples representing P. novopanici treated with different concentrations of phosphite. In addition, the protein sequences from the Uniprot database (https://www.uniprot.org/) and Joint Genome Institute phytozome (https://phytozome.jgi.doe.gov/pz/portal.html) annotation of P. graminis, P. striiformis, and P. triticina were included as input for MAKER. Repeat Mask (http://repeatmasker.org) was applied to remove retrotransposon sequences and low-complexity regions in the genome during gene model prediction in MAKER.
Gill, US, Nandety, RS, Krom, N, Dai, X, Zhuang, Z, Tang Y, Zhao PX, Mysore KS. Draft Genome Sequence Resource of Switchgrass Rust Pathogen, Puccinia novopanici Isolate Ard-01. Phytopathology. 2019 Sep;109(9):1513-1515. doi: 10.1094/PHYTO-04-19-0118-A. Epub 2019 Jul 30. pubmed