Oryza australiensis disease resistance genes

The collapsed O. australiensis genome was run through two tools, NLR-Annotator and RGAugury, to identify disease resistance gene candidates. NLR-Annotator was run against both the O. australiensis unmasked assembly and the annotated CDS sequence file. The annotated O. australiensis amino acid sequence file was run through RGAugury, using BLAST, nCoils, pfam_scan, Phobius, and InterProScan. Cloned disease resistance gene sequences in rice compiled from a previous paper (Simon et al., 2023) were searched and downloaded from the Rice Annotation Project (RAP) and MSU Rice Genome Annotation Project databases. This compiled list of genes was designated as the cloned disease resistance homologue (CDRH) list. An additional database, RefPlantNLR, containing 481 amino acid sequences corresponding to experimentally-verified plant NLRs within a number of important plant species was also retrieved (Kourelis et al., 2021). The RefPlantNLR database and compiled CDRH gene lists were searched for orthologues within the O. australiensis genome using OrthoFinder v2.5.5 with default parameters.