Oryza australiensis disease resistance genes

The collapsed <i>O. australiensis</i> genome was run through two tools, NLR-Annotator and RGAugury, to identify disease resistance gene candidates. NLR-Annotator was run against both the <i>O. australiensis</i> unmasked assembly and the annotated CDS sequence file. The annotated<i> O. australiensis</i> 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.将澳洲稻（O. australiensis）的折叠基因组分别通过NLR-Annotator和RGAugury两款工具进行分析，以鉴定候选抗病基因。其中，NLR-Annotator分别针对澳洲稻的未屏蔽基因组组装序列与注释后的CDS序列文件进行比对分析；将注释得到的澳洲稻氨基酸序列文件通过RGAugury进行分析，分析过程中调用了BLAST、nCoils、pfam_scan、Phobius以及InterProScan多款工具。研究人员从以往发表的论文（Simon等，2023）中整理得到的水稻克隆抗病基因序列，从水稻注释项目（Rice Annotation Project, RAP）与MSU水稻基因组注释项目数据库中检索并下载。该整理得到的基因序列列表被命名为克隆抗病同源基因（cloned disease resistance homologue, CDRH）列表。此外还检索得到RefPlantNLR数据库，该数据库包含481条对应多个重要植物物种中经实验验证的植物NLR的氨基酸序列（Kourelis等，2021）。使用默认参数的OrthoFinder v2.5.5工具，在澳洲稻基因组中检索RefPlantNLR数据库与上述CDRH基因列表的直系同源基因。