Oryza australiensis species-specific gene and protein candidates

<i>O. sativa</i> subsp. <i>japonica </i>Illumina read data was extracted from the NCBI (SRR15967546 &amp; SRR15967547) and mapped against the <i>O. australiensis </i>gene list to identify candidate unique coding sequences. Data was mapped using the Map Reads to Reference tool (length fraction: 0.9 and similarity fraction: 0.9) on the QIAGEN CLC Genomics Workbench 24.0.2. <i>O. australiensis</i> genes that were not mapped with any <i>O. sativa</i> Illimuna reads were designated as ‘unmapped’ genes and were functionally annotated with OmicsBox 3.1.11. OmicsBox was used with FatiGO to conduct a two-tailed Fisher’s Exact test to assess for enriched GO functions in the unmapped genes compared to the overal<i>l O. australiensis</i> gene set. .The protein sequence data for both <i>O. australiensis</i> and <i>O. sativa</i> (Osativa323v7 protein file Phytozome). were filtered for the longest isomer and then analysed for orthologous and unique protein clusters within the O. australiensis genome using OrthoVenn3 (parameters: OrthoFinder algorithm, E-value: 1e-2, Inflation value:1.50) (Sun et al., 2023, Emms and Kelly, 2019). GO enrichment analyses and annotation for unique <i>O. australiensis</i> clusters containing three or more protein sequences were automatically run through the Orthovenn3 platform.<br>