Oryza australiensis species-specific gene and protein candidates

O. sativa subsp. japonica Illumina read data was extracted from the NCBI (SRR15967546 & SRR15967547) and mapped against the O. australiensis 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.
O. australiensis genes that were not mapped with any O. sativa 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 overall O. australiensis gene set. .
The protein sequence data for both O. australiensis and O. sativa (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 O. australiensis clusters containing three or more protein sequences were automatically run through the Orthovenn3 platform.