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>

<i>水稻（Oryza sativa）</i>亚种<i>粳稻（Oryza sativa subsp. japonica）</i>的Illumina读段数据取自美国国家生物技术信息中心（NCBI，SRR15967546和SRR15967547），并与<i>澳洲稻（Oryza australiensis）</i>基因列表进行比对，以识别候选独特编码序列。数据比对使用QIAGEN CLC Genomics Workbench 24.0.2软件中的"Map Reads to Reference"工具进行，参数设置为长度分数0.9、相似性分数0.9。未被任何<i>水稻（Oryza sativa）</i>Illumina读段比对上的<i>澳洲稻（Oryza australiensis）</i>基因被标记为"未比对"基因，并使用OmicsBox 3.1.11进行功能注释。利用OmicsBox中的FatiGO工具进行双尾Fisher精确检验，评估未比对基因相对于整体<i>澳洲稻（Oryza australiensis）</i>基因集的富集基因本体（GO，Gene Ontology）功能。<i>澳洲稻（Oryza australiensis）</i>和<i>水稻（Oryza sativa）</i>的蛋白质序列数据（Osativa323v7蛋白文件来自Phytozome）被过滤以保留最长异构体，随后使用OrthoVenn3工具（参数：OrthoFinder算法、E值1e-2、Inflation值1.50）分析<i>澳洲稻（Oryza australiensis）</i>基因组内的直系同源和独特蛋白簇（Sun等，2023；Emms和Kelly，2019）。包含三个及以上蛋白质序列的独特<i>澳洲稻（Oryza australiensis）</i>簇的GO富集分析和注释通过OrthoVenn3平台自动完成。