Fig 1. Overview of LongiGAD. A, Proportion of orthologous genes and singleton genes in the haplotype-resolved and telomere to telomere (T2T) genome of Oryza longistaminata. ‘Three-way’ denotes genes that have orthologs in all three assemblies [haplotype 1 (Hap1), haplotype 2 (Hap2), and the T2T genome]. ‘Two-way’ denotes genes that have orthologs in any two of the three assemblies but are absent from the third. B, Framework of LongiGAD, including data source, orthologous gene identification, and application scenarios. RBH, Reciprocal bast hit; SBH, Single base hit. C, Main content of Browse module (T2T, Hap1, and Hap2). D, Search interface of Search module. E, Outputs of Search module primarily include genomic coordinates of O. longistaminata gene and the correlations with orthologous genes in cultivated rice (O. sativa). F, Visualization of gene structure, where green boxes represent coding sequence (CDS) regions, blue box represents 5′ untranslated region (5′UTR), and red box represents 3′UTR. G, Download functionality of Search results (gene, CDS, and protein sequences); format: FASTA). H, Visual annotation of gene sequences with color-highlighted features, including green for CDS, blue for 5′UTRs, and red for 3′UTRs. I, Relative expression levels of gene C1H1g26676 in different tissues of O. longistaminata. TPM, Transcripts per million. J, Visualizing and interactively exploring multiple sequence alignments of genes between O. longistaminata and O. sativa.