Hayai-Annotation v3.0: A functional gene prediction tool that integrates orthologs and gene ontology for network analysis

Hayai-Annotation v3, an R-package integrated with the R-Shiny browser interface, utilizes two methods for functional annotation: DIAMOND for sequence alignment using UniProtKB Plants as the database, and OrthoLoger, the official OrthoDB tool for ortholog inferences. The GO enrichment accuracy was assessed by a CAFA-evaluator, demonstrating that Hayai-Annotation v3s accuracy was comparable to that of the benchmark, BLAST2GO. We here propose a method to explore genome evolution and adaptation from a different perspective, by creating networks and heatmaps correlating orthologs with gene ontology (molecular function and biological process) from their co-occurrence tables. This approach enhances the ability to infer functions of uncharacterized genes by associating orthologs with gene ontology terms and the ability to visualize the distribution of gene numbers correlated with co-occurrence patterns across different species. To our knowledge, this is the first attempt to correlate orthologs with GO (MF and BP) to construct a gene network, providing a comprehensive, cross-species view of gene distribution and function. Hayai-Annotation v3 not only retains the convenience of previous versions but also enhances ortholog analysis functionality, allowing for evolutionary insights from gene sequences. Hayai-Annotation v3 is expected to contribute significantly to the future development of plant genome analysis.