GSAman: a Gene Structure Annotation Manual Curator for Functional Genomics Research

A high-quality reference genome requires not only accurate DNA sequences but also well-defined gene structure annotations. However, many existing tools depend predominantly on automated pipelines that perform poorly when confronted with complex gene architectures, such as overlapping loci, alternative splicing patterns, and lowly expressed isoforms, resulting in incomplete or inaccurate annotations. To overcome these limitations, we developed GSAman, a standalone, ready-to-use tool that enables intuitive, WYSIWYG (What You See Is What You Get) editing of gene structure annotations. In contrast to web-based platforms such as Apollo2, which generally require server deployment and do not provide full offline functionality, GSAman delivers a fully local, responsive interface for real-time annotation refinement, thereby improving accessibility across research settings. GSAman supports both fine-scale curations of individual genes and large-scale annotation of entire genomes. By enabling precise curation of gene models across varied genomic contexts, it directly facilitates downstream applications including pan-genome construction, gene family evolutionary analyses, and precision crop enhancement. Using a telomere-to-telomere rice genome (MH63) annotation project as a case study, we demonstrate the practical utility of GSAman in producing a complete and accurate reference annotation, improving BUSCO completeness to 99.63% following manual curation. We believe GSAman will serve as a critical resource for advancing functional genomics across diverse species. The software is freely available for non-commercial users at https://github.com/CJ-Chen/GSAman/releases.