The digital map of homologous gene clusters across Poaceae species unveils the complex evolutionary trajectories of genes in Triticeae

Nevertheless, the fine-scale evolutionary trajectories of genes within their local genomic contexts across diverse genera remain poorly characterized. Here, we developed an approach, GoldMiner, that uses homologous gene clusters (HOCs) as evolutionary units for investigating gene evolution and enables hierarchical alignment of pan-genomic HOCs across species and genera.

We constructed a genus-level pangenomic map of half a million indexed HOCs across 248 diploid genomes from 25 Poaceae species. Finally, an interactive web platform, waGOLD (wheat.cau.edu.cn/TGT/waGOLD), was developed for the community to explore evolutionary trajectories of HOCs. Overall, we presented a digital atlas of gene evolution for Poaceae species as a resource that opens new avenues for fine-scale gene family evolution and provides a practical framework for constructing genus-level gene-based pangenomes.