GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts.

Automated summary

This study proposes a crop pangenome approach using individual cultivar assemblies to access conserved genes more easily. However, the variability in genome content and inconsistent identifiers have hindered exploration. To overcome these challenges, the concept of pangenes is introduced to summarize a species coding potential and link back to original annotations. The protocol get_pangenes utilizes whole genome alignments to identify syntenic gene models based on coordinate overlaps. Benchmark tests with both small and large plant genomes demonstrate that pangenes accurately recapitulate phylogeny-based orthologies and generate complete soft-core gene sets.