Evolutionary graph pangenome of the order Poales from chloroplast genomes highlight phylogenetic inconsistencies

With the increased accessibility and democratization of genomic sequencing, the number of fully sequenced genomes across all taxonomies is exploding. To benefit from the availability of complete genomes in evolutionary studies a complex frameworks such as graph-pangenomes are increasingly embraced. However, the high computational cost and precarious interpretation of graph-pangenomes at higher taxonomic levels hinder their broad implementation in evolutionary genomics. Here, we describe the development and application of an evolutionary graph pangenomes aproach which facilitates the analysis and interpretation of diversity across species and families. We applied our approach to 709 chloroplast genomes spanning the order Poales , overcoming key limitations of traditional phylogenetic approaches by uncovering structural variation and evolutionary signals. Our results show that despite overarching structural conservation, most genomic diversity arises from species-specific “cloud” variation. We also recover from the graph, a 77.7Kbp consensus core genome for Poales encoding essential cellular functions, while accessory regions capture adaptive traits. Graph-theory metrics were further implemented revealing distinct genus-level evolutionary signatures, with Triticum appearing homogeneous and highly connected, in contrast to the divergent, lineage-specific structure of Elymus . Collectively, we propose evolutionary graph pangenomes (evographs) as a powerful and nuanced framework for resolving structural and evolutionary complexity across species and higher taxonomies.