Plastome analysis and phylogenetic reconstruction of Iris (Iridaceae)

Iris L. is a group of perennial herbs with important horticultural value, comprising more than 300 species worldwide. Previous studies based on limited chloroplast fragments have provided insufficient phylogenetic resolution. In this study, we aimed to reconstruct a robust plastid-based phylogenetic framework of Iris using complete chloroplast genomes and to investigate the plastome features and plastid-based evolutionary history of the genus. We sequenced, assembled, and annotated the plastomes of 17 Iris species and combined them with 62 publicly available chloroplast genomes, ultimately analyzing 79 species. All plastomes exhibited a typical quadripartite structure, ranging from 150,169–155,878 bp. The GC content of the Iris plastomes was highly conserved across the studied species, ranging from 37.74–38.23%. Each genome contained 123–137 genes, including 84–88 protein-coding, 34–41 tRNA, and eight rRNA genes. Phylogenetic analyses resolved the genus into four major clades. Ancestral state reconstruction based on the maternal framework indicated that the common ancestor of Iris was beardless (State C, P = 1.00). Clades B and D largely preserved the primitive beardless condition, whereas Clade A converted to bearded and Clade C evolved to crested state. Divergence time estimation suggested that Iris diverged from the outgroup Crocus approximately 39.45 Ma. Subsequent diversification of major chloroplast lineages occurred from the Oligocene to the Quaternary, indicating a prolonged evolutionary history of Iris . Given that the chloroplast genome is maternally inherited and represents only a single genetic lineage, our inferences should be interpreted as a plastid‑based hypothesis that may not fully reflect the species tree. Our results indicate that the overall chloroplast genome structure of Iris is highly conserved. Complete plastome sequences provide richer phylogenetic information than CDS or isolated hypervariable regions, offering a chloroplast-based phylogeny for the genus. Ancestral state reconstruction based on maternal framework reveals that the beardless petals represent the primitive state of Iris , with bearded and crested appendages evolving secondarily.