Phylogenomics, divergence time estimation, and biogeography of Iris species from Kazakhstan using plastome sequence analysis.

The genus Iris Tourn. ex L. (Iridaceae Juss.) comprises more than 300 accepted species distributed across the Northern Hemisphere and widely valued for its medicinal and ornamental significance. However, Iris is a taxonomically complex genus with controversial circumscription and unresolved phylogenetic relationships, emphasizing the need for comprehensive systematic studies. In this study, plastomes of 14 Iris species collected in Kazakhstan were sequenced, assembled, and annotated. Comparative genomic analyses, divergence time estimation, and biogeographic reconstruction were performed based on complete plastome data. All plastomes exhibited the typical quadripartite circular structure, with genome sizes ranging from 150, 612 bp (I. tenuifolia) to 155, 046 bp (I. kuschakewiczii). The gene content was highly conserved among the studied species, with 133 genes identified, including 87 protein-coding genes (PCGs), 38 tRNA genes, and eight rRNA genes. Among these, eight PCGs (ndhB, rpl2, rpl23, rps7, rps12, rps19, ycf1, and ycf2), seven tRNA genes (trnA-UGC, trnH-GUG, trnIGAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and all four rRNA genes (rrn4.5, rrn5, rrn16, and rrn23) were duplicated. Ten highly variable regions were identified, namely rps16, rps16-trnQ(UUG), trnS(GCU)-trnG(UCC), trnG(UCC), trnY(GUA), trnD(GUC), rpl32, rps15, clpP, and ycf1, most of which were located in the large single-copy region. A total of 2, 401 simple sequence repeats (SSRs) were detected across the 14 plastomes, with an average of 171.5 SSRs per species. Mononucleotide repeats were the most abundant type, accounting for 65.7% of all SSRs, with a strong bias toward A/T motifs. Phylogenetic analyses resolved three major clades corresponding to the subgenera Iris, Scorpiris, Limniris, and Hermodactyloides. Molecular dating suggested that Iris originated approximately 49.31 Ma (95% CI: 40.13-59.60 Ma), with crown group diversification beginning around 41.43 Ma (95% CI: 33.97-50.97 Ma). Ancestral area reconstruction indicated a combined Eastern Asia-Central Asia origin for the genus. Overall, this study provides comprehensive plastome-based insights that may contribute to resolving phylogenetic relationships, improving population genetic studies, and elucidating the evolutionary history and biogeography of Iris.