Abstract
The genus Allium L. represents one of the largest and taxonomically complex groups of monocots, with Central Asia recognized as a major center of its diversity. Despite the high species richness of Allium in Kazakhstan, genomic data for many native taxa remain limited. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of 12 Allium species from Kazakhstan. All chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes ranging from 152,029 to 153,521 bp and a uniform gene content of 137 genes, including 88 protein-coding genes, 38 tRNAs, 8 rRNAs, and 3 pseudogenes. Comparative analyses revealed high structural conservation, with most sequence divergence concentrated in intergenic regions. Several highly variable regions, including ycf1, matK, rpoC2, and ycf2, were identified as potential molecular markers. Phylogenetic analyses based on chloroplast genome sequences using Maximum Likelihood and Bayesian approaches recovered three major chloroplast genome-based lineages within Allium, largely consistent with previous phylogenomic studies. Divergence-time analyses suggested that major chloroplast lineage diversification events within the genus occurred during the early Eocene (ca. 47.97 Mya). Overall, this study expands the currently available chloroplast genomic resources for Allium from Kazakhstan, provides insights into chloroplast genome evolution and chloroplast genome-based relationships, and establishes a valuable foundation for future phylogenetic, taxonomic, and evolutionary studies of this diverse genus.