A genomic resource for a hidden endemic: the complete chloroplast genome of Allium aktauense from Uzbekistan

Allium aktauense is a narrow endemic species from the Aktau Range in the Nurotau Mountains, Western Pamir-Alay, Uzbekistan, where it grows in rocky limestone crevices. Genomic resources for this species have previously been limited, restricting molecular assessment of its phylogenetic placement. In this study, we sequenced, assembled and characterized the complete chloroplast genome of A. aktauense and evaluated its phylogenetic position within Allium using comparative plastome data. The plastome is 152,443 bp long and has the typical quadripartite organization, comprising a large single-copy region of 81,522 bp, a small single-copy region of 17,907 bp and two inverted repeat regions of 26,507 bp each. Annotation identified 131 gene copies, including 85 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Across the broad comparative dataset, the highest nucleotide diversity was observed in the ndhF-rpl32 region (Pi approximately 0.044), followed by ycf1 (Pi approaching 0.030); these regions are treated here as candidate variable loci requiring further validation within closely related taxa. Maximum-likelihood analysis of complete plastome sequences placed A. aktauense within subgenus Allium , with A. ophiophyllum as its closest sampled plastome lineage (bootstrap support 100%). The plastome provides a genomic resource for future phylogenetic, taxonomic and conservation-related research on endemic Central Asian Allium .