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

Abstract

<ns5:p> <ns5:italic>Allium aktauense</ns5:italic> is a narrow endemic species from the Aktau Range in the Nurotau Mountains, Western Pamir-Alay, where it grows in rocky limestone crevices. Genomic resources for this species have not previously been available, limiting molecular understanding of its phylogenetic placement and conservation value. In this study, we sequenced, assembled and characterized the complete chloroplast genome of <ns5:italic>A. aktauense</ns5:italic> and evaluated its phylogenetic position within <ns5:italic>Allium</ns5:italic> using comparative plastome data. The plastome exhibited the typical circular quadripartite structure of angiosperms, with a total length of 152,443 bp, including 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. The overall genome organization, gene order and plastome structure were conserved, with no major rearrangements detected. The highest nucleotide diversity was observed in the <ns5:italic>ndhF–rpl32</ns5:italic> region, suggesting its potential utility as a molecular marker for future studies. Phylogenetic analysis based on complete chloroplast genome sequences placed <ns5:italic>A. aktauense</ns5:italic> within subgenus <ns5:italic>Allium</ns5:italic> , close to <ns5:italic>A. ophiophyllum</ns5:italic> , with <ns5:italic>A. nikolaii</ns5:italic> and <ns5:italic>A. filidens</ns5:italic> forming a neighbouring lineage. These results provide the first plastome resource for <ns5:italic>A. aktauense</ns5:italic> and contribute to future phylogenetic, taxonomic and conservation-related studies of endemic <ns5:italic>Allium</ns5:italic> species in Central Asia. </ns5:p>