DOI: 10.12688/f1000research.184132.1 ISSN: 2046-1402

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

Ibrokhimjon Ergashov, Farkhodjon Mingboev, Ziyoviddin Yusupov, Farruhbek Rasulov, Diyorjon Hamrayev, Mashrab Turdiyev, Gulirukhsor Ganiyeva, Movlon Bekmirzayev, Yulduz Fayzulloyeva, Saidkamol Xaydarov, Shohruh Fayzulloyev, Zera Moldakhmetova, Laylo Mirzoyeva
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Allium aktauense 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 A. aktauense and evaluated its phylogenetic position within Allium 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 ndhF–rpl32 region, suggesting its potential utility as a molecular marker for future studies. Phylogenetic analysis based on complete chloroplast genome sequences placed A. aktauense within subgenus Allium , close to A. ophiophyllum , with A. nikolaii and A. filidens forming a neighbouring lineage. These results provide the first plastome resource for A. aktauense and contribute to future phylogenetic, taxonomic and conservation-related studies of endemic Allium species in Central Asia.

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