Comparative Chloroplast Genomics of Calligonum leucocladum from Kazakhstan: Genetic Basis for Arid Adaptation and Agroforestry Applications

Mussina М. Kyrbassova E. Tynybekov B. Hou W. Bassygarayev Z. Bozhbanov A. Imаnova E. Kurmanbay U. Ydyrys A. Imanaliyeva M.
December 2025 Engineered Science Publisher

ES Food and Agroforestry
2025 #22

Calligonum leucocladum (Schrenk) Bunge is a key desert shrub in Central Asia that plays an important role in dune stabilization and maintaining the ecological sustainability of arid landscapes. To elucidate the genetic mechanisms underlying ecological adaptation and to assess the species’ potential for agroforestry applications, we sequenced and compared the complete chloroplast genomes of three geographically distinct populations from Kazakhstan. The chloroplast genome size ranged from 162,085 to 162,187 base pairs and exhibited the typical quadripartite structure, consisting of large and small single-copy regions (LSC, SSC) and two inverted repeat (IR) regions. Comparative genomic analysis revealed a conserved plastome organization in populations P1 and P2, whereas population P3 showed contraction of the IR region and expansion of the SSC region, indicating localized genomic adaptation. Analyses of codon usage and SSR motifs revealed a predominance of A/T content and identified potential loci for population-level marker development. Phylogenetic analysis confirmed a close intraspecific relationship among Calligonum leucocladum populations, supporting the taxonomic integrity of the species within the Polygonaceae family. These findings provide novel genomic insights into the adaptive evolution of Calligonum leucocladum and establish a valuable foundation for its conservation, ecological restoration, and application in sustainable agroforestry practices in the arid regions of Kazakhstan.

Agroforestry , C. leucocladum , Chloroplast genome, Arid adaptation , Ecological restoration , Kazakhstan

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Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
Department of biology, Institute of Natural Sciences, NPJSC Kazakh women’s teacher training university, Almaty, 05000, Kazakhstan
School of Medicine, Shenzhen University, Shenzhen, 518060, China
Department of Food Biotechnology, Faculty of Food Technologies, Almaty Technological University, Almaty, 050040, Kazakhstan
Zh. Tashenev University, 21 Konaev, Shymkent, 160000, Kazakhstan
Ahmet Yassawi University, 29 Bekzat Sattarhanov Street, Turkestan, 161200, Kazakhstan
Biomedical Research Centre, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan

Faculty of Biology and Biotechnology
Department of biology
School of Medicine
Department of Food Biotechnology
Zh. Tashenev University
Ahmet Yassawi University
Biomedical Research Centre

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