Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences

Yermagambetova M. Imanbayeva A. Ishmuratova M. Sumbembayev A. Almerekova S.
August 2025 Multidisciplinary Digital Publishing Institute (MDPI)

Genes
2025 #16 Issue 8

Background: Rosa L. is an economically significant genus with species that are notable for their rich content of phenolic compounds. Despite its importance, the taxonomy of Rosa remains complex and unresolved. Methods: We sequenced, assembled, and performed comparative analyses of the complete plastomes of four Rosa species: R. acicularis, R. iliensis, R. laxa, and R. spinosissima. In addition to the plastome, we sequenced the nuclear ribosomal internal transcribed spacer (ITS). Results: Plastomes ranged in size from 157,148 bp (R. iliensis) to 157,346 bp (R. laxa). In each plastome, 136 genes were annotated, comprising 90 protein-coding, 38 tRNA, and eight rRNA genes. A total of 905 SSRs were identified, ranging from 224 (R. acicularis) to 229 in R. spinosissima. Nine highly variable regions were detected, including two coding genes (rps16 and ycf1) and seven intergenic spacers (ycf3-trnS(GGA), trnT(UGU)-trnL(UAA), rpl14-rpl16, trnR(UCU)-atpA, trnD(GUC), trnG(UCC)-trnfM(CAU), and psbE-petL). Maximum Likelihood (ML) phylogenetic analyses based on the complete plastome and ycf1 gene datasets consistently resolved the Rosa species into three major clades, with strong bootstrap support. In contrast, the ML tree based on ITS resolved species into four clades but showed lower bootstrap values, indicating reduced resolution compared to plastid datasets. Conclusions: Our findings underscore the value of plastome data in resolving phylogenetic relationships within the genus Rosa.

comparative analysis , ITS , Kazakhstan , phylogeny , plastome , Rosa , ycf1

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Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
Mangyshlak Experimental Botanical Garden, Aktau, 130000, Kazakhstan
Biology and Geography Faculty, Karaganda Buketov University, Karaganda, 100028, Kazakhstan
Altai Botanical Garden, Ridder, 071300, Kazakhstan

Institute of Plant Biology and Biotechnology
Mangyshlak Experimental Botanical Garden
Biology and Geography Faculty
Altai Botanical Garden

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