Complete plastome sequences of Lonicera L. species: implications for phylogeny and comparative analysis
Полные последовательности пластомов видов Lonicera L.: значение для филогении и сравнительный анализ
Almerekova S.S. Yermagambetova M.M. Yerbolatov D.Y. Ishmuratova M.Y. Turuspekov Y.K.
2025Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Vavilovskii Zhurnal Genetiki i Selektsii
2025#29Issue 6883 - 895 pp.
Lonicera L. is one of the largest and economically significant genera in the family Caprifoliaceae Juss., with a controversial taxonomy. To contribute to its molecular taxonomy, we sequenced the plastomes of Lonicera species: Lonicera caerulea (two subspecies), L. tatarica, and L. micrantha - using next-generation sequencing technology and conducted a comparative analysis. Plastome sizes ranged from 153,985 bp in L. micrantha to 164,000 bp in L. caerulea subsp. pallasii, each containing 130 genes, including 85 protein-coding, 37 tRNA, and 8 rRNA genes. Five protein-coding (rps7, rps12, ndhB, ycf2, and ycf15), 7 tRNA (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and 4 rRNA (rrn4.5, rrn5, rrn16, and rrn23) genes were duplicated. Comparative analysis of Lonicera plastome boundaries revealed structural variations in L. caerulea subsp. altaica and L. caerulea subsp. pallasii, particularly in ndhA gene distribution. Three highly variable, two intergenic (ycf1-trnN-GUU and trnN-GUU-ndhF) and one genic (accD) region were identified. A total of 641 simple sequence repeats were detected in four plastomes. Phylogenetic analyses grouped Lonicera samples into two clades corresponding to subgenera Periclymenum and Chamaecerasus. In this study, the plastid genomes of two subspecies of L. caerulea and species L. micrantha were sequenced for the first time. The maximum likelihood tree derived from complete plastid genome sequences proved to be the most informative, showing a topology consistent with previous studies. The nucleotide sequences of variable regions (accD-ycf1-ndhF-trnN-GUU) demonstrate high potential for use in DNA barcoding and may serve as valuable molecular markers for species phylogenetic studies within the genus Lonicera.
DNA-barcoding markers , Kazakhstan , Lonicera , next-generation sequencing , simple sequence repeats , variable regions
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Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
Karaganda Buketov University, Karaganda, Kazakhstan
Institute of Plant Biology and Biotechnology
Karaganda Buketov University
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