Phylogenetic Analysis of Lonicera Sect. Nintooa Based on Chloroplast Genomes Data

doi:10.13560/j.cnki.biotech.bull.1985.2025-0116

Abstract

Abstract:

Objective Evolutionary analysis of chloroplast genomes of Sect. Nintooa (Lonicera) species is significant for the scientific conservation and development of resources related to Sect. Nintooa. It also provides references for the subsequent species identification of the genus Lonicera. Method Using the leaves of Lonicera similis and Lonicera pampaninii as materials, the chloroplast genomes of the two plants were sequenced, assembled and annotated, and the whole chloroplast genomes were obtained. Result The sequence of whole chloroplast genome of L. similis was 155 312 bp and that of L. pampaninii was 155 360 bp. The chloroplast genome of L. similis and L. pampaninii contained the same type and number of genes, 130 genes were identified, and GC content was 38.5%. The chloroplast genome structure of the two species were highly similar to other Lonicera plants, there were no significant expansion or contraction observed. There was gene deletion in L. calcarata. A total of 102 SSR loci were detected, with the highest proportion of mono-nucleotide repeat SSRs dominated by (A/T). Three regions with high variation were identified from the chloroplast genomes, each for LSC, SSC and IRb region. There were 32 high-frequency codons in the two plants which preferred to end with A/U. Phylogenetic analysis indicates that the Lonicera showed a close relationship to the Leycesteria. Among the species within Sect. Nintooa, the Subsect. Volubilis wereclustered to be a branch, and L. similis and L. pampaninii had the closest relationship. L. calcarata in Subsect. Calcaratae had long distance to Subsect. Volubilis. The reconstruction of ancestral area revealed that Himalaya and Southwest China probably were the original location of Sect. Nintooa as well as the species mainly migrated to the Southeast China, and then region F becomes the major settlement place. Conclusion The chloroplast genome of Sect. Nintooa contains a conserved genomic structure and gene composition. However, there are differences in the non-coding areas of L. calcarata. The Sect. Nintooa shows higher preference for codons ending in A/U. The ancestral distribution area of the Sect. Nintooa species is the Himalayas and the southwestern region of China.

Key words: Lonicera, Sect. Nintooa, chloroplast genome, structural characteristic, codon preference, phylogeny, ancestral range

WEI Yao, ZHANG Jing-jing, CUI Yun-xiao, LIU Yu, LIU Hai-rui. Phylogenetic Analysis of Lonicera Sect. Nintooa Based on Chloroplast Genomes Data[J]. Biotechnology Bulletin, 2025, 41(8): 276-288.

Figures/Tables 10

References 47

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