忍冬属忍冬组植物叶绿体基因组进化分析

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

摘要/Abstract

摘要：

目的探究忍冬组植物的分子进化和系统发育关系，对忍冬组植物相关资源的科学保护和开发具有重要的现实意义，为后续忍冬属物种鉴定提供借鉴。方法以细毡毛忍冬以及短柄忍冬叶片为材料，对2种植物的叶绿体全基因组进行测序、组装、注释，得到完整的叶绿体基因组。结果细毡毛忍冬完整叶绿体基因组序列全长155 312 bp，短柄忍冬为155 360 bp，细毡毛忍冬以及短柄忍冬叶绿体基因组包含基因类型与数目相同，共鉴定出130个编码基因，GC含量为38.5%，其基因组结构与其他忍冬属植物的叶绿体基因组高度相似，无明显边界收缩扩张的情况，长距忍冬存在基因缺失现象。共检测到该组物种102个SSR位点，其中单核苷酸重复位点数量最多，主要以A、T碱基为主。高变区有3个，其中LSC区、SSC区、IRb区各1个。2种植物的高频密码子均为32个，偏好使用以A/U结尾。属间亲缘关系显示，忍冬属与鬼吹箫属较近，组内亲缘关系显示，缠绕亚组物种聚为一支，细毡毛忍冬与短柄忍冬的亲缘关系最为密切。长距亚组的长距忍冬与缠绕亚组相距较远。通过重建忍冬组物种祖先分布区，发现喜马拉雅与中国西南地区可能是忍冬组物种的最初分布地，且该组物种主要向东南方向迁移，F区为主要建殖地。结论忍冬组植物的叶绿体基因组具有保守的基因组结构和基因组成，但长距忍冬的非编码区存在差异。忍冬组植物对A/U结尾的密码子有更高的偏好性，且忍冬组与空枝组的亲缘关系更近。忍冬组物种的祖先分布区为喜马拉雅与中国西南地区。

关键词: 忍冬属, 忍冬组, 叶绿体基因组, 结构特征, 密码子偏好性, 系统发育, 祖先分布区

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

魏瑶, 张晶晶, 崔云晓, 刘钰, 刘海瑞. 忍冬属忍冬组植物叶绿体基因组进化分析[J]. 生物技术通报, 2025, 41(8): 276-288.

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.

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