Phylogenetic Relationships and Characterization of the Complete Chloroplast Genomes of Dendrobium Section Densiflora

doi:10.11733/j.issn.1007-0435.2025.05.004

Acta Agrestia Sinica ›› 2025, Vol. 33 ›› Issue (5): 1372-1386.DOI: 10.11733/j.issn.1007-0435.2025.05.004

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Phylogenetic Relationships and Characterization of the Complete Chloroplast Genomes of Dendrobium Section Densiflora

CHEN Yu-ming^1,2, WEI Chun-yi², ZHANG Sai³, HUANG Si-ming², LAN Si-ren², LI Ming-he^1,2

1. College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China;
2. Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China;
3. Academy of Forestry Inventory and Planting, National Forestry and Grassland Administration, Beijing 100714, China

Received:2024-12-16 Revised:2025-02-06 Online:2025-05-15 Published:2025-05-20

石斛属灯笼组物种叶绿体基因组特征及系统发育分析

陈育明^1,2, 韦春怡², 张赛³, 黄思铭², 兰思仁², 李明河^1,2

1. 福建农林大学林学院, 福建福州 350002;
2. 福建农林大学风景园林与艺术学院/兰科植物保护与利用国家林业和草原局重点实验室, 福建福州 350002;
3. 国家林业和草原局林草调查规划院, 北京 100714

通讯作者: 李明河,E-mail:fjalmh@126.com
作者简介:陈育明（2001-），女，汉族，福建泉州人，硕士研究生，主要从事园林植物与观赏园艺研究，E-mail：12304022001@fafu.edu.cn
基金资助:
国家自然科学基金面上项目“石斛属植物亲缘关系及其碳同化途径的育种潜力研究”（32271957）；福建省自然科学基金杰出青年项目“中国兰科植物景天酸代谢途径物种多样性及其系统演化”（2024J010023）资助

Abstract

Abstract: To analyze the chloroplast （CP） genome structure and phylogenetic relationships ofsection Densiflora in the genus of Dendrobium， this study used high-throughput sequencing technology for the first time to sequence the CP genomes of four species in the section， including D. farmer， D. palpebrae， D. sulcatum， and D. thyrsiflorum. The genomes of section Densiflora were assembled， annotated， mapped and analyzed by bioinformatics software. Phylogenetic trees of 42 species of Dendrobium， including ten species of section Densiflora， were constructed based on cp genomes. The complete cp genomes of section Densiflora were 151 717-160 123 bp in size with 37.1%-37.6% GC content. Additionally， 46-63 simple sequence repeats （SSRs） and 48-49 interspersed nuclear elements （INEs） were identified in section Densiflora. Codon usage in protein-coding genes is biased toward A and U （or T）. There were significant differences in the coding regions of six genes， including trnK^UUU， atpF， rpoC， trnL^UAA， clpP and rpl16 among section Densiflora. Phylogenetic analyses revealed that ten species of section Densiflora were clustered into four different clades， indicating that this section defined by traditional morphology is non-monophyletic.

Key words: Dendrobium section Densiflora, Chloroplast genome, Genomic comparison, Phylogenetic analysis

摘要： 为解析石斛属（Dendrobium）灯笼组（Section Densiflora）物种的叶绿体基因组特征及其系统发育关系，本研究采用高通量测序技术首次对该组的四角石斛（D.farmer）、角茎灯笼石斛（D.palpebrae）、具槽石斛（D.sulcatum）和球花石斛（D. thyrsiflorum）叶绿体基因组进行测序，利用生物信息学相关软件对其基因组进行组装、注释、图谱绘制以及序列特征分析，并构建石斛属42个物种（灯笼组10个）的系统发育树。结果显示：灯笼组物种叶绿体基因组全长范围为151 717~160 123 bp，总GC含量为37.1%~37.6%，共注释到129~133个基因；同时检测到46~63个简单重复序列（Simple repeat sequence，SSR）以及48~49个分散重复序列（Interspersed repetitive sequence，INE）；蛋白编码基因的密码子偏好以A/U（T）结尾；灯笼组物种中的trnK^UUU，atpF，rpoC，trnL^UAA，clpP，rpl16等6个基因的编码区具有显著差异。系统发育树表明，灯笼组10个物种聚类为4个不同演化分支，传统形态学界定的灯笼组为非单系。

关键词: 灯笼组石斛, 叶绿体基因组, 基因组比较, 系统发育分析

CLC Number:

Q943.2

CHEN Yu-ming, WEI Chun-yi, ZHANG Sai, HUANG Si-ming, LAN Si-ren, LI Ming-he. Phylogenetic Relationships and Characterization of the Complete Chloroplast Genomes of Dendrobium Section Densiflora[J]. Acta Agrestia Sinica, 2025, 33(5): 1372-1386.

陈育明, 韦春怡, 张赛, 黄思铭, 兰思仁, 李明河. 石斛属灯笼组物种叶绿体基因组特征及系统发育分析[J]. 草地学报, 2025, 33(5): 1372-1386.

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Phylogenetic Relationships and Characterization of the Complete Chloroplast Genomes of Dendrobium Section Densiflora

石斛属灯笼组物种叶绿体基因组特征及系统发育分析

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