龙石斛叶绿体基因组特征及系统发育分析

doi:10.3969/j.issn.1009-7791.2025.04.002

亚热带植物科学 ›› 2025, Vol. 54 ›› Issue (4): 378-386.DOI: 10.3969/j.issn.1009-7791.2025.04.002

龙石斛叶绿体基因组特征及系统发育分析

张翊凡1，颜茵2，陈育明2，黄思铭1，李明河1,2*

(1. 福建农林大学风景园林与艺术学院，福建福州 350002；2. 福建农林大学林学院，福建福州 350002)

收稿日期:2024-12-27 接受日期:2025-02-05 出版日期:2025-08-30 发布日期:2025-10-13
通讯作者: 李明河
基金资助:
国家自然科学基金项目(32271957)

Chloroplast Genome and Phylogenetic Analysis of Dendrobium draconis

ZHANG Yi-fan1, YAN Yin2, CHEN Yu-ming2, HUANG Si-ming1, LI Ming-he1,2*

(1. College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian China; 2. College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian China)

Received:2024-12-27 Accepted:2025-02-05 Online:2025-08-30 Published:2025-10-13
Contact: LI Ming-he

摘要/Abstract

摘要： 以龙石斛Dendrobium draconis新鲜叶片为材料，对其叶绿体基因组进行组装、注释和分析，探究该物种的叶绿体基因组序列特征及其与同属其他物种的系统发育关系。结果表明，龙石斛叶绿体基因组呈典型四分体结构，基因组大小为159 080 bp (GC含量37.3%)，大单拷贝区域为86 613 bp (GC 35.0%)，小单拷贝区域为18 409 bp (GC 30.4%)，两个反向重复区域为27 029 bp (GC 43.2%)；共注释得到132个基因，包括86个蛋白质编码基因，38个tRNA基因，8个rRNA基因。简单重复序列检测表明，叶绿体基因组包括50个简单重复系列位点，其中以A和T组成的单核苷酸重复次数最多，占46.0%。叶绿体基因组结构中IR区边界相对保守。核苷酸多样性分析获得8个高变异热点区域：rpoB-trnC^GCA、petN-psbM、accD-psaI、clpP-psbB、ndhF-rpl32、ndhK、ndhF、ycf1，可作为物种鉴定和遗传多样性研究的潜在分子标记。系统发育分析显示，龙石斛与高山石斛D. wattii、毛鞘石斛D. christyanum、黑毛石斛D. williamsonii、翅萼石斛D. cariniferum组成的分支构成姐妹类群。本研究首次解析了龙石斛叶绿体基因组特征，为该物种及石斛属植物的分子标记开发和系统发育分析等研究提供理论依据。

关键词: 龙石斛, 叶绿体基因组, 系统发育分析, 分子标记

Abstract: The chloroplast genome sequence was assembled, annotated and analyzed using fresh leaves of Dendrobium draconis to explore the sequence characteristics and the phylogenetic relationships with other species in the same genus. The results showed that the chloroplast genome of D. draconis exhibited a typical quadripartite structure with a total genome size of 159 080 bp and a GC content of 37.3%. The large single-copy region, small single-copy region and inverted repeat region were 86 613 bp (GC content 35.0%), 18 409 bp (GC content 30.4%), and 27 029 bp (GC content 43.2%), respectively. A total of 132 genes, including 86 protein-coding, 38 tRNA and 8 rRNA, were annotated. Simple sequence repeat (SSR) analysis showed that the chloroplast genome contained 50 SSR loci, with the single nucleotide repeats consisting of A and T being the most numerous and accounting for 46.0%. Comparative analysis of chloroplast genome structure showed that the boundary regions of inverted repeat regions were relatively conserved. Nucleotide diversity analysis obtained eight highly variable hotspot regions: rpoB-trnC^GCA, petN-psbM, accD-psaI, clpP-psbB, ndhF-rpl32, ndhK, ndhF, and ycf1, which could be used as potential molecular markers for identification and genetic diversity research. Phylogenetic analysis showed that D. draconis was sister to the clade formed by D. wattii, D. christyanum, D. williamsonii and D. cariniferum. This study is the first to elucidate the chloroplast genome characteristics of D. draconis, providing a foundation for molecular marker development and phylogenetic studies of D. draconis and other Dendrobium species.

Key words: Dendrobium draconis, chloroplast genome, phylogenetic analysis, molecular marker

中图分类号:

Q943

张翊凡, 颜茵, 陈育明, 黄思铭, 李明河. 龙石斛叶绿体基因组特征及系统发育分析[J]. 亚热带植物科学, 2025, 54(4): 378-386.

ZHANG Yi-fan, YAN Yin, CHEN Yu-ming, HUANG Si-ming, LI Ming-he. Chloroplast Genome and Phylogenetic Analysis of Dendrobium draconis[J]. Subtropical Plant Science, 2025, 54(4): 378-386.

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龙石斛叶绿体基因组特征及系统发育分析

Chloroplast Genome and Phylogenetic Analysis of Dendrobium draconis

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