棱枝槲寄生叶绿体基因组结构特征及系统发育分析

张煜冰<sup>1</sup>; 曾晓丽<sup>1; 2</sup>; 班启明<sup>3</sup>; 郑红军<sup>4</sup>; 邱建生<sup>1; 5*</sup>

引用本文:	张煜冰, 曾晓丽, 班启明, 郑红军, 邱建生.棱枝槲寄生叶绿体基因组结构特征及系统发育分析[J].广西植物,2025,45(12):2255-2270.[点击复制]
	ZHANG Yubing, ZENG Xiaoli, BAN Qiming, ZHENG Hongjun, QIU Jiansheng.Chloroplast genome structure characteristics and phylogenetic analysis of Viscum diospyrosicola[J].Guihaia,2025,45(12):2255-2270.[点击复制]

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棱枝槲寄生叶绿体基因组结构特征及系统发育分析
张煜冰¹, 曾晓丽^1,2, 班启明³, 郑红军⁴, 邱建生^1,5*
1. 贵州大学林学院, 贵阳 550025;2. 贵定县人民政府宝山街道办事处, 贵州贵定 551300;3. 望谟县林业局, 贵州望谟 552300;4. 毕节市林业局, 贵州毕节 551700;5. 贵州省林业科学研究院, 贵阳 550011

摘要:

为了阐明棱枝槲寄生(Viscum diospyrosicola)的叶绿体基因组特征并解析槲寄生属物种的亲缘关系,该研究基于Illumina高通量测序平台完成其叶绿体基因组的测序,并采用生物信息学分析方法进行组装、注释与比较基因组分析。结果表明:(1)棱枝槲寄生叶绿体基因组具有典型环状四分体结构,全长126 315 bp,总GC含量为36.40%,注释得到111个基因,其中包括69个蛋白编码基因、34个tRNA基因和8个rRNA基因,未检测到转录起始因子infA。(2)比较基因组分析结果显示,5种槲寄生属物种叶绿体基因组LSC区变异率显著高于IR区,其中ycf1、ycf2、ycf3、atpA、rpoC2、rpoC1等基因的编码区存在特异性变异,为分子标记开发提供潜在靶点。(3)密码子使用偏好性分析表明,密码子第3位碱基以A/U结尾为主,密码子使用模式主要受到自然选择的影响。(4)系统发育分析结果表明,主要分为桑寄生科和檀香科2个主要分支,棱枝槲寄生与枫香槲寄生聚为一支,亲缘关系最近。该研究首次解析了棱枝槲寄生叶绿体基因组特征,明晰了槲寄生属系统发育关系,以及为槲寄生属植物分子鉴定和系统发育相关研究提供理论依据。

关键词: 棱枝槲寄生, 槲寄生属, 叶绿体基因组, 序列比对, 密码子偏好性, 系统发育分析

DOI：10.11931/guihaia.gxzw202409026

分类号:Q943

文章编号:1000-3142(2025)12-2255-16

基金项目:贵州省科技计划项目(黔科合服企 [2020]4010)。

Chloroplast genome structure characteristics and phylogenetic analysis of Viscum diospyrosicola

ZHANG Yubing¹, ZENG Xiaoli^1,2, BAN Qiming³, ZHENG Hongjun⁴, QIU Jiansheng^1,5*

1. College of Forestry, Guizhou University, Guiyang 550025, China;2. Baoshan Sub-District Office of Guiding County People's Government, Guiding 551300, Guizhou, China;3. Wangmo County Forestry Bureau, Wangmo 552300, Guizhou, China;4. Bijie City Forestry Bureau, Bijie 551700, Guizhou, China;5. Guizhou Academy of Forestry Sciences, Guiyang 550011, China

Abstract:

To elucidate the characteristics of chloroplast genome of Viscum diospyrosicola and resolve the phylogenetic relationships within the Viscum genus. Utilizing the Illumina high-throughput sequencing platform, we sequenced its chloroplast genome and performed bioinformatics analyses, including assembly, annotation, and comparative genomic analysis. The results were as follows:(1)The chloroplast genome of V. diospyrosicola exhibited a typical circular quadripartite structure, with the total length of 126 315 bp and the total GC content of 36.40%. A total of 111 genes were annotated, including 69 protein-coding genes, 34 tRNA genes, and 8 rRNA genes, with no detection of the transcription initiation factor infA.(2)Comparative genomic analysis revealed that the variation rate in the LSC region of the chloroplast genome was significantly higher than that in the IR region among five Viscum species. Specific variations were found in the coding regions of genes such as ycf1, ycf2, ycf3, atpA, rpoC2, and rpoC1, providing potential targets for molecular marker development.(3)Codon usage bias analysis showed that the third base of codons predominantly ended with A/U, and the codon usage pattern was mainly influenced by natural selection.(4)Phylogenetic analysis results indicated that the species were divided into two main branches, Loranthaceae and Santalaceae, with V. diospyrosicola clustering with V. liquidambaricola, indicating the closest genetic relationship. This study is the first to elucidate the characteristics of the chloroplast genome of V. diospyrosicola and to clarify the phylogenetic relationships within the Viscum, providing a theoretical basis for molecular identification and phylogenetic research of Viscum species.

Key words: Viscum diospyrosicola, Viscum, chloroplast genome, sequence alignment, codon usage bias, phylogenetic analysis