三种不同栽培类型菊花品种的叶绿体基因组特征对比分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-1432

摘要/Abstract

摘要：

目的探究不同栽培类型菊花品种的叶绿体基因组特征和系统发育关系，为菊属植物的系统发育、物种鉴定及资源保护等研究提供理论依据。方法对地被菊Chrysanthemum × morifolium ‘Bei Lin Qiu Yun’、单头切花菊C. morifolium ‘Sheng Xue’和传统大菊C. morifolium ‘Fen Shi Ba’进行叶绿体基因组测序、组装与注释，分析其基因组结构、简单重复序列、密码子偏好性、反向重复序列边界及共线性特征；从GenBank下载9个菊属植物叶绿体基因组序列（包括8个菊属物种和1个菊科外类群）开展系统发育分析。结果 3个品种叶绿体基因组均呈典型双链环状四分体结构，长度151 060‒151 073 bp，GC含量均为37.5%，均注释出131个基因（86个蛋白质编码基因、37个tRNA基因、8个rRNA基因）。全基因组比对显示基因组整体高度保守，IR区保守性高于单拷贝区，非编码区突变频率高于编码区，且无大片段基因重排。各样本边界分布基因类型一致。C. morifolium ‘Sheng Xue’与C. morifolium ‘Fen Shi Ba’各含68个SSR（simple sequence repeats），C. morifolium ‘Bei Lin Qiu Yun’含70个，均以A/T型单核苷酸重复为主，无六核苷酸重复。密码子偏好性较弱（CAI 0.168‒0.169，ENC 49.127‒49.420），偏好A/U结尾密码子，选择压力是影响密码子偏好性的关键因素。系统发育分析表明，C. morifolium ‘Sheng Xue’与C. morifolium ‘Fen Shi Ba’与菊花栽培种亲缘关系更近，C. morifolium ‘Bei Lin Qiu Yun’则与菊属野生种亲缘关系较近。结论 3个栽培类型菊花叶绿体基因组结构与基因组成保守；地被菊样本与野生种亲缘关系更近，切花菊和传统大菊样本则与栽培种亲缘关系更近。

关键词: 菊属, 菊花, 叶绿体基因组, 系统发育分析, 序列特征, 密码子偏好性, SSR

Abstract:

Objective To explore the chloroplast genome characteristics and phylogenetic relationships of Chrysanthemum cultivars of different cultivation types, providing a theoretical basis for research on the phylogeny, species identification and germplasm conservation of the genus Chrysanthemum. Method Chloroplast genome sequencing, assembly and annotation were performed on the groundcover Chrysanthemum × morifolium ‘Bei Lin Qiu Yun’, the single-headed cut flower C. morifolium ‘Sheng Xue’, and the traditional large-flowered C. morifolium ‘Fen Shi Ba’. Analysis of genomic structure, simple sequence repeats (SSRs), codon usage bias, inverted repeat (IR) boundary regions and collinearity characteristics was conducted. For phylogenetic analysis, nine chloroplast genome sequences, including eight from Chrysanthemum species and one outgroup from the Asteraceae family, were downloaded from GenBank. Result The chloroplast genomes of the three cultivars all exhibited a typical double-stranded circular quadripartite structure, ranging in length from 151 060 to 151 073 bp, with a GC content of 37.5%. A total of 131 genes were annotated in each genome, including 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Whole-genome alignment revealed high overall conservation of the chloroplast genomes: the IR regions showed higher conservation than the single-copy (SC) regions, and the non-coding regions had a higher mutation frequency than the coding regions, with no large-scale gene rearrangements detected. Boundary gene types were consistent across all samples. C. morifolium ‘Sheng Xue’ and C. morifolium ‘Fen Shi Ba’ each contained 68 SSRs, whereas C. morifolium ‘Bei Lin Qiu Yun’ contained 70 SSRs. Mononucleotide repeats (A/T-type) dominated the SSRs in all three cultivars, with no hexanucleotide repeats detected. Codon usage bias was weak (CAI: 0.168‒0.169; ENC: 49.127‒49.420), with a preference for A/U-ending codons. Selection pressure was identified as the key factor influencing codon usage bias. Phylogenetic analysis showed that C. morifolium ‘Sheng Xue’ and C. morifolium ‘Fen Shi Ba’ were closely related to cultivated C. morifolium, while C. morifolium ‘Bei Lin Qiu Yun’ was closely related to wild Chrysanthemum species. Conclusion The three Chrysanthemum cultivars of different cultivation types have a conserved chloroplast genomic structure and gene content. The groundcover C. morifolium is more closely related to wild species, whereas the traditional large-flowered C. morifolium and single-headed cut C. morifolium are more closely related to cultivated varieties.

Key words: Chrysanthemum, Chrysanthemum × morifolium, chloroplast genome, phylogenetic analysis, sequence characteristics, codon usage bias, SSR

刘柔知, 吴嘉琦, 吴辉烨, 袁婧怡, 程堂仁, 张启翔, 袁存权. 三种不同栽培类型菊花品种的叶绿体基因组特征对比分析[J]. 生物技术通报, 2026, 42(8): 239-250.

LIU Rou-zhi, WU Jia-qi, WU Hui-ye, YUAN Jing-yi, CHENG Tang-ren, ZHANG Qi-xiang, YUAN Cun-quan. Comparative Analysis of Chloroplast Genome Characteristics among Three Cultivated Types of Chrysanthemum Varieties[J]. Biotechnology Bulletin, 2026, 42(8): 239-250.

图/表 12

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功能 Functions	基因分组 Gene grouping	基因名 Gene name
自我复制 Self-replication	核糖体大亚基 Large ribosomal subunit	rpl32， rpl23（2）， rpl2（2）， rpl22， rpl16， rpl14， rpl36， rpl20， rpl33*
自我复制 Self-replication	核糖体小亚基 Small ribosomal subunit	rps15， rps12， rps12-5end， rps12-3end， rps7（2）， rps19， rps3， rps8， rps11， rps18， rps4， rps14， rps2， rps16*
	RNA聚合酶 RNA polymerase	rpoA， rpoC2， rpoC1， rpoB
	核糖体RNA Ribosomal RNA	rrn5（2）， rrn4.5（2）， rrn23（2）， rrn16（2）
	转运RNA Transfer RNA	trnL-UAG， trnN-GUU（2）， trnR-ACG（2）， trnA-UGC（2）， trnI-GAU（2）， trnI-CAU（2）， trnV-GAC（2）， trnL-CAA（2）， trnM-CAU（2）， trnP-UGG， trnW-CCA， trnV-UAC， trnF-GAA， trnL-UAA， trnT-UGU， trnS-GGA， trnG-GCC， trnS-UGA， trnT-GGU， trnG-UCC， trnR-UCU， trnE-UUC， trnY-GUA， trnD-GUC， trnC-GCA， trnS-GCU， trnQ-UUG， trnK-UUU， trnH-GUG
光合作用 Photosynthesis	光系统I基因 Photosystem I gene	psaC， psaJ， psaI， psaA， psaB
	光系统II基因 Photosystem II gene	psbH，，psbT， psbB， psbE， psbF， psbL， psbJ， psbZ， psbC， psbD， psbM， psbI， psbK， psbA
	NADH氧化还原酶 NADH dehydrogenase	ndhH， ndhA， ndhI， ndhG， ndhE， ndhD， ndhF， ndhB（2）， ndhC， ndhK， ndhJ*
	细胞色素复合物基因 Cytochrome complex gene	petB， petG， petL， petA， petN*
	ATP合酶 ATP synthase	atpB， atpE， atpA， atpF， atpH， atpI*
	Rubisco大亚基 Large subunit of Rubisco	rbcL
其他基因 Other gene	成熟酶 Maturase	matK
其他基因 Other gene	翻译起始因子 Translational initiation factor	infA
	蛋白酶 Protease	clpP1**
	被膜蛋白 Envelop membrane protein	cemA
	乙酰辅酶A亚基 Acetyl-CoA carboxylase subunit	accD
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
功能未知基因Genes of unknown function	保守的假定叶绿体开放阅读框ORF Conserved hypothetical chloroplast ORF	ycf1， φycf1， ycf15（2）， ycf2（2）， ycf3， ycf4

功能 Functions	基因分组 Gene grouping	基因名 Gene name
自我复制 Self-replication	核糖体大亚基 Large ribosomal subunit	rpl32， rpl23（2）， rpl2（2）， rpl22， rpl16， rpl14， rpl36， rpl20， rpl33*
自我复制 Self-replication	核糖体小亚基 Small ribosomal subunit	rps15， rps12， rps12-5end， rps12-3end， rps7（2）， rps19， rps3， rps8， rps11， rps18， rps4， rps14， rps2， rps16*
	RNA聚合酶 RNA polymerase	rpoA， rpoC2， rpoC1， rpoB
	核糖体RNA Ribosomal RNA	rrn5（2）， rrn4.5（2）， rrn23（2）， rrn16（2）
	转运RNA Transfer RNA	trnL-UAG， trnN-GUU（2）， trnR-ACG（2）， trnA-UGC（2）， trnI-GAU（2）， trnI-CAU（2）， trnV-GAC（2）， trnL-CAA（2）， trnM-CAU（2）， trnP-UGG， trnW-CCA， trnV-UAC， trnF-GAA， trnL-UAA， trnT-UGU， trnS-GGA， trnG-GCC， trnS-UGA， trnT-GGU， trnG-UCC， trnR-UCU， trnE-UUC， trnY-GUA， trnD-GUC， trnC-GCA， trnS-GCU， trnQ-UUG， trnK-UUU， trnH-GUG
光合作用 Photosynthesis	光系统I基因 Photosystem I gene	psaC， psaJ， psaI， psaA， psaB
	光系统II基因 Photosystem II gene	psbH，，psbT， psbB， psbE， psbF， psbL， psbJ， psbZ， psbC， psbD， psbM， psbI， psbK， psbA
	NADH氧化还原酶 NADH dehydrogenase	ndhH， ndhA， ndhI， ndhG， ndhE， ndhD， ndhF， ndhB（2）， ndhC， ndhK， ndhJ*
	细胞色素复合物基因 Cytochrome complex gene	petB， petG， petL， petA， petN*
	ATP合酶 ATP synthase	atpB， atpE， atpA， atpF， atpH， atpI*
	Rubisco大亚基 Large subunit of Rubisco	rbcL
其他基因 Other gene	成熟酶 Maturase	matK
其他基因 Other gene	翻译起始因子 Translational initiation factor	infA
	蛋白酶 Protease	clpP1**
	被膜蛋白 Envelop membrane protein	cemA
	乙酰辅酶A亚基 Acetyl-CoA carboxylase subunit	accD
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
功能未知基因Genes of unknown function	保守的假定叶绿体开放阅读框ORF Conserved hypothetical chloroplast ORF	ycf1， φycf1， ycf15（2）， ycf2（2）， ycf3， ycf4

品种名 Cultivar	密码子适应指数CAI	密码子偏性指数CBI	有效密码子数ENC	GC1 （%）	GC2 （%）	GC3 （%）
C. morifolium ‘Bei Lin Qiu Yun’	0.168	-0.107	49.127	45.95	38.05	29.08
C. morifolium ‘Sheng Xue’	0.169	-0.102	49.420	46.64	38.70	29.46
C. morifolium ‘Fen Shi Ba’	0.169	-0.103	49.407	46.89	38.88	29.44

品种名 Cultivar	密码子适应指数CAI	密码子偏性指数CBI	有效密码子数ENC	GC1 （%）	GC2 （%）	GC3 （%）
C. morifolium ‘Bei Lin Qiu Yun’	0.168	-0.107	49.127	45.95	38.05	29.08
C. morifolium ‘Sheng Xue’	0.169	-0.102	49.420	46.64	38.70	29.46
C. morifolium ‘Fen Shi Ba’	0.169	-0.103	49.407	46.89	38.88	29.44