青钱柳叶片叶绿体基因组结构特征与系统发育分析

doi:10.3969/j.issn.1004-1524.20250193

浙江农业学报 ›› 2026, Vol. 38 ›› Issue (2): 284-300.DOI: 10.3969/j.issn.1004-1524.20250193

青钱柳叶片叶绿体基因组结构特征与系统发育分析

尹明华¹^,²(), 康海燕¹, 钟可情¹, 吴利鹃³^,⁴, 胡烈新³^,⁴, 吴春发³^,⁴, 龚水飞³^,⁴

1.上饶师范学院生命科学学院, 江西上饶 334001
2.上饶市药食同源植物资源保护与利用重点实验室, 江西上饶 334001
3.江西琪格轩生态农业开发有限公司, 江西上饶 334699
4.上饶县琪轩种植专业合作社, 江西上饶 334699

收稿日期:2025-03-12 出版日期:2026-02-25 发布日期:2026-03-24
作者简介:尹明华,研究方向为药用植物生物技术。E-mail:yinminghua04@163.com
基金资助:
国家自然科学基金(31960079);国家自然科学基金(32060092);江西省现代农业产业技术体系建设专项(JXARS-13-赣东站)

Structural characterization and phylogenetic analysis of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja leaves

YIN Minghua¹^,²(), KANG Haiyan¹, ZHONG Keqing¹, WU Lijuan³^,⁴, HU Liexin³^,⁴, WU Chunfa³^,⁴, GONG Shuifei³^,⁴

1. College of Life Sciences, Shangrao Normal University, Shangrao 334001, Jiangxi, China
2. Shangrao Key Laboratory of Protection and Utilization of Medicinal and Edible Plant Resources, Shangrao 334001, Jiangxi, China
3. Jiangxi Qigexuan Ecological Agriculture Development Co., Ltd., Shangrao 334699, Jiangxi, China
4. Shangrao Qixuan Planting Professional Cooperative, Shangrao 334699, Jiangxi, China

Received:2025-03-12 Online:2026-02-25 Published:2026-03-24

摘要/Abstract

摘要：

为探究青钱柳[Cyclocarya paliurus(Batal.) Iljinskaja]叶绿体基因组的结构特征与系统进化关系,本研究以江西省上饶市广信区青钱柳叶片为材料,通过高通量测序获得其叶绿体基因组序列,利用生物信息学方法分析其序列特征、密码子使用偏好性与系统发育关系。结果显示,上饶市广信区青钱柳叶绿体基因组全长为160 992 bp,平均GC含量为37.48%;共注释到133个基因,包括88个蛋白质编码基因、37个tRNA基因和8个rRNA基因;鉴定到84个简单重复序列(SSR),以A/T重复为主;52个长重复序列,以正向重复和回文重复为主。与15个近缘种比较显示,青钱柳叶绿体基因组在LSC-IRB边界(JLB)、SSC-IRB边界(JSB)、SSC-IRA边界(JSA)和LSC-IRA边界(JLA)4个边界区域的基因类型与排列顺序基本一致,边界扩张与收缩程度差异不明显;在LSC和SSC共鉴定出10个高变异区域,分别为matK_rps16、rps16_trnQ-UUG、psbK_psbI、trnS-GCU_trnG-GCC、trnT-GGU_psbD、ndhC_trnV-UAC、trnV-UAC、rpl22、ycf1和rps15_ycf1。青钱柳叶绿体基因组密码子整体偏好性较弱,主要受自然选择影响;共鉴定出15个最优密码子:AAU、GAA、CAU、AAA、AUU、AUG、GGA、GGU、CCU、ACA、GUA、GUU、CGU、UUG和AGU,多数以U或A结尾。系统发育分析表明,上饶市广信区青钱柳与南京青钱柳二倍体(MW531677,Cyclocarya paliurus isolate 2nPA)聚为一支,亲缘关系较近。本研究结果可为青钱柳遗传多样性研究、分子育种和物种鉴定提供理论依据。

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

Abstract:

To investigate the structural characteristics and phylogenetic relationships of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja, this study used leaves of C. paliurus from Guangxin District, Shangrao City, Jiangxi Province as material. The complete chloroplast genome sequence was obtained through high-throughput sequencing, and its sequence characteristics, codon usage bias, and phylogenetic relationships were analyzed using bioinformatics methods. The results showed that the complete chloroplast genome of C. paliurus from Guangxin District, Shangrao City, was 160 992 bp in length, with an average GC content of 37.48%. A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes and 8 rRNA genes. 84 simple sequence repeats (SSR) were identified, predominantly consisting of A/T repeats, along with 52 long repeats, mainly forward repeats and palindromic repeats. Comparison with 15 related species revealed that the gene types and arrangement order in the four boundary regions [LSC-IRB(JLB), SSC-IRB(JSB), SSC-IRA(JSA) and LSC-IRA(JLA)] of the C. paliurus chloroplast genome were largely consistent, with no significant differences in the extent of boundary expansion or contraction. Ten highly variable regions were identified in the LSC and SSC: matK_rps16, rps16_trnQ-UUG, psbK_psbI, trnS-GCU_trnG-GCC, trnT-GGU_psbD, ndhC_trnV-UAC, trnV-UAC, rpl22, ycf1, and rps15_ycf1. The overall codon usage bias in the C. paliurus chloroplast genome was weak and primarily influenced by natural selection. 15 optimal codons were identified: AAU, GAA, CAU, AAA, AUU, AUG, GGA, GGU, CCU, ACA, GUA, GUU, CGU, UUG and AGU, most of which end with U or A. Phylogenetic analysis indicated that C. paliurus from Guangxin District, Shangrao City, clusters closely with the diploid C. paliurus from Nanjing (MW531677, Cyclocarya paliurus isolate 2nPA), showing a close genetic relationship. The findings of this study provided a theoretical basis for research on genetic diversity, molecular breeding, and species identification of C. paliurus.

Key words: Cyclocarya paliurus(Batal.) Iljinskaja, chloroplast genome, sequence characteristic, codon bias, phylogenetic analysis

中图分类号:

S792.99

尹明华, 康海燕, 钟可情, 吴利鹃, 胡烈新, 吴春发, 龚水飞. 青钱柳叶片叶绿体基因组结构特征与系统发育分析[J]. 浙江农业学报, 2026, 38(2): 284-300.

YIN Minghua, KANG Haiyan, ZHONG Keqing, WU Lijuan, HU Liexin, WU Chunfa, GONG Shuifei. Structural characterization and phylogenetic analysis of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja leaves[J]. Acta Agriculturae Zhejiangensis, 2026, 38(2): 284-300.

图/表 13

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基因功能 Gene function	基因类型 Gene type	基因名 Gene name	基因数量 Number of genes
光合作用	光系统Ⅰ Photosystem Ⅰ	psaA、psaB、psaC、psaI、psaJ	5
Photosynthesis	光系统Ⅱ Photosystem Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psaJ、psbK、psbL、psbM、psbT、psbZ、psbN(pbf1)	15
	NADH脱氢酶 NADH dehydrogenase	ndhA、ndhB^、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK*	12
	细胞色素b/f复合体 Cytochrome b/f complex	petA、petB、petD、petG、petL、petN	6
	ATP合成酶ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI	6
自我复制 Self replication	核糖体大亚基蛋白质 Ribosomal large subunit protein	rpl14、rpl16、rpl2^、rpl20、rpl22、rpl23^、rpl32、rpl33、rpl36	11
	核糖体小亚基蛋白质 Ribosomal small subunit protein	rps11、rps12^、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7^、rps8	14
	核糖体大亚基Ribosomal large subunit	rbcL	1
	RNA聚合酶RNA polymerase	rpoA、rpoB、rpoC1、rpoC2	4
	核糖体RNA Ribosomal RNA	rrn16^、rrn23^、rrn4.5^、rrn5^	8
	转运RNA transfer RNA	trnA-UGC^、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、trnfM-CAU、trnG-GCC、trnG-UCC、trnH-GUG、trnI-CAU^、trnI-GAU^、trnK-UUU、trnL-CAA^、trnL-UAA、trnL-UAG、trnM-CAU、trnN-GUU^、trnP-UGG、trnQ-UUG、trnR-ACG^、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、trnV-GAC^、trnV-UAC、trnW-CCA、trnY-GUA*	37
其他基因Other genes	成熟酶Mature enzyme	matK	1
	蛋白酶Protease	clpP1	1
	囊膜蛋白Envelope protein	cemA	1
	乙酰辅酶A羧化酶 Acetyl-CoA carboxylase	accD	1
	C-型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA	1
	翻译起始因子Translation initiation factor	infA	1
未知功能基因 Unknown genes	保守假设叶绿体阅读框架 Conservative assumption of chloroplast reading framework	ycf1^、ycf15^、ycf2^、ycf3(pafI)、ycf4(pafII*)	8

基因功能 Gene function	基因类型 Gene type	基因名 Gene name	基因数量 Number of genes
光合作用	光系统Ⅰ Photosystem Ⅰ	psaA、psaB、psaC、psaI、psaJ	5
Photosynthesis	光系统Ⅱ Photosystem Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psaJ、psbK、psbL、psbM、psbT、psbZ、psbN(pbf1)	15
	NADH脱氢酶 NADH dehydrogenase	ndhA、ndhB^、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK*	12
	细胞色素b/f复合体 Cytochrome b/f complex	petA、petB、petD、petG、petL、petN	6
	ATP合成酶ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI	6
自我复制 Self replication	核糖体大亚基蛋白质 Ribosomal large subunit protein	rpl14、rpl16、rpl2^、rpl20、rpl22、rpl23^、rpl32、rpl33、rpl36	11
	核糖体小亚基蛋白质 Ribosomal small subunit protein	rps11、rps12^、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7^、rps8	14
	核糖体大亚基Ribosomal large subunit	rbcL	1
	RNA聚合酶RNA polymerase	rpoA、rpoB、rpoC1、rpoC2	4
	核糖体RNA Ribosomal RNA	rrn16^、rrn23^、rrn4.5^、rrn5^	8
	转运RNA transfer RNA	trnA-UGC^、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、trnfM-CAU、trnG-GCC、trnG-UCC、trnH-GUG、trnI-CAU^、trnI-GAU^、trnK-UUU、trnL-CAA^、trnL-UAA、trnL-UAG、trnM-CAU、trnN-GUU^、trnP-UGG、trnQ-UUG、trnR-ACG^、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、trnV-GAC^、trnV-UAC、trnW-CCA、trnY-GUA*	37
其他基因Other genes	成熟酶Mature enzyme	matK	1
	蛋白酶Protease	clpP1	1
	囊膜蛋白Envelope protein	cemA	1
	乙酰辅酶A羧化酶 Acetyl-CoA carboxylase	accD	1
	C-型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA	1
	翻译起始因子Translation initiation factor	infA	1
未知功能基因 Unknown genes	保守假设叶绿体阅读框架 Conservative assumption of chloroplast reading framework	ycf1^、ycf15^、ycf2^、ycf3(pafI)、ycf4(pafII*)	8

密码子 Codon	氨基酸 Amino acid	相对同义密码子使用度 Relative synonymous codon usage	RSCU低表达 RSCU low expression	RSCU高表达 RSCU high expression	RSCU差值 RSCU difference
AAU	天冬酰胺Asn	1.535	1.375	1.500	0.125
GAA	谷氨酸Glu	1.508	1.556	1.714	0.159
CAU	组氨酸His	1.574	1.000	1.200	0.200
AAA	赖氨酸Lys	1.494	1.000	1.333	0.333
AUU	异亮氨酸Ile	1.461	1.200	1.800	0.600
AUG	蛋氨酸Met	2.981	1.000	1.556	0.556
GGA	甘氨酸Gly	1.634	1.647	1.846	0.199
GGU	甘氨酸Gly	1.333	0.706	0.923	0.217
CCU	脯氨酸Pro	1.502	1.143	1.500	0.357
ACA	苏氨酸Thr	1.213	1.091	1.500	0.409
GUA	缬氨酸Val	1.566	0.923	2.000	1.077
GUU	缬氨酸Val	1.445	1.154	1.333	0.179
CGU	精氨酸Arg	1.304	0.278	0.545	0.268
UUG	亮氨酸Leu	1.187	0.938	1.059	0.121
AGU	丝氨酸Ser	1.216	1.053	1.455	0.402

密码子 Codon	氨基酸 Amino acid	相对同义密码子使用度 Relative synonymous codon usage	RSCU低表达 RSCU low expression	RSCU高表达 RSCU high expression	RSCU差值 RSCU difference
AAU	天冬酰胺Asn	1.535	1.375	1.500	0.125
GAA	谷氨酸Glu	1.508	1.556	1.714	0.159
CAU	组氨酸His	1.574	1.000	1.200	0.200
AAA	赖氨酸Lys	1.494	1.000	1.333	0.333
AUU	异亮氨酸Ile	1.461	1.200	1.800	0.600
AUG	蛋氨酸Met	2.981	1.000	1.556	0.556
GGA	甘氨酸Gly	1.634	1.647	1.846	0.199
GGU	甘氨酸Gly	1.333	0.706	0.923	0.217
CCU	脯氨酸Pro	1.502	1.143	1.500	0.357
ACA	苏氨酸Thr	1.213	1.091	1.500	0.409
GUA	缬氨酸Val	1.566	0.923	2.000	1.077
GUU	缬氨酸Val	1.445	1.154	1.333	0.179
CGU	精氨酸Arg	1.304	0.278	0.545	0.268
UUG	亮氨酸Leu	1.187	0.938	1.059	0.121
AGU	丝氨酸Ser	1.216	1.053	1.455	0.402

青钱柳叶片叶绿体基因组结构特征与系统发育分析

Structural characterization and phylogenetic analysis of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja leaves

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重复单元碱基类型 Repetitive unit base type	重复单元重复次数Repetitive unit repetition times													总数 Total number
重复单元碱基类型 Repetitive unit base type	5	6	7	8	9	10	11	12	13	14	15	16	17	总数 Total number
A/T	0	0	0	0	0	27	20	13	5	6	0	1	1	73
C/G	0	0	0	0	0	2	0	0	0	0	0	0	0	2
AT/AT	0	2	4	2	0	0	0	0	0	0	0	0	0	8
AAT/ATT	1	0	0	0	0	0	0	0	0	0	0	0	0	1

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