岗梅叶绿体基因组序列特征、密码子使用偏好性和系统发育分析

doi:10.11924/j.issn.1000-6850.casb2025-0638

中国农学通报 ›› 2026, Vol. 42 ›› Issue (8): 67-76.doi: 10.11924/j.issn.1000-6850.casb2025-0638

岗梅叶绿体基因组序列特征、密码子使用偏好性和系统发育分析

洪森荣¹^,²(), 张芝瑶¹, 闵凌瑞¹, 杜静怡¹, 阿迪莱·吾马尔¹, 何凌婷¹, 哈丽米兰·艾合买提¹, 吴利鹃³^,⁴, 胡烈新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:2025-07-28 修回日期:2025-12-11 出版日期:2026-04-25 发布日期:2026-04-23
作者简介:
洪森荣，男，1974年出生，教授，硕士，研究方向：药用植物生物技术研究。通信地址：334001 江西省上饶市信州区志敏大道401号上饶师范学院生命科学学院，Tel：0793-8153721，E-mail：864035356@qq.com。
基金资助:
江西省科技厅重点研发项目“三叶青种质资源离体保存及其核心种质筛选、脱毒和大棚基质栽培关键技术研究与示范”(20202BBG73010); 国家自然科学基金资助项目“江西铅山红芽芋超低温疗法脱毒抑制细胞凋亡抗早衰的机理研究”(32060092)

Sequence Characteristics, Codon Bias, and Phylogenetic Analysis of Chloroplast Genome of Ilex asprella (Hook.et Arn.) Champ. ex Benth

HONG Senrong¹^,²(), ZHANG Zhiyao¹, MIN Lingrui¹, DU Jingyi¹, ADILE Wumar¹, HE Lingting¹, HARIMILLAN Ahemaiti¹, WU Lijuan³^,⁴, HU Liexin³^,⁴

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

Received:2025-07-28 Revised:2025-12-11 Published:2026-04-25 Online:2026-04-23

摘要/Abstract

摘要：

针对岗梅分子生物学研究薄弱、叶绿体基因组进化与密码子偏好性机制不清的问题，为阐明岗梅叶绿体基因组序列特征、密码子使用模式及系统发育关系，以江西上饶广信区野生岗梅叶片为材料，采用DNBSEQ-T7测序技术对叶绿体基因组进行测序、组装、注释，联合生物信息学方法分析序列特征、重复序列、边界保守性、密码子偏好性及亲缘关系。结果表明：岗梅的叶绿体基因组大小为157871 bp，GC的平均含量为37.62%，具有1个LSC、1个SSC和2个IR的四分区环状结构；136个基因在岗梅的叶绿体基因组中被注释，其中包括CDS基因91个、tRNA基因37个、rRNA基因8个；共检测到56个SSR和43个Longrepeat，其中包括A/T单核苷酸重复53个、AT/AT二核苷酸重复2个、AAT/ATT三核苷酸重复1个、正向重复22个、回文重复21个；IR边界高度保守，基因位置和边界之间的差异较小，具有10个高变异区域(rps16_trnQ-UUG、trnS-UGA、trnS-UGA_lhbA、lhbA、ycf4_cemA、petD、rpl32_trnL-UAG、ndhD、ndhD_psaC、psaC)；密码子使用偏好性较弱，自然选择和内部突变压力是影响岗梅叶绿体基因组的密码子使用偏向性的主要因素和次要因素，鉴定出5个最优密码子（UAA、GUA、CGU、CUU、UCA），均以U或A结尾。系统发育显示岗梅与满树星Ilex aculeolata OP104164的亲缘关系较近。结论：岗梅叶绿体基因组结构保守、变异位点丰富、密码子偏好性弱，研究结果可为冬青属药用植物鉴定、遗传进化及分子标记开发提供理论基础。

关键词: 岗梅, 叶绿体基因组, 序列结构特征, 密码子使用偏好性, 系统进化

Abstract:

In order to understand the sequence characteristics, codon usage preferences, and phylogenetic relationships of the chloroplast genome of Ilex asprella (Hook.et Arn.) Champ.ex Benth, the leaves of wild Ilex asprella (Hook.et Arn.) Champ.ex Benth from Guangxin District, Shangrao were used as materials. The DNBSEQ-T7 BGI gene sequencer was used to sequence, assemble, annotate, and analyze the chloroplast genome of Ilex asprella (Hook.et Arn.) Champ.ex Benth, and bioinformatics analysis software was used to analyze its codon usage preferences and species relationships. The results showed that the chloroplast genome size of Ilex asprella was 157871 bp, with an average GC content of 37.62%. It had a four zone circular structure consisting of one LSC, one SSC, and two IRs. The chloroplast genome of Ilex asprella was annotated with a total of 136 genes, including 91 CDS genes, 37 tRNA genes, and 8 rRNA genes. A total of 56 SSRs (including only 53 A/T single nucleotide repeats, 2 AT/AT dinucleotide repeats, and 1 AAT/ATT trinucleotide repeat) and 43 Longrepeats (including only 22 forward repeats and 21 palindromic repeats) were detected in the chloroplast genome of Ilex asprella. The chloroplast genome boundaries of Ilex asprella were highly conserved, with small differences in gene location and boundaries, and 10 highly variable regions (rps16_trnQ-UUG, trnS-UGA, trnS-UGA_lhbA, lhbA, ycf4_cemA, petD, rpl32_trnL-UAG, ndhD, ndhD_psaC, psaC); The codon usage bias of the chloroplast genome in Ilex asprella was relatively weak, mainly influenced by natural selection, followed by internal mutation pressure. The chloroplast genes of Ilex asprella had five optimal codons (UAA, GUA, CGU, CUU, and UCA), all ending in U or A. The genetic relationship between Ilex asprella and Ilex asprella OP104164 was relatively close. A high-quality chloroplast genome of Ilex asprella (Hook.et Arn.) Champ. ex BenthWe had been successfully assembled, obtaining the sequence structure, sequence characteristics, and codon usage preference information of its chloroplast genome, which laying the foundation for the identification, evolution, and phylogenetic research of medicinal plants in the genus Ilex.

Key words: Ilex asprella (Hook.et Arn.) Champ.ex Benth, chloroplast genome, sequence structure characteristics, codon bias, phylogenetic evolution

中图分类号:

S793.9

洪森荣, 张芝瑶, 闵凌瑞, 杜静怡, 阿迪莱·吾马尔, 何凌婷, 哈丽米兰·艾合买提, 吴利鹃, 胡烈新. 岗梅叶绿体基因组序列特征、密码子使用偏好性和系统发育分析[J]. 中国农学通报, 2026, 42(8): 67-76.

HONG Senrong, ZHANG Zhiyao, MIN Lingrui, DU Jingyi, ADILE Wumar, HE Lingting, HARIMILLAN Ahemaiti, WU Lijuan, HU Liexin. Sequence Characteristics, Codon Bias, and Phylogenetic Analysis of Chloroplast Genome of Ilex asprella (Hook.et Arn.) Champ. ex Benth[J]. Chinese Agricultural Science Bulletin, 2026, 42(8): 67-76.

图/表 5

参考文献 36

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基因功能	基因类型	基因名	基因数量
光合作用	光系统Ⅰ	psaA、psaB、psaC、psaI、psaJ	5
	光系统Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbG、psbH、psbI、psaJ、psbK、psbL、psbM、psbT、psbZ、psbN(pbf1)	16
	NADH脱氢酶	ndhA、ndhB、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK*	12
	细胞色素b/f复合体	petA、petB、petD、petG、petL、petN	6
	ATP合成酶	atpA、atpB、atpE、atpF、atpH、atpI	6
自我复制	核糖体大亚基蛋白质	rpl14、rpl16、rpl2、rpl20、rpl22、rpl23*、rpl32、rpl33、rpl36*	11
	核糖体小亚基蛋白质	rps11、rps12、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7*、rps8*	14
	核糖体大亚基	rbcL	1
	RNA聚合酶	rpoA、rpoB、rpoC1、rpoC2	4
	核糖体	rrn16、rrn23*、rrn4.5*、rrn5**	8
	转运	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	成熟酶	matK	1
	蛋白酶	clpP1	1
	囊膜蛋白	cemA	1
	乙酰辅酶A羧化酶	accD	1
	c-型细胞色素合成基因	ccsA	1
	翻译起始因子	infA	1
未知功能基因	保守假设叶绿体阅读框架	ycf1、ycf15*、ycf2、ycf68、ycf3(pafI)、ycf4(pafII*)	10

基因功能	基因类型	基因名	基因数量
光合作用	光系统Ⅰ	psaA、psaB、psaC、psaI、psaJ	5
	光系统Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbG、psbH、psbI、psaJ、psbK、psbL、psbM、psbT、psbZ、psbN(pbf1)	16
	NADH脱氢酶	ndhA、ndhB、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK*	12
	细胞色素b/f复合体	petA、petB、petD、petG、petL、petN	6
	ATP合成酶	atpA、atpB、atpE、atpF、atpH、atpI	6
自我复制	核糖体大亚基蛋白质	rpl14、rpl16、rpl2、rpl20、rpl22、rpl23*、rpl32、rpl33、rpl36*	11
	核糖体小亚基蛋白质	rps11、rps12、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7*、rps8*	14
	核糖体大亚基	rbcL	1
	RNA聚合酶	rpoA、rpoB、rpoC1、rpoC2	4
	核糖体	rrn16、rrn23*、rrn4.5*、rrn5**	8
	转运	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	成熟酶	matK	1
	蛋白酶	clpP1	1
	囊膜蛋白	cemA	1
	乙酰辅酶A羧化酶	accD	1
	c-型细胞色素合成基因	ccsA	1
	翻译起始因子	infA	1
未知功能基因	保守假设叶绿体阅读框架	ycf1、ycf15*、ycf2、ycf68、ycf3(pafI)、ycf4(pafII*)	10

密码子	氨基酸	相对同义密码子使用度	RSCU低表达	RSCU高表达	RSCU差值
UAA	Ter	1.54945	1.000000	1.800000	0.800
GUA	Val	1.46402	1.234040	1.666670	0.433
CGU	Arg	1.28024	0.726115	0.857143	0.131
CUU	Leu	1.28587	1.209880	1.666670	0.457
UCA	Ser	1.22864	1.681320	2.000000	0.319

密码子	氨基酸	相对同义密码子使用度	RSCU低表达	RSCU高表达	RSCU差值
UAA	Ter	1.54945	1.000000	1.800000	0.800
GUA	Val	1.46402	1.234040	1.666670	0.433
CGU	Arg	1.28024	0.726115	0.857143	0.131
CUU	Leu	1.28587	1.209880	1.666670	0.457
UCA	Ser	1.22864	1.681320	2.000000	0.319

岗梅叶绿体基因组序列特征、密码子使用偏好性和系统发育分析

Sequence Characteristics, Codon Bias, and Phylogenetic Analysis of Chloroplast Genome of Ilex asprella (Hook.et Arn.) Champ. ex Benth

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