食用百合叶绿体基因组的密码子使用偏性分析

doi:10.16178/j.issn.0528-9017.20240675

摘要/Abstract

摘要：

食用百合是原产于我国的具有重要经济、药用和观赏价值的多年生宿根草本植物,本文采用CodonW和SPSS等软件对不同食用百合品种的叶绿体基因组进行密码子使用偏性分析,并基于叶绿体基因组序列构建了系统发育树。结果表明,食用百合的叶绿体基因组密码子适应指数(codon adaptation index,CAI)为0.642~0.644,有效密码子数(effective number of codon,ENC)为55.185~55.529,叶绿体基因组密码子使用偏性较弱。密码子不同位置的GC含量分别为37.19%(第1位)、37.29%(第2位)和 36.56%(第3位)。利用ENC-plot、PR2-plot和中性绘图分析表明,选择压力是影响食用百合叶绿体基因组密码子使用偏性的重要因素。比较不同密码子碱基位置的影响,第3位碱基组成对密码子使用偏性存在显著(p<0.05)影响。通过最优密码子分析获得12个最优密码子。系统发育分析显示,百合属近缘种之间密码子使用特征相似,龙牙百合与兰州百合亲缘关系较近。而在叶绿体基因组假基因化方面,龙牙百合与卷丹更为相似,该研究为百合属植物系统进化、物种分类及叶绿体基因工程的相关研究提供了理论依据。

关键词: 食用百合, 叶绿体基因组, 密码子使用偏性, 系统发育分析

Abstract:

Edible lilies are perennial herbaceous plants with important economic, medicinal, and ornamental values originating from China. In this study, CodonW and SPSS software were used to perform codon usage bias analysis on the chloroplast genomes of different edible lily varieties, and a phylogenetic tree was constructed based on chloroplast genome sequences. The results showed that the codon adaptation index (CAI) of the chloroplast genome of edible lily ranged from 0.642 to 0.644, and the effective number of codons (ENC) ranged from 55.185 to 55.529. The codon usage bias of the chloroplast genome was relatively weak. The GC contents at different positions of codons were 37.19% (1st position), 37.29% (2nd position), and 36.56% (3rd position), respectively. Using ENC-plot, PR2-plot, and neutral plot analysis, it was found that selection pressure was an important factor affecting the codon usage bias in the chloroplast genome of edible lily. Comparing the effects of different base positions of codon, the composition of the third base has a significant (p<0.05) impact on codon usage bias. Twelve optimal codons were obtained through optimal codon analysis. Phylogenetic analysis showed that the codon usage characteristics of closely related species in the edible lily genus were similar, and the genetic relationship between Lilium brownii var. viridulum and Lilium davidii var. unicolor was relatively close. In terms of pseudogenomics of chloroplast genomes, the Lilium brownii var. viridulum was more similar to the Lilium lancifolium. This study provides a theoretical basis for the systematic evolution, species classification, and chloroplast genetic engineering of lily.

Key words: edible lily, chloroplast genome, codon usage bias, phylogenetic analysis

中图分类号:

S644.1

吴超, 彭娟, 蒋沅均, 付曼曼, 杜俊宇, 黎侠. 食用百合叶绿体基因组的密码子使用偏性分析[J]. 浙江农业科学, 2025, 66(12): 2965-2972.

WU Chao, PENG Juan, JIANG Yuanjun, FU Manman, DU Junyu, LI Xia. Analysis of codon usage bias in the chloroplast genome of edible lily[J]. Journal of Zhejiang Agricultural Sciences, 2025, 66(12): 2965-2972.

图/表 9

参考文献 18

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物种	登录号	ENC	GC₁/%	GC₂/%	GC₃/%	GC all/%	CAI
卷丹	NC_035589.1	55.529	37.17	36.82	37.09	37.03	0.644
龙牙百合	KX347245.1	55.185	37.20	37.52	36.30	37.01	0.642
兰州百合	MK954110.1	55.185	37.20	37.52	36.30	37.01	0.642
均值		55.300	37.19	37.29	36.56	37.02	0.643

物种	登录号	ENC	GC₁/%	GC₂/%	GC₃/%	GC all/%	CAI
卷丹	NC_035589.1	55.529	37.17	36.82	37.09	37.03	0.644
龙牙百合	KX347245.1	55.185	37.20	37.52	36.30	37.01	0.642
兰州百合	MK954110.1	55.185	37.20	37.52	36.30	37.01	0.642
均值		55.300	37.19	37.29	36.56	37.02	0.643

	GC₁	GC₂	GC₃	GC all	ENC
GC₁		0.457^**	0.306^*	0.847^**	0.129
GC₂	0.457^**		0.287^*	0.785^**	0.013
GC₃	0.306^*	0.287^*		0.603^**	0.294^*
GC all	0.847^**	0.785^**	0.603^**		0.167
ENC	0.13	0.013	0.294^*	0.167

	GC₁	GC₂	GC₃	GC all	ENC
GC₁		0.457^**	0.306^*	0.847^**	0.129
GC₂	0.457^**		0.287^*	0.785^**	0.013
GC₃	0.306^*	0.287^*		0.603^**	0.294^*
GC all	0.847^**	0.785^**	0.603^**		0.167
ENC	0.13	0.013	0.294^*	0.167

氨基酸	密码子	RSCU值	氨基酸	密码子	RSCU值
Ter	UAG	0.72	Asn	AAC	0.44
	UGA	0.76		AAU	1.57
	UAA	1.52	Pro	CCC	0.85
Ala	GCA	1.18		CCA	1.14
	GCG	0.43		CCU	1.59
	GCU	1.79		CCG	0.43
	GCC	0.60	Gln	CAG	0.50
Cys	UGC	0.48		CAA	1.50
	UGU	1.52	Arg	CGC	0.37
Asp	GAC	0.39		CGA	1.34
	GAU	1.61		CGU	1.39
Glu	GAG	0.49		AGG	0.54
	GAA	1.51		AGA	1.86
Phe	UUC	0.68		CGG	0.49
	UUU	1.32	Ser	UCU	1.67
Gly	GGC	0.47		UCA	1.26
	GGU	1.28		UCC	0.97
	GGG	0.68		AGC	0.28
	GGA	1.57		UCG	0.51
His	CAC	0.41		AGU	1.31
	CAU	1.59	Thr	ACC	0.71
Ile	AUC	0.56		ACG	0.42
	AUA	1.00		ACU	1.64
	AUU	1.44		ACA	1.22
Lys	AAA	1.51	Val	GUA	1.50
	AAG	0.83		GUU	1.50
Leu	UUA	2.02		GUG	0.53
	CUC	0.37		GUC	0.47
	UUG	1.16	Trp	UGG	1.00
	CUG	0.33	Tyr	UAU	1.65
	CUU	1.31		UAC	0.35
	CUA	0.80
Met	AUG	1.00