Analysis of codon usage bias in the chloroplast genome of edible lily

doi:10.16178/j.issn.0528-9017.20240675

Abstract

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

CLC Number:

S644.1

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.

Figures/Tables 9

References 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