Analysis on codon usage patterns of chloroplast genome of Lonicera japonica cv. Damaohua

doi:10.3969/j.issn.1004-1524.2023.04.09

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (4): 821-830.DOI: 10.3969/j.issn.1004-1524.2023.04.09

• Horticultural Science • Previous Articles Next Articles

Analysis on codon usage patterns of chloroplast genome of Lonicera japonica cv. Damaohua

ZHANG Jiaqiang¹(), LIU Huichun¹, WANG Jie², XU Wenting¹, ZHOU Jianghua¹, ZHU Kaiyuan¹^,^*()

1. Zhejiang Institute of Landscape Plants and Flowers, Hangzhou 311251, China
2. The Crop Technology Extension Center of Suichang County, Suichang 323300, Zhejiang, China

Received:2022-01-26 Online:2023-04-25 Published:2023-05-05

Abstract

Abstract:

By analyzing the codon usage bias of the chloroplast genome of Lonicera japonica cv. Damaohua, we explored the main factors affecting the formation of its codon bias, and provided references for the study of the phylogeny of Lonicera japonica and the evolution of codons in the chloroplast genome. The codon usage bias of 50 chloroplast protein-coding genes of Lonicera japonica cv. Damaohua were analyzed using the bioinformatics software. The GC content of the chloroplast genome of Lonicera japonica cv. Damaohua was 39.18%, the ENc value was 48.81, and the bias for codon usage was weak. The correlation coefficient of GC and GC1, GC2, GC3, GC3s, GC and CAI all reached significant or extremely significant levels. There were 30 codons with RSCU values greater than 1, of which, 28 condons ending with A and T. Comprehensive ENc-plot analysis, PR2-plot analysis, neutral plot analysis and correspondence analysis showed that during the formation of codon usage bias in the chloroplast genome of Lonicera japonica cv. Damaohua, selection pressure and mutations and other factors played an important role together. Based on the analysis of relative synonymous codon usage, 30 high-frequency codons and 5 optimal codons were determined, the optimal codons all ended with A or T. This study clarified that the codon usage bias of the chloroplast genome of Lonicera japonica cv. Damaohua was jointly affected by factors such as selection pressure and mutation, and screened out five optimal codons.

Key words: Lonicera japonica, codon usage pattern, chloroplast genome, optimal codon

CLC Number:

S567

ZHANG Jiaqiang, LIU Huichun, WANG Jie, XU Wenting, ZHOU Jianghua, ZHU Kaiyuan. Analysis on codon usage patterns of chloroplast genome of Lonicera japonica cv. Damaohua[J]. Acta Agriculturae Zhejiangensis, 2023, 35(4): 821-830.

Figures/Tables 8

References 40

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基因 Gene	GC1/ %	GC2/ %	GC3/ %	GC3s/ %	GC/ %	ENc	CAI	基因 Gene	GC1/ %	GC2/ %	GC3/ %	GC3s/ %	GC/ %	ENc	CAI
atpA	55.51	39.96	27.56	26.01	41.01	50.92	0.208	psbB	55.40	46.17	32.61	28.90	44.73	50.54	0.198
atpB	55.31	41.88	31.46	29.55	42.89	49.03	0.201	psbC	52.95	45.99	32.49	28.79	43.81	45.58	0.171
atpE	51.49	41.04	29.10	26.56	40.55	48.98	0.166	psbD	52.54	43.22	33.62	29.31	43.13	45.34	0.257
atpF	49.19	32.97	35.14	33.33	39.10	45.26	0.132	rbcL	57.98	43.07	33.40	31.00	44.82	50.43	0.265
atpI	49.19	38.31	27.02	24.37	38.17	48.65	0.170	rpl14	55.28	38.21	30.89	28.81	41.46	45.75	0.160
ccsA	34.06	38.44	25.00	20.86	32.50	49.21	0.126	rpl16	49.64	51.09	27.74	23.44	42.82	38.92	0.158
cemA	41.74	27.83	34.35	30.23	34.64	59.11	0.196	rpl20	40.31	44.96	29.46	26.83	38.24	46.78	0.115
clpP	54.38	37.33	36.87	33.98	42.86	55.47	0.181	rpl22	43.48	37.27	26.09	21.33	35.61	49.79	0.213
matK	42.18	32.87	30.69	28.78	35.25	48.92	0.164	rpl2	51.10	48.16	34.19	32.20	44.49	57.60	0.140
ndhA	44.51	38.19	22.80	19.77	35.16	44.75	0.132	rpoB	50.66	39.23	29.31	26.94	39.73	48.10	0.146
ndhB	41.68	38.36	30.92	26.92	36.99	47.30	0.160	rpoC1	51.32	38.68	28.97	26.82	39.66	50.80	0.153
ndhC	45.45	33.88	29.75	23.42	36.36	54.08	0.224	rpoC2	46.29	37.49	31.00	29.24	38.26	50.85	0.149
ndkD	42.80	37.60	28.40	23.99	36.27	47.25	0.131	rps11	53.24	56.83	28.06	25.37	46.04	56.15	0.141
ndhE	41.18	33.33	25.49	21.65	33.33	49.30	0.134	rps12	52.38	47.62	28.57	28.23	42.86	48.70	0.140
ndkF	37.53	35.81	24.27	19.94	32.54	44.55	0.142	rps14	43.56	47.52	37.62	36.08	42.90	38.38	0.124
ndhG	46.33	33.90	27.68	25.29	35.97	51.10	0.125	rps2	43.04	43.04	29.96	26.34	38.68	49.35	0.168
ndhH	51.02	35.53	29.70	24.59	38.75	51.45	0.159	rps3	44.93	30.84	24.23	20.83	33.33	48.85	0.155
ndkI	42.17	34.94	28.92	26.88	35.34	48.37	0.181	rps4	51.52	36.87	29.80	28.50	39.39	52.10	0.160
ndhJ	50.94	37.11	31.45	27.52	39.83	51.40	0.159	rps7	48.08	43.59	23.72	20.81	38.46	44.14	0.212
ndhK	45.13	43.36	29.20	25.93	39.23	52.65	0.167	rps8	40.88	41.61	25.55	23.48	36.01	41.16	0.100
petA	52.02	35.83	33.96	32.70	40.60	56.09	0.193	yef 1	38.80	31.60	28.49	25.66	32.96	48.98	0.158
petB	49.54	41.20	31.02	25.50	40.59	46.20	0.209	yef2	43.53	35.35	36.57	33.92	38.48	52.09	0.159
petD	50.29	40.57	24.57	21.08	38.48	39.19	0.161	ycf3	47.93	39.05	33.73	31.06	40.24	47.84	0.141
psaA	53.13	43.41	32.89	28.85	43.14	51.28	0.200	ycf4	42.16	43.24	32.43	29.55	39.28	51.44	0.169
psaB	48.84	42.99	32.24	27.66	41.36	48.45	0.186	平均值	47.66	39.82	30.05	26.96	39.18	48.81	0.169
psbA	50.56	43.50	33.62	29.31	42.56	41.96	0.285	Average

基因 Gene	GC1/ %	GC2/ %	GC3/ %	GC3s/ %	GC/ %	ENc	CAI	基因 Gene	GC1/ %	GC2/ %	GC3/ %	GC3s/ %	GC/ %	ENc	CAI
atpA	55.51	39.96	27.56	26.01	41.01	50.92	0.208	psbB	55.40	46.17	32.61	28.90	44.73	50.54	0.198
atpB	55.31	41.88	31.46	29.55	42.89	49.03	0.201	psbC	52.95	45.99	32.49	28.79	43.81	45.58	0.171
atpE	51.49	41.04	29.10	26.56	40.55	48.98	0.166	psbD	52.54	43.22	33.62	29.31	43.13	45.34	0.257
atpF	49.19	32.97	35.14	33.33	39.10	45.26	0.132	rbcL	57.98	43.07	33.40	31.00	44.82	50.43	0.265
atpI	49.19	38.31	27.02	24.37	38.17	48.65	0.170	rpl14	55.28	38.21	30.89	28.81	41.46	45.75	0.160
ccsA	34.06	38.44	25.00	20.86	32.50	49.21	0.126	rpl16	49.64	51.09	27.74	23.44	42.82	38.92	0.158
cemA	41.74	27.83	34.35	30.23	34.64	59.11	0.196	rpl20	40.31	44.96	29.46	26.83	38.24	46.78	0.115
clpP	54.38	37.33	36.87	33.98	42.86	55.47	0.181	rpl22	43.48	37.27	26.09	21.33	35.61	49.79	0.213
matK	42.18	32.87	30.69	28.78	35.25	48.92	0.164	rpl2	51.10	48.16	34.19	32.20	44.49	57.60	0.140
ndhA	44.51	38.19	22.80	19.77	35.16	44.75	0.132	rpoB	50.66	39.23	29.31	26.94	39.73	48.10	0.146
ndhB	41.68	38.36	30.92	26.92	36.99	47.30	0.160	rpoC1	51.32	38.68	28.97	26.82	39.66	50.80	0.153
ndhC	45.45	33.88	29.75	23.42	36.36	54.08	0.224	rpoC2	46.29	37.49	31.00	29.24	38.26	50.85	0.149
ndkD	42.80	37.60	28.40	23.99	36.27	47.25	0.131	rps11	53.24	56.83	28.06	25.37	46.04	56.15	0.141
ndhE	41.18	33.33	25.49	21.65	33.33	49.30	0.134	rps12	52.38	47.62	28.57	28.23	42.86	48.70	0.140
ndkF	37.53	35.81	24.27	19.94	32.54	44.55	0.142	rps14	43.56	47.52	37.62	36.08	42.90	38.38	0.124
ndhG	46.33	33.90	27.68	25.29	35.97	51.10	0.125	rps2	43.04	43.04	29.96	26.34	38.68	49.35	0.168
ndhH	51.02	35.53	29.70	24.59	38.75	51.45	0.159	rps3	44.93	30.84	24.23	20.83	33.33	48.85	0.155
ndkI	42.17	34.94	28.92	26.88	35.34	48.37	0.181	rps4	51.52	36.87	29.80	28.50	39.39	52.10	0.160
ndhJ	50.94	37.11	31.45	27.52	39.83	51.40	0.159	rps7	48.08	43.59	23.72	20.81	38.46	44.14	0.212
ndhK	45.13	43.36	29.20	25.93	39.23	52.65	0.167	rps8	40.88	41.61	25.55	23.48	36.01	41.16	0.100
petA	52.02	35.83	33.96	32.70	40.60	56.09	0.193	yef 1	38.80	31.60	28.49	25.66	32.96	48.98	0.158
petB	49.54	41.20	31.02	25.50	40.59	46.20	0.209	yef2	43.53	35.35	36.57	33.92	38.48	52.09	0.159
petD	50.29	40.57	24.57	21.08	38.48	39.19	0.161	ycf3	47.93	39.05	33.73	31.06	40.24	47.84	0.141
psaA	53.13	43.41	32.89	28.85	43.14	51.28	0.200	ycf4	42.16	43.24	32.43	29.55	39.28	51.44	0.169
psaB	48.84	42.99	32.24	27.66	41.36	48.45	0.186	平均值	47.66	39.82	30.05	26.96	39.18	48.81	0.169
psbA	50.56	43.50	33.62	29.31	42.56	41.96	0.285	Average

指标Index	GC1	GC2	GC3	GC3s	GC	ENc
GC2	0.385 1^**
GC3	0.336 5^*	0.094 2
GC3s	0.373 4^**	0.115	0.951 3^**
GC	0.826 7^**	0.747 1^**	0.559 1^**	0.572 3^**
ENc	0.134 8	-0.221	0.267 1	0.260 6	0.045 0
CAI	0.441 2^**	0.046 9	0.272 2	0.147 4	0.342 9^*	0.103 5

指标Index	GC1	GC2	GC3	GC3s	GC	ENc
GC2	0.385 1^**
GC3	0.336 5^*	0.094 2
GC3s	0.373 4^**	0.115	0.951 3^**
GC	0.826 7^**	0.747 1^**	0.559 1^**	0.572 3^**
ENc	0.134 8	-0.221	0.267 1	0.260 6	0.045 0
CAI	0.441 2^**	0.046 9	0.272 2	0.147 4	0.342 9^*	0.103 5

氨基酸 Amino acid	密码子 Codons	数目 Number	RSCU	氨基酸 Amino acid	密码子 Codons	数目 Number	RSCU
Phe	TTT	757	1.40	Ala	GCC	197	0.73
	TTC	399	0.60		GCA	329	1.12
Leu	TTA	663	1.81		GCG	135	0.48
	TTG	455	1.30	Tyr	TAT	599	1.56
	CTT	467	1.35		TAC	150	0.36
	CTC	157	0.43	His	CAT	380	1.50
	CTA	300	0.78		CAC	110	0.46
	CTG	131	0.33	Gln	CAA	557	1.58
Ile	ATT	798	1.46		CAG	181	0.42
	ATC	339	0.58	Asn	AAT	701	1.48
	ATA	544	0.96		AAC	221	0.48
Val	GTT	432	1.49	Lys	AAA	764	1.46
	GTC	140	0.46		AAG	282	0.50
	GTA	415	1.48	Asp	GAT	655	1.53
	GTG	171	0.57		GAC	166	0.47
Ser	TCT	442	1.70	Glu	GAA	767	1.50
	TCC	241	1.01		GAG	273	0.46
	TCA	285	1.17	Cys	TGT	150	1.41
	TCG	128	0.46		TGC	64	0.47
	AGT	300	1.32	Arg	CGT	263	1.62
	AGC	86	0.35		CGC	85	0.49
Pro	CCT	327	1.38		CGA	291	1.39
	CCC	171	0.71		CGG	91	0.43
	CCA	264	1.18		AGA	358	1.45
	CCG	127	0.57		AGG	136	0.62
Thr	ACT	413	1.61	Gly	GGT	473	1.35
	ACC	190	0.72		GGC	168	0.44
	ACA	308	1.18		GGA	539	1.49
	ACG	109	0.49		GGG	273	0.72
Ala	GCT	507	1.67	平均值Average		329	0.99

Analysis on codon usage patterns of chloroplast genome of Lonicera japonica cv. Damaohua

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氨基酸 Amino acid	密码子 Codon	高表达 High expression	低表达 Low expression	△RSCU	氨基酸 Amino acid	密码子 Codon	高表达 High expression	低表达 Low expression	△RSCU
Phe	TTT	1.276 0	1.372 0	-0.096 0	Ala	GCC	0.848 0	0.288 0	0.560 0
	TTC	0.724 0	0.628 0	0.096 0		GCA	1.498 0	1.624 0	-0.126 0
Leu	TTA	1.088 0	1.410 0	-0.322 0		GCG	0.576 0	0.640 0	-0.064 0
	TTG	1.410 0	1.418 0	-0.008 0	Tyr	TAT	1.184 0	1.754 0	-0.570 0
	CTT	1.404 0	2.082 0	-0.678 0		TAC	0.416 0	0.246 0	0.170 0
	CTC	0.990 0	0.000 0	0.990 0	His	CAT	1.510 0	1.460 0	0.050 0
	CTA	0.694 0	0.966 0	-0.272 0		CAC	0.490 0	0.540 0	-0.050 0
	CTG	0.410 0	0.124 0	0.286 0	Gln	CAA	1.574 0	1.634 0	-0.060 0
Ile	ATT	1.330 0	1.412 0	-0.082 0		CAG	0.426 0	0.366 0	0.060 0
	ATC	0.464 0	0.586 0	-0.122 0	Asn	AAT	1.308 0	1.262 0	0.046 0
	ATA	1.208 0	1.002 0	0.206 0		AAC	0.692 0	0.738 0	-0.046 0
Val	GTT	1.448 0	2.232 0	-0.784 0	Lys	AAA	1.210 0	1.286 0	-0.076 0
	GTC	0.546 0	0.106 0	0.440 0		AAG	0.790 0	0.314 0	0.476 0
	GTA	1.466 0	1.476 0	-0.010 0	Asp	GAT	1.450 0	0.846 0	0.604 0
	GTG	0.538 0	0.188 0	0.350 0		GAC	0.550 0	1.154 0	-0.604 0
Ser	TCT	1.860 0	1.606 0	0.254 0	Glu	GAA	1.098 0	1.652 0	-0.554 0
	TCC	0.904 0	1.682 0	-0.778 0		GAG	0.502 0	0.348 0	0.154 0
	TCA	1.008 0	0.764 0	0.244 0	Cys	TGT	1.466 0	2.000 0	-0.534 0
	TCG	0.316 0	0.722 0	-0.406 0		TGC	0.534 0	0.000 0	0.534 0
	AGT	1.434 0	0.896 0	0.538 0	Arg	CGT	1.918 0	2.098 0	-0.180 0
	AGC	0.476 0	0.328 0	0.148 0		CGC	0.936 0	0.302 0	0.634 0
Pro	CCT	1.368 0	1.766 0	-0.398 0		CGA	0.756 0	1.140 0	-0.384 0
	CCC	0.994 0	0.704 0	0.290 0		CGG	0.360 0	0.270 0	0.090 0
	CCA	0.968 0	0.766 0	0.202 0		AGA	1.152 0	1.662 0	-0.510 0
	CCG	0.672 0	0.762 0	-0.090 0		AGG	0.880 0	0.522 0	0.358 0
Thr	ACT	1.130 0	1.248 0	-0.118 0	Gly	GGT	1.314 0	1.920 0	-0.606 0
	ACC	0.938 0	0.890 0	0.048 0		GGC	0.612 0	0.394 0	0.218 0
	ACA	1.428 0	1.580 0	-0.152 0		GGA	1.566 0	1.208 0	0.358 0
	ACG	0.506 0	0.280 0	0.226 0		GGG	0.512 0	0.480 0	0.032 0
Ala	GCT	1.076 0	1.450 0	-0.374 0

[1]	HAN Lihong, TIAN Xuelian, LIU Chao, FU Xiaolin, WANG Yuanxian. Codon usage bias and its influencing factors in the whole genome of three truffles [J]. Acta Agriculturae Zhejiangensis, 2022, 34(7): 1439-1448.
[2]	LI Xilian， YANG Yuanjie， LI Qian， LIU Jindian，GU Zhimin* . Analysis on codon bias of functional gene of Astacidea [J]. , 2014, 26(4): 862-.