镰翅羊耳蒜叶绿体基因组密码子偏好性分析

刘江枫

doi:10.19303/j.issn.1008-0384.2021.06.002

镰翅羊耳蒜叶绿体基因组密码子偏好性分析

doi: 10.19303/j.issn.1008-0384.2021.06.002

刘江枫

福州市于山风景名胜公园管理处，福建　福州　350001

基金项目: 国家自然科学基金项目（31700618）；福建省自然科学基金项目（2016J01703）

详细信息

作者简介:
刘江枫（1977−），男，博士，高级工程师，研究方向：兰科植物保育与利用（E-mail：fengye1202@126.com）

中图分类号: S567.23+9
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出版历程
- 收稿日期: 2021-02-20
- 修回日期: 2021-04-22
- 网络出版日期: 2021-05-17
- 刊出日期: 2021-06-28

Codon Usage Bias of Chloroplast Genome in Liparis bootanensis

LIU Jiangfeng

Management Office of Yushan Scenic Park, Fuzhou, Fujian　350001, China

摘要

摘要: 目的分析镰翅羊耳蒜叶绿体基因组密码子偏好性，并探讨影响密码子偏好性形成的主要因素。方法从镰翅羊耳蒜叶绿体基因组中筛选出47条编码序列，通过CodonW和CUSP软件计算不同基因的GC含量，分析密码子使用模式。结果 GC3含量为27.99%，低于GC1（47.00%）和GC2（39.41%）；ENC取值范围为40.85～56.80，平均值为47.27；ENC与GC1、GC2之间均无显著相关，与GC3呈极显著正相关；GC12与GC3的相关性不显著，相关系数为0.05；47%基因的ENC比值频数分布在−0.05～0.05区间，53%基因的ENC比值频数分布在−0.05～0.05区间之外；碱基的使用频率为A＞T、G＞C；17个密码子被确定为最优密码子。结论镰翅羊耳蒜叶绿体基因组密码子对A或T碱基结尾有偏好性；密码子偏好性较弱；密码子偏好性主要受选择和突变作用共同影响，同时还受其他因素影响，是多因素综合影响的结果。
- 镰翅羊耳蒜 /
- 叶绿体基因组 /
- 密码子偏好性
Abstract: Objective The coden usage bias and its infulence factor in the chloroplast genome of Liparis bootanensis were analyzed in this study. Method CodonW and CUSP software were used to analyze the codon usage bias based on 47 codon DNA sequences of the chloroplast genome of L. bootanensis. Result The GC content in the 3^rd position of the codons was 27.99%, which was lower than those in the 1^st and the 2^nd. The effective number of codons ranged from 40.85 to 56.80, averaging 47.27. The ENC showed no significant correlation to GC1 and GC2 but a significant positive correlation to GC3. The correlation between GC12 and GC3 was not significant with a coefficient of 0.05. The frequency of ENC ratio of 47% genes was distributed between −0.05 and 0.05, while that of 53% genes outside -0.05 and 0.05 range. A PR2-plot analysis indicated the base usage frequencies to be A＞T and G＞C. There were 17 codons selected after screening. Conclusion The 3^rd position of codons was rich in A or T. The codon usage bias was weak, complex, and affected by mutation and selection besides other factors.
- Liparis bootanensis /
- chloroplast genome /
- codon usage bias

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图 1 中性绘图分析

Figure 1. Neutrality plot

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图 2 ENC-plot绘图分析

Figure 2. ENC-plot

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图 3 PR2-plot绘图分析

Figure 3. PR2 bias plot

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表 1 编码基因密码子不同位置GC含量

Table 1. GC content in various positions of codon in chloroplast gene

基因 Gene	GC1/%	GC2/%	GC3/%	GCall/%	ENC	基因 Gene	GC1/%	GC2/%	GC3/%	GCall/%	ENC
rps12	52.42	47.58	25.00	41.67	43.84	petA	53.89	35.51	26.17	38.53	48.43
psbA	49.44	43.22	32.20	41.62	43.05	rps18	37.25	45.1	30.39	37.58	43.24
atpA	54.72	40.35	23.43	39.50	43.05	rpl20	36.67	44.17	29.17	36.67	54.03
atpF	45.95	33.51	28.65	36.04	48.25	clpP	57.56	37.07	28.29	40.98	56.80
atpI	48.39	36.69	24.60	36.56	45.27	psbB	53.83	46.17	31.04	43.68	48.68
rps2	43.22	40.25	27.97	37.15	47.67	petB	47.69	41.2	30.09	39.66	43.21
rpoC2	45.91	37.29	27.30	36.83	48.68	petD	50.61	37.8	24.39	37.60	43.52
rpoC1	50.15	38.09	29.85	39.36	49.05	rpoA	45.00	34.71	26.47	35.39	48.64
rpoB	49.30	38.38	28.10	38.59	48.53	rps11	53.24	51.8	23.74	42.93	43.04
psbD	52.26	42.94	30.23	41.81	42.10	rps8	40.15	37.12	18.94	32.07	40.85
psbC	53.38	45.99	33.97	44.44	45.89	rpl14	53.66	35.77	27.64	39.02	43.44
rps14	43.56	46.53	27.72	39.27	41.37	rpl16	52.21	52.94	25.74	43.63	41.93
psaA	52.06	43.41	32.22	42.57	49.71	rps3	44.29	33.79	22.83	33.64	45.82
ycf3	47.34	39.05	24.85	37.08	53.43	rpl22	41.40	35.67	22.93	33.33	44.99
rps4	48.02	38.12	30.20	38.78	51.44	ycf2	42.53	35.21	37.34	38.36	53.23
ndhJ	47.17	37.74	30.82	38.57	53.38	ndhB	41.88	39.92	32.29	38.03	47.85
ndhK	41.53	42.80	30.08	38.14	50.43	rps7	53.85	46.15	23.72	41.24	47.64
ndhC	49.59	34.71	29.75	38.02	51.42	ccsA	34.37	38.08	29.10	33.85	47.69
atpE	50.37	42.22	28.15	40.25	44.72	ndhE	43.14	33.33	30.39	35.62	54.50
atpB	55.29	41.32	31.74	42.78	51.77	ndhG	40.11	36.16	25.42	33.9	45.14
rbcL	57.69	42.31	28.54	42.85	47.79	ndhA	42.03	37.09	20.05	33.06	42.54
accD	36.44	34.99	25.67	32.37	44.91	ndhH	48.22	35.79	27.66	37.23	47.50
ycf4	43.78	41.08	31.89	38.92	48.68	ycf1	35.72	26.67	25.69	29.36	46.69
cemA	41.74	26.52	33.04	33.77	47.70	平均值 AVG	47.00	39.41	27.99	38.13	47.27

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表 2 编码基因密码子参数的相关性

Table 2. Correlations among individual related parameters of genes

项目 Items	GC1	GC2	GC3	GCall	ENC	N
GC1	1.000
GC2	0.390**	1.000
GC3	0.047	0.035	1.000
GCall	0.802**	0.758**	0.396**	1.000
ENC	0.022	−0.277	0.455**	0.029
N	−0.126	−0.286	0.296*	−0.118	0.196	1.000
注：表示在0.05水平上显著相关；表示在0.01水平上极显著相关。 Note: means significant correlation at 0.05 level; ** means extremely significant correlation at 0.01 level.

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表 3 相对同义密码子使用度分析

Table 3. RSCU analysis on protein coding region

氨基酸Amino acid	密码子 Coden	数量 Number	RSCU	氨基酸 Amino acid	密码子 Coden	数量 Number	RSCU
Phe	UUU	649	1.37	Ser	UCU	410	1.71
Phe	UUC	359	0.63		UCC	231	0.98
Leu	UUA	584	2.09		UCA	283	1.25
	UUG	379	1.16		UCG	114	0.43
	CUU	384	1.31	Pro	CCU	287	1.47
	CUC	127	0.38		CCC	172	0.89
	CUA	259	0.74		CCA	206	1.15
	CUG	126	0.32		CCG	75	0.31
	AUU	770	1.48	Thr	ACU	379	1.69
Ile	AUC	312	0.57		ACC	154	0.68
	AUA	492	0.95		ACA	289	1.16
Met	AUG	432	1.00		ACG	103	0.47
Val	GUU	369	1.45	Ala	GCU	444	1.82
	GUC	119	0.39		GCC	133	0.59
	GUA	377	1.44		GCA	309	1.23
	GUG	165	0.73		GCG	93	0.36
Tyr	UAU	527	1.68	Cys	UGU	157	1.51
	UAC	130	0.32		UGC	53	0.36
Ter	UAA	22	1.40	Ter	UGA	11	0.70
	UAG	14	0.89	Trp	UGG	322	0.87
His	CAU	330	1.45	Arg	CGU	260	1.60
	CAC	97	0.47		CGC	63	0.37
Gln	CAA	528	1.59		CGA	246	1.31
	CAG	162	0.41		CGG	83	0.43
Asn	AAU	695	1.50		AGA	359	1.71
	AAC	190	0.45		AGG	116	0.59
Lys	AAA	772	1.50	Ser	AGU	292	1.31
	AAG	249	0.41		AGC	75	0.31
Asp	GAU	638	1.62	Gly	GGU	405	1.30
	GAC	131	0.38		GGC	122	0.41
Glu	GAA	822	1.52		GGA	499	1.68
	GAG	271	0.48		GGG	206	0.62
注：Phe：苯丙氨酸，Leu：亮氨酸，Ile：异亮氨酸，Met：蛋氨酸， Val：缬氨酸，Tyr：酪氨酸，His：组氨酸，Gln：谷氨酰胺， Asn：天冬酰胺，Lys：赖氨酸，Asp：天冬氨酸，Glu：谷氨酸，Ser：丝氨酸， Pro：脯氨酸，Thr：苏氨酸，Ala：丙氨酸，Cys：半胱氨酸，Trp：色氨酸，Arg：精氨酸，Gly：甘氨酸，Ter：终止密码子。表5同。 Note: Phe: phenylalanine; Leu: leucine; Ile: isoleucine; Met: methionine; Val: valine; Tyr: tyrosine; His: histidine; Gln: glutamine; Asn: asparagine; Lys: lysine; Asp: aspartic acid; Glu: glutamic acid; Ser: serine; Pro: proline; Thr: threonine; Ala: alanine; Cys: cysteine; Trp: tryptophane; Arg: argnine; Gly: glycine; Ter: termination codon. Same for Table 5.

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表 4 ENC比值频数分布

Table 4. Distribution of ENC ratios

组限 Class limits	组中值 Class mid value	组数 Frequency number	组频 Frequency
−0.25～−0.15	−0.20	1	0.02
−0.15～−0.05	−0.75	5	0.11
−0.05～0.05	0.00	22	0.47
0.05～0.15	0.10	19	0.40
合计 total		47	1.00

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表 5 最优密码子分析

Table 5. Analysis on preferred codon

氨基酸 Amino acid	密码子 Coden	高表达基因 High expressed gene		低表达基因 Low expressed gene		ΔRSCU	氨基酸 Amino acid	密码子 Coden	高表达基因 High expressed gene		低表达基因 Low expressed gene		ΔRSCU
氨基酸 Amino acid	密码子 Coden	数量 Number	RSCU	数量 Number	RSCU	ΔRSCU	氨基酸 Amino acid	密码子 Coden	数量 Number	RSCU	数量 Number	RSCU	ΔRSCU
Phe	UUU*	53	1.61	25	1.46	0.15	Ser	UCU***	28	1.86	11	1.15	0.71
	UUC	19	0.39	9	0.54	-0.15		UCC*	12	1.14	9	0.93	0.21
Leu	UUA	47	1.70	21	1.89	-0.19		UCA	16	1.07	14	1.55	−0.48
	UUG*	17	1.05	9	0.81	0.24		UCG	2	0.28	5	0.57	−0.29
	CUU*	26	1.76	18	1.48	0.28	Pro	CCU***	21	1.89	10	0.91	0.98
	CUC	6	0.43	5	0.37	0.06		CCC***	10	1.03	3	0.29	0.74
	CUA	24	0.84	10	0.90	−0.06		CCA	11	0.93	9	0.90	0.03
	CUG	8	0.22	7	0.56	−0.34		CCG	2	0.15	3	0.29	−0.14
Ile	AUU*	47	1.36	28	1.22	0.14	Thr	ACU*	23	1.53	13	1.36	0.17
	AUC	10	0.30	13	0.61	−0.31		ACC*	11	0.97	8	0.76	0.21
	AUA*	39	1.33	26	1.16	0.17		ACA*	18	1.37	9	1.14	0.23
Met	AUG	27	1.00	20	1.00	0.00		ACG	3	0.13	6	0.74	−0.61
Val	GUU***	27	2.19	17	1.55	0.64	Ala	GCU	37	1.69	27	2.08	−0.39
	GUC*	10	0.41	4	0.29	0.12		GCC	6	0.47	8	0.52	−0.05
	GUA	20	1.15	14	1.43	−0.28		GCA***	26	1.50	14	0.93	0.57
	GUG	4	0.24	5	0.73	−0.49		GCG	6	0.34	6	0.47	−0.13
Tyr	UAU*	31	1.88	30	1.67	0.21	Cys	UGU	10	1.73	5	1.73	0.00
	UAC	4	0.12	6	0.33	−0.21		UGC	2	0.27	2	0.27	0.00
Ter	UAA	3	1.80	3	1.80	0.00	Ter	UGA	1	0.60	1	0.60	0.00
	UAG	1	0.60	1	0.60	0.00	Trp	UGG	28	1.00	13	0.80	0.20
His	CAU	15	1.50	15	1.54	−0.04	Arg	CGU**	21	1.60	12	1.21	0.39
	CAC	2	0.50	5	0.46	0.04		CGC	3	0.26	3	0.36	−0.10
Gln	CAA	28	1.61	24	1.75	−0.14		CGA*	21	1.64	13	1.38	0.26
	CAG*	7	0.39	4	0.25	0.14		CGG	1	0.08	7	0.79	−0.71
Asn	AAU	27	1.50	33	1.82	−0.32		AGA**	22	1.83	15	1.50	0.33
	AAC**	10	0.50	4	0.18	0.32		AGG	7	0.60	8	0.76	−0.16
Lys	AAA	34	1.61	23	1.61	0.00	Ser	AGU**	17	1.37	12	1.21	0.16
	AAG	10	0.39	7	0.39	0.00		AGC	2	0.28	5	0.59	−0.16
Asp	GAU	18	0.97	31	1.92	−0.95	Gly	GGU***	35	1.31	7	0.68	0.63
	GAC*	8	0.24	2	0.08	0.16		GGC	13	0.44	8	0.60	−0.16
Glu	GAA***	44	1.76	32	1.03	0.73		GGA	29	1.73	18	1.92	−0.19
	GAG	6	1.03	15	0.97	0.06		GGG	11	0.52	5	0.79	−0.27
注:＿表示RSCU 值大于1 的密码子；表示△RSCU≥0.08；表示ΔRSCU≥0.3； *表示ΔRSCU≥0.5。 Note: Underlining indicates RSCU＞1; means △RSCU≥0.08; means △RSCU≥0.3; * means ΔRSCU≥0.5.

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