3个茶树品种WOX基因家族的进化及密码子偏好性比较

doi:10.12302/j.issn.1000-2006.202108049

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (2): 71-80.doi: 10.12302/j.issn.1000-2006.202108049

3个茶树品种WOX基因家族的进化及密码子偏好性比较

王占军¹^,²(), 吴子琦¹(), 王朝霞¹, 欧祖兰¹, 李杰¹, 蔡倩文¹, 徐忠东¹, 张照亮²^,^*()

1.合肥师范学院生命科学学院,安徽合肥 230601
2.安徽农业大学茶树生物学与资源利用国家重点实验室,安徽合肥 230036

收稿日期:2021-08-29 接受日期:2021-11-29 出版日期:2022-03-30 发布日期:2022-04-08
通讯作者: 张照亮
基金资助:
国家自然科学基金项目(32072624);安徽农业大学茶树生物学与资源利用国家重点实验室开放基金资助项目(SKLTOF20200129);安徽省高校优秀青年人才支持计划项目(gxyq2020040)

A comparative study of the evolution and codon usage bias in WOX gene family of three Camellia sinensis cultivars

WANG Zhanjun¹^,²(), WU Ziqi¹(), WANG Zhaoxia¹, OU Zulan¹, LI Jie¹, CAI Qianwen¹, XU Zhongdong¹, ZHANG Zhaoliang²^,^*()

1. College of Life Science, Hefei Normal University, Hefei 230601, China
2. State Key Laboratory of Camellia sinensis Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China

Received:2021-08-29 Accepted:2021-11-29 Online:2022-03-30 Published:2022-04-08
Contact: ZHANG Zhaoliang

摘要/Abstract

摘要：

【目的】WOX基因家族在模式植物组织培养中扮演着重要的分子调控角色。非模式植物WOX基因家族的系统发育和密码子使用偏好性研究有助于探索遗传进化规律和基因表达特征,进而为其转基因体系构建提供指导。【方法】利用生物信息学方法在3个茶树品种全基因组数据中鉴定WOX基因;通过ClustalX 2.1和MEGA X软件探索它们的进化规律。运用Perl语言、Codon W 1.4.2程序和SPSS 23.0等软件分析3个茶树品种WOX基因编码序列,探究它们的密码子使用偏好模式;基于ENc-GC_3s、PR2分析和中性分析结果解析影响密码子偏好的主要因素。【结果】共鉴定出42个WOX成员,其中‘云抗10号’(CSA)11个,‘舒茶早’(CSS)18个,‘云南野生古茶DASZ’(DASZ)13个,系统发育揭示3个茶树品种WOX基因在进化上存在较强的保守性。密码子偏好性分析揭示,3个茶树品种WOX基因密码子都偏好使用A/T和以A/T结尾;CSA和DASZ的WOX基因密码子使用模式相似,表明两者亲缘关系较近;以CSA和CSS作为转基因受体时,3个茶树品种WOX基因中个别密码子需优化;烟草是3个茶树品种WOX基因的最佳异源表达受体;ENc-GC_3s绘图、PR2分析和中性分析表明自然选择是影响3个茶树品种WOX基因密码子使用偏倚的主要因素。【结论】3个茶树品种WOX基因进化上较保守,密码子偏好使用A/T和以A/T结尾,且密码子偏好原因主要是自然选择;揭示出转茶树时密码子的优化信息和烟草为最佳异源表达受体的结果。

关键词: 茶树, WOX基因家族, 进化分析, 密码子偏好性, 转基因表达

Abstract:

【Objective】The WOX gene family plays an important molecular regulatory role in model plant tissue culture. Phylogeny studies and research on the codon usage bias in the WOX gene family in non-model plants are helpful for exploring genetic evolution and gene expression characteristics, which serve as a guideline for establishing a transgenic system.【Method】In this study, bioinformatics were used to identify the WOX genes among all coding sequences of three Camellia sinensis cultivars. The evolutionary patterns were analyzed using ClustalX 2.1 and MEGA X software. The codon usage index of the coding sequence of the WOX gene was analyzed, and the codon usage pattern and the source of codon variation were explored using Perl language, Codon W1.4.2, and SPSS 23.0. The main factors affecting codon usage bias were analyzed based on the results of ENc-GC_3s, a PR2-plot analysis, and a neutral analysis.【Result】A total of 42 WOX members were identified in this study, of which 11 were CSA, 18 were CSS and 13 were DASZ. The phylogenetic analysis revealed that the evolution of WOX genes of the three Camellia sinensis cultivars is highly conserved. The codon bias analysis revealed that the codons of WOX genes preferred to use A/T and end with A/T in the three Camellia sinensis cultivars; the codon usage patterns of WOX genes in CSA and DASZ are similar, indicating that they are closely related. When CSA and CSS are used as transgenic receptors, individual codons in WOX genes of three Camellia sinensis cultivars need to be optimized. Nicotiana tabacum is the best heterologous expression receptor for WOX genes of three Camellia sinensis cultivars. ENc-GC_3s mapping the PR2 analysis, and the neutrality analysis indicate that the natural selection is the main reason for the codon usage bias of WOX genes in the three Camellia sinensis cultivars.【Conclusion】This study showed that WOX genes of three Camellia sinensis cultivars are evolutionarily conserved, codons prefer to use A/T and end with A/T, and the codon usage bias is mainly due to the natural selection. The results reveal the optimization information of codons when transforming tea plants, and tobacco is the best heterologous expression receptor.

Key words: Camellia sinensis, WOX gene family, evolutionary analysis, codon usage bias, transgene expression

中图分类号:

Q786
S794.4

王占军,吴子琦,王朝霞,等. 3个茶树品种WOX基因家族的进化及密码子偏好性比较[J]. 南京林业大学学报（自然科学版）, 2022, 46(2): 71-80.

WANG Zhanjun, WU Ziqi, WANG Zhaoxia, OU Zulan, LI Jie, CAI Qianwen, XU Zhongdong, ZHANG Zhaoliang. A comparative study of the evolution and codon usage bias in WOX gene family of three Camellia sinensis cultivars[J].Journal of Nanjing Forestry University (Natural Science Edition), 2022, 46(2): 71-80.DOI: 10.12302/j.issn.1000-2006.202108049.

图/表 6

表1

3个茶树品种WOX基因家族信息"

基因名称 gene name	基因ID gene ID	氨基酸数量 amino acid quantity	等电点 isoelectric point	分子质量/ku molecular weight	不稳定系数 instability coefficient	脂溶性指数 aliphatic index	亲水性 hydrophilicity	亚细胞定位 subcellular localization
CsaWUS	CSA016122.1	292	5.91	32 238.09	78.16	43.42	-1.001	细胞核
CsaWOX1a	CSA009146.1	326	8.45	37 982.71	64.95	60.18	-0.913	细胞核
CsaWOX1b	CSA021658.1	125	9.26	14 771.54	72.38	66.96	-1.003	细胞核
CsaWOX1c	CSA017712.1	197	9.94	22 734.74	64.44	60.00	-1.076	细胞核
CsaWOX3	CSA034617.1	195	8.77	22 724.70	63.00	52.00	-0.835	细胞核
CsaWOX4	CSA021808.1	231	9.30	26 338.67	58.94	61.21	-0.905	细胞核
CsaWOX5	CSA035970.1	289	9.01	32 485.00	55.84	77.27	-0.522	细胞核
CsaWOX8a	CSA024131.1	285	5.54	32 067.08	56.18	68.07	-0.698	细胞核
CsaWOX8b	CSA032010.1	296	6.06	33 503.17	58.29	53.34	-0.963	细胞核
CsaWOX9	CSA016734.1	287	9.10	31 373.27	52.17	55.71	-0.574	细胞核
CsaWOX11	CSA027532.1	275	5.63	29 686.28	67.31	72.62	-0.286	细胞核
CssWUS	TEA008786.1	297	6.00	32 659.55	79.08	44.34	-0.986	细胞核
CssWOX1a	TEA025042.1	271	7.71	31 693.58	66.28	61.22	-0.913	细胞核
CssWOX1b	TEA006406.1	361	6.47	40 838.38	57.69	60.30	-0.804	细胞核
CssWOX2a	TEA014651.1	220	5.41	23 858.01	51.73	57.68	-0.771	细胞核
CssWOX2b	TEA032867.1	256	6.22	27 928.90	59.25	59.06	-0.702	细胞核
CssWOX3a	TEA018015.1	172	9.27	19 461.41	69.67	63.49	-0.553	细胞核
CssWOX3b	TEA012714.1	195	8.77	22 724.70	63.00	52.00	-0.835	细胞核
CssWOX4a	TEA029435.1	214	8.96	24 865.11	48.74	59.25	-1.007	细胞核
CssWOX4b	TEA022717.1	231	9.30	26 334.68	58.61	61.21	-0.910	细胞核
CssWOX4c	TEA007699.1	316	8.96	36 018.54	60.02	59.91	-0.736	细胞核
CssWOX8a	TEA027235.1	288	5.53	32 224.21	56.12	67.36	-0.695	细胞核
CssWOX8b	TEA017348.1	288	6.06	32 745.31	57.53	53.47	-0.984	细胞核
CssWOX9a	TEA033789.1	279	8.85	31 274.79	61.41	55.91	-0.834	细胞核
CssWOX9b	TEA029851.1	459	8.93	49 770.50	74.52	56.91	-0.550	细胞核
CssWOX11	TEA027449.1	212	5.09	22 791.41	79.30	67.12	-0.395	细胞核
CssWOX13a	TEA021703.1	410	6.84	46 513.77	50.56	76.49	-0.594	细胞核
CssWOX13b	TEA020072.1	706	7.84	81 150.51	49.65	80.88	-0.630	细胞核
CssWOX13c	TEA007801.1	287	7.72	32 557.99	58.76	74.36	-0.630	细胞核
DaszWOX1a	GWHPABKB016733	326	8.45	38 010.72	65.95	60.18	-0.915	细胞核
DaszWOX1b	GWHPABKB013155	916	6.51	102 942.02	48.18	76.12	-0.433	细胞核
DaszWOX2a	GWHPABKB014366	118	9.72	13 333.89	62.71	54.58	-0.840	细胞核
DaszWOX2b	GWHPABKB001060	254	6.53	27 823.75	59.93	59.53	-0.731	细胞核
DaszWOX4a	GWHPABKB015660	226	9.10	26 222.65	52.45	60.00	-0.977	细胞核
DaszWOX4b	GWHPABKB020125	234	9.30	26 676.05	57.99	61.67	-0.909	细胞核
DaszWOX5	GWHPABKB000744	157	9.62	17 769.22	53.75	75.03	-0.569	细胞核
DaszWOX8a	GWHPABKB020522	286	5.54	32 080.10	57.59	67.83	-0.698	细胞核
DaszWOX8b	GWHPABKB001976	287	6.07	32 259.75	61.39	53.66	-0.959	细胞核
DaszWOX9	GWHPABKB030319	354	8.63	38 729.50	49.81	59.18	-0.459	细胞核
DaszWOX11	GWHPABKB008034	197	5.25	21 261.58	82.03	63.35	-0.488	细胞核
DaszWOX13a	GWHPABKB017606	252	7.05	28 500.77	59.30	61.11	-0.928	细胞核
DaszWOX13b	GWHPABKB010750	183	9.10	20 592.04	61.42	56.50	-0.949	细胞核

表1

图1

表2

表3

3个茶树品种WOX基因密码子的URSCU和fRFSC"

氨基酸 amino acid	密码子 codon	U_RSCU			f_RFSC			氨基酸 amino acid	密码子 codon	U_RSCU			f_RFSC
氨基酸 amino acid	密码子 codon	CSA	CSS	DASZ	CSA	CSS	DASZ	氨基酸 amino acid	密码子 codon	CSA	CSS	DASZ	CSA	CSS	DASZ
Phe	TTT	1.09	0.98	1.09	54.26	49.21	54.35	Ala	GCA	1.47	1.35	1.15	36.84	33.86	28.78
	TTC	0.91	1.02	0.91	45.74	50.79	45.65		GCG	0.18	0.29	0.43	4.51	7.17	10.73
Leu	TTA	0.78	0.70	0.84	13.07	11.60	13.95	Tyr	TAT	1.10	1.03	1.20	54.93	51.75	59.77
	TTG	1.53	1.59	1.60	25.57	26.52	26.75		TAC	0.90	0.97	0.80	45.07	48.25	40.23
	CTT	1.43	1.39	1.42	23.86	23.20	23.64		TAA	1.36	1.50	1.15	45.46	50.00	38.46
	CTC	1.16	1.23	1.21	19.32	20.44	20.16	TER	TAG	0.55	0.33	0.00	18.18	11.11	0.00
	CTA	0.48	0.55	0.47	7.95	9.12	7.75		TGA	1.09	1.17	1.85	36.36	38.89	61.54
	CTG	0.61	0.55	0.47	10.23	9.12	7.75	His	CAT	0.99	0.77	1.04	49.44	38.73	52.07
	ATT	1.18	1.22	1.37	39.39	40.66	45.61		CAC	1.01	1.23	0.96	50.56	61.27	47.93
Ile	ATC	0.93	0.98	0.98	31.06	32.60	32.75	Gln	CAA	1.15	1.20	1.21	57.50	60.12	60.32
	ATA	0.89	0.80	0.65	29.55	26.74	21.64		CAG	0.85	0.80	0.79	42.50	39.88	39.68
Met	ATG	1.00	1.00	1.00	100.00	100.00	100.00	Asn	AAT	1.10	1.06	1.18	55.13	52.94	59.19
Val	GTT	1.64	1.24	1.53	40.94	30.98	38.26		AAC	0.90	0.94	0.82	44.87	47.06	40.81
	GTC	0.54	0.74	0.51	13.39	18.43	12.76	Lys	AAA	0.78	0.71	0.67	38.96	35.42	33.50
	GTA	0.57	0.45	0.51	14.17	11.37	12.76		AAG	1.22	1.29	1.33	61.04	64.58	66.50
	GTG	1.26	1.57	1.45	31.50	39.22	36.22	Asp	GAT	0.98	1.11	1.21	49.02	55.61	60.54
Ser	TCT	1.40	1.45	1.59	23.31	24.09	26.59		GAC	1.02	0.89	0.79	50.98	44.39	39.46
	TCC	0.77	1.01	0.76	12.90	16.85	12.60	Glu	GAA	1.14	1.13	1.03	56.78	56.43	51.70
	TCA	1.33	1.11	1.38	22.22	18.48	23.01		GAG	0.86	0.87	0.97	43.22	43.57	48.30
	TCG	0.41	0.46	0.43	6.81	7.61	7.12	Cys	TGT	0.89	1.03	1.08	44.68	51.65	54.17
	AGT	1.18	1.03	1.04	19.71	17.21	17.26		TGC	1.11	0.97	0.92	55.32	48.35	45.83
	AGC	0.90	0.95	0.81	15.05	15.76	13.42	Trp	TGG	1.00	1.00	1.00	100.00	100.00	100.00
Pro	CCT	1.05	1.26	1.33	26.35	31.40	33.18	Arg	CGT	0.78	0.83	0.89	13.02	13.85	14.85
	CCC	0.77	0.69	0.73	19.16	17.36	18.18		CGC	0.85	0.85	0.71	14.20	14.19	11.79
	CCA	1.75	1.62	1.47	43.71	40.50	36.82		CGA	0.43	0.45	0.52	7.10	7.43	8.73
	CCG	0.43	0.43	0.47	10.78	10.74	11.82		CGG	0.43	0.41	0.71	7.10	6.76	11.79
Thr	ACT	1.47	1.47	1.66	36.69	36.87	41.49		AGA	1.74	1.78	1.60	28.99	29.73	26.64
	ACC	0.90	1.02	0.94	22.49	25.42	23.58		AGG	1.78	1.68	1.57	29.59	28.04	26.20
	ACA	1.30	1.21	1.05	32.54	30.17	26.20	Gly	GGT	1.14	1.17	1.26	28.43	29.14	31.52
	ACG	0.33	0.30	0.35	8.28	7.54	8.73		GGC	0.93	0.99	1.00	23.35	24.86	24.90
Ala	GCT	1.47	1.48	1.64	36.85	37.06	40.98		GGA	1.18	1.13	0.95	29.44	28.29	23.74
	GCC	0.87	0.88	0.78	21.80	21.91	19.51		GGG	0.75	0.71	0.79	18.78	17.71	19.84

表3

表4

3个茶树品种WOX基因与6种植物的密码子使用频率比较"

氨基酸 amino acid	密码子 codon	CsaWOX						CssWOX						DaszWOX
氨基酸 amino acid	密码子 codon	CSA	CSS	A	N	P	O	CSA	CSS	A	N	P	O	CSA	CSS	A	N	P	O
Phe	TTT	0.95	1.03	0.83	0.72	0.70	1.39	0.87	0.93	0.79	0.68	0.66	1.31	0.96	1.03	0.90	0.79	0.76	1.51
	TTC	1.06	0.97	0.74	0.85	0.87	0.68	1.18	1.08	0.86	0.98	1.01	0.79	1.06	0.97	0.80	0.92	0.95	0.74
Leu	TTA	1.06	1.07	0.64	0.61	0.55	1.34	0.94	0.95	0.60	0.57	0.51	1.26	1.14	1.14	0.75	0.71	0.64	1.55
	TTG	0.96	0.98	0.77	0.72	0.63	1.09	1.00	1.02	0.84	0.79	0.68	1.19	1.00	1.03	0.87	0.81	0.71	1.23
	CTT	1.04	1.22	0.62	0.62	0.52	0.98	1.01	1.18	0.64	0.64	0.53	1.01	1.03	1.20	0.67	0.67	0.55	1.06
	CTC	1.28	1.22	0.75	0.98	0.86	0.47	1.35	1.29	0.84	1.10	0.96	0.52	1.33	1.27	0.85	1.11	0.97	0.53
	CTA	0.77	0.75	0.50	0.53	0.41	0.65	0.88	0.86	0.61	0.64	0.50	0.78	0.75	0.73	0.53	0.56	0.43	0.68
	CTG	0.81	0.83	0.65	0.63	0.44	0.31	0.72	0.74	0.61	0.59	0.41	0.29	0.61	0.63	0.54	0.52	0.36	0.25
	ATT	0.83	0.92	0.86	0.67	0.63	1.30	0.85	0.95	0.94	0.73	0.69	1.43	0.96	1.07	0.95	0.74	0.70	1.44
Ile	ATC	1.12	0.96	0.79	1.05	0.96	0.75	1.17	1.01	0.88	1.17	1.07	0.84	1.18	1.01	0.80	1.06	0.97	0.76
	ATA	1.21	1.18	1.10	0.99	0.93	1.58	1.09	1.07	1.06	0.95	0.89	1.51	0.88	0.87	0.77	0.69	0.65	1.11
Met	ATG	1.00	1.00	1.32	1.30	1.38	1.36	1.00	1.00	1.09	1.07	1.14	1.13	1.00	1.00	1.11	1.08	1.15	1.14
Val	GTT	1.07	1.19	0.68	0.69	0.76	1.19	0.81	0.90	0.53	0.54	0.60	0.93	1.00	1.11	0.73	0.74	0.81	1.27
	GTC	0.76	0.70	0.47	0.55	0.54	0.30	1.05	0.96	0.67	0.77	0.76	0.43	0.73	0.66	0.51	0.59	0.58	0.33
	GTA	0.92	0.87	0.65	0.56	0.63	0.94	0.74	0.70	0.53	0.46	0.52	0.78	0.83	0.78	0.66	0.58	0.64	0.97
	GTG	1.09	1.05	0.82	0.85	0.84	0.59	1.36	1.31	1.05	1.09	1.08	0.75	1.26	1.21	1.07	1.12	1.10	0.77
Ser	TCT	0.94	1.10	0.92	1.16	1.13	1.82	0.97	1.13	0.96	1.21	1.18	1.91	1.07	1.25	1.01	1.28	1.24	2.01
	TCC	0.93	0.85	1.14	1.26	1.49	0.79	1.22	1.10	1.52	1.66	1.97	1.04	0.91	0.83	1.08	1.19	1.41	0.74
	TCA	0.99	0.98	1.21	1.25	1.12	1.78	0.82	0.82	1.02	1.06	0.94	1.50	1.03	1.02	1.21	1.25	1.12	1.78
	TCG	0.78	0.72	0.73	1.28	1.35	0.55	0.87	0.80	0.82	1.45	1.53	0.62	0.82	0.75	0.74	1.29	1.37	0.56
	AGT	1.17	1.23	1.40	1.47	1.30	2.22	1.02	1.08	1.24	1.30	1.15	1.97	1.02	1.08	1.18	1.25	1.10	1.88
	AGC	1.14	0.98	1.32	1.50	1.32	0.93	1.19	1.02	1.40	1.59	1.40	0.99	1.01	0.87	1.14	1.29	1.14	0.81
Pro	CCT	0.76	0.91	0.84	0.84	0.98	1.15	0.91	1.09	1.11	1.11	1.30	1.53	0.96	1.15	1.03	1.03	1.20	1.41
	CCC	1.13	0.97	2.15	1.73	2.19	0.94	1.02	0.88	2.17	1.74	2.21	0.95	1.07	0.92	1.98	1.59	2.02	0.87
	CCA	1.21	1.19	1.61	1.31	1.56	1.83	1.12	1.10	1.67	1.35	1.61	1.89	1.02	1.00	1.32	1.08	1.28	1.50
	CCG	0.87	0.74	0.75	1.28	1.60	0.36	0.87	0.74	0.83	1.42	1.78	0.40	0.95	0.81	0.79	1.37	1.71	0.38
Thr	ACT	1.07	1.26	1.26	1.09	1.53	2.08	1.07	1.27	1.38	1.19	1.67	2.27	1.20	1.42	1.43	1.23	1.73	2.36
	ACC	1.00	0.93	1.31	1.39	1.63	0.91	1.13	1.06	1.61	1.71	2.00	1.11	1.04	0.98	1.38	1.46	1.71	0.95
	ACA	0.99	0.93	1.25	1.13	1.28	1.69	0.92	0.86	1.26	1.13	1.29	1.70	0.80	0.75	1.00	0.91	1.03	1.36
	ACG	0.82	0.70	0.65	1.11	1.13	0.44	0.75	0.64	0.64	1.09	1.12	0.43	0.87	0.74	0.68	1.17	1.20	0.46
Ala	GCT	0.96	1.10	0.62	0.56	0.79	0.89	0.97	1.10	0.60	0.54	0.77	0.87	1.07	1.22	0.78	0.71	1.00	1.13
	GCC	1.11	1.01	1.00	0.83	1.05	0.34	1.12	1.02	0.97	0.80	1.02	0.33	0.99	0.91	1.02	0.84	1.07	0.34
	GCA	1.13	1.09	1.00	0.76	0.87	1.01	1.04	1.00	0.89	0.67	0.77	0.90	0.88	0.85	0.89	0.67	0.77	0.90
	GCG	0.48	0.41	0.24	0.37	0.58	0.08	0.76	0.64	0.36	0.57	0.89	0.12	1.13	0.96	0.64	1.00	1.56	0.22
Tyr	TAT	0.94	0.95	0.95	0.78	0.85	1.39	0.88	0.90	0.92	0.76	0.83	1.35	1.02	1.04	0.94	0.77	0.84	1.37
	TAC	1.09	1.06	0.83	0.84	1.20	0.75	1.16	1.14	0.92	0.93	1.33	0.83	0.97	0.95	0.67	0.68	0.97	0.61
	TAA	1.68	1.84	1.98	1.62	4.45	2.54	1.85	2.02	1.82	1.49	4.11	2.35	1.42	1.55	1.46	1.20	3.29	1.88
TER	TAG	0.82	0.86	1.42	1.42	1.78	0.89	0.50	0.53	0.73	0.73	0.91	0.46	0.00	0.00	0.00	0.00	0.00	0.00
	TGA	0.72	0.67	1.19	1.42	2.03	1.19	0.77	0.72	1.06	1.28	1.82	1.06	1.21	1.14	1.75	2.10	3.01	1.75
His	CAT	0.80	0.83	1.14	1.17	0.99	1.39	0.63	0.65	0.89	0.91	0.77	1.08	0.84	0.88	1.20	1.24	1.04	1.47
	CAC	1.33	1.24	1.84	1.84	1.93	1.16	1.61	1.50	2.22	2.22	2.33	1.40	1.26	1.18	1.75	1.75	1.84	1.11
Gln	CAA	1.00	0.94	2.11	1.98	1.96	3.03	1.04	0.98	1.93	1.81	1.79	2.77	1.05	0.99	2.02	1.89	1.87	2.90
	CAG	1.00	1.10	1.99	2.02	1.72	1.45	0.94	1.03	1.63	1.65	1.41	1.19	0.94	1.02	1.70	1.72	1.46	1.24
Asn	AAT	0.90	0.95	1.37	1.09	1.11	2.03	0.86	0.91	1.33	1.06	1.07	1.96	0.97	1.02	1.56	1.24	1.25	2.30
Asn	AAC	1.16	1.07	1.19	1.39	1.60	1.35	1.22	1.12	1.26	1.47	1.68	1.42	1.06	0.97	1.14	1.34	1.53	1.29
Lys	AAA	0.82	0.77	0.69	0.66	0.63	1.33	0.74	0.70	0.67	0.63	0.60	1.29	0.70	0.66	0.56	0.53	0.51	1.08
	AAG	1.17	1.24	1.02	1.00	1.03	1.04	1.24	1.31	1.15	1.12	1.16	1.16	1.27	1.35	1.05	1.03	1.06	1.07
Asp	GAT	0.72	0.75	0.49	0.48	0.43	0.70	0.82	0.85	0.62	0.61	0.54	0.89	0.89	0.92	0.64	0.63	0.56	0.93
	GAC	1.60	1.48	1.08	1.10	1.29	0.66	1.40	1.29	1.05	1.07	1.26	0.64	1.24	1.15	0.89	0.90	1.07	0.54
氨基酸 amino acid	密码子 codon	CsaWOX						CssWOX						DaszWOX
氨基酸 amino acid	密码子 codon	CSA	CSS	A	N	P	O	CSA	CSS	A	N	P	O	CSA	CSS	A	N	P	O
Glu	GAA	1.08	1.00	1.17	1.12	0.99	1.86	1.07	1.00	1.14	1.09	0.97	1.82	0.98	0.91	1.05	1.00	0.89	1.67
	GAG	0.91	1.00	0.95	1.04	0.94	0.79	0.92	1.00	0.94	1.03	0.93	0.78	1.02	1.11	1.05	1.14	1.04	0.87
Cys	TGT	0.81	0.87	0.71	0.76	0.67	1.21	0.93	1.00	0.82	0.88	0.77	1.38	0.98	1.05	0.98	1.05	0.92	1.65
	TGC	1.24	1.14	1.29	1.29	1.04	0.75	1.08	1.00	1.12	1.12	0.90	0.65	1.03	0.95	1.21	1.21	0.97	0.70
Trp	TGG	1.00	1.00	1.31	1.34	1.18	1.19	1.00	1.00	1.27	1.30	1.14	1.15	1.00	1.00	1.26	1.29	1.14	1.14
Arg	CGT	1.12	1.55	0.87	1.04	1.06	1.09	1.19	1.65	0.83	1.00	1.01	1.04	1.27	1.77	0.99	1.19	1.21	1.24
	CGC	1.66	1.97	2.25	2.19	1.90	0.53	1.66	1.97	2.02	1.97	1.70	0.48	1.38	1.64	1.87	1.82	1.58	0.44
	CGA	0.56	0.53	0.68	0.81	0.78	0.67	0.59	0.55	0.64	0.76	0.73	0.63	0.69	0.65	0.83	0.99	0.96	0.82
	CGG	0.68	0.69	0.87	1.15	0.75	0.32	0.65	0.66	0.74	0.99	0.64	0.27	1.13	1.14	1.45	1.92	1.25	0.53
	AGA	0.94	0.81	0.92	1.09	0.89	1.66	0.97	0.83	0.85	1.00	0.82	1.53	0.87	0.75	0.84	1.00	0.82	1.53
	AGG	1.14	1.18	1.62	1.46	1.40	1.11	1.08	1.12	1.38	1.24	1.19	0.95	1.01	1.05	1.43	1.29	1.24	0.99
Gly	GGT	0.96	1.14	0.90	0.89	1.11	1.35	0.99	1.17	0.84	0.83	1.03	1.26	1.07	1.26	0.96	0.96	1.18	1.44
	GGC	1.31	1.20	1.78	1.46	1.61	0.56	1.39	1.28	1.73	1.42	1.56	0.54	1.39	1.28	1.83	1.50	1.65	0.57
	GGA	0.95	0.86	0.85	0.89	0.91	1.30	0.92	0.82	0.75	0.78	0.80	1.14	0.77	0.69	0.66	0.69	0.71	1.01
	GGG	0.87	0.88	1.29	1.25	1.15	0.77	0.82	0.83	1.11	1.08	0.98	0.66	0.92	0.93	1.31	1.28	1.17	0.78

表4

图2

参考文献 37

[1]	XIA E H, ZHANG H B, SHENG J, et al. The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J]. Mol Plant, 2017, 10(6):866-877. DOI: 10.1016/j.molp.2017.04.002. doi: 10.1016/j.molp.2017.04.002
[2]	WEI C L, YANG H, WANG S B, et al. Draft genome sequence of Camellia sinensis var.sinensis provides insights into the evolution of the tea genome and tea quality[J]. Proc Natl Acad Sci USA, 2018, 115(18):E4151-E4158. DOI: 10.1073/pnas.1719622115. doi: 10.1073/pnas.1719622115
[3]	ZHANG W Y, ZHANG Y J, QIU H J, et al. Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties[J]. Nat Commun, 2020, 11(1):3719. DOI: 10.1038/s41467-020-17498-6. doi: 10.1038/s41467-020-17498-6
[4]	SINGH K, PAUL A, KUMAR S, et al. Cloning and differential expression of QM like protein homologue from tea[Camellia sinensis (L.) O.Kuntze][J]. Mol Biol Rep, 2009, 36(5):921-927. DOI: 10.1007/s11033-008-9264-x. doi: 10.1007/s11033-008-9264-x
[5]	CAO Y P, HAN Y H, MENG D D, et al. Genome-wide analysis suggests the relaxed purifying selection affect the evolution of WOX genes in Pyrus bretschneideri,Prunus persica,Prunus mume,and Fragaria vesca[J]. Front Genet, 2017, 8:78. DOI: 10.3389/fgene.2017.00078. doi: 10.3389/fgene.2017.00078
[6]	WU X L, CHORY J, WEIGEL D. Combinations of WOX activities regulate tissue proliferation during Arabidopsis embryonic development[J]. Dev Biol, 2007, 309(2):306-316. DOI: 10.1016/j.ydbio.2007.07.019. doi: 10.1016/j.ydbio.2007.07.019
[7]	GALLOIS J L, NORA F R, MIZUKAMI Y, et al. WUSCHEL induces shoot stem cell activity and developmental plasticity in the root meristem[J]. Genes Dev, 2004, 18(4):375-380. DOI: 10.1101/gad.291204. doi: 10.1101/gad.291204
[8]	GORDON S P, HEISLER M G, REDDY G V, et al. Pattern formation during de novo assembly of the Arabidopsis shoot meristem[J]. Development, 2007, 134(19):3539-3548. DOI: 10.1242/dev.010298. doi: 10.1242/dev.010298
[9]	WANG P J, GUO Y C, CHEN X J, et al. Genome-wide identification of WOX genes and their expression patterns under different hormone and abiotic stress treatments in tea plant (Camellia sinensis)[J]. Trees, 2019, 33(4):1129-1142. DOI: 10.1007/s00468-019-01847-0. doi: 10.1007/s00468-019-01847-0
[10]	LIU H M, HE R, ZHANG H Y, et al. Analysis of synonymous codon usage in Zea mays[J]. Mol Biol Rep, 2010, 37(2):677-684. DOI: 10.1007/s11033-009-9521-7. doi: 10.1007/s11033-009-9521-7
[11]	PERLAK F J, DEATON R W, ARMSTRONG T A, et al. Insect resistant cotton plants[J]. Biotechnology (N Y), 1990, 8(10):939-943. DOI: 10.1038/nbt1090-939. doi: 10.1038/nbt1090-939
[12]	张乐, 金龙国, 罗玲, 等. 大豆基因组和转录组的核基因密码子使用偏好性分析[J]. 作物学报, 2011, 37(6):965-974.
	ZHANG L, JIN L G, LUO L, et al. Analysis of nuclear gene codon bias on soybean genome and transcriptome[J]. Acta Agron Sin, 2011, 37(6):965-974. DOI: 10.3724/SP.J.1006.2011.00965. doi: 10.3724/SP.J.1006.2011.00965
[13]	时慧, 王玉, 杨路成, 等. 茶树抗寒调控转录因子ICE1密码子偏性分析[J]. 园艺学报, 2012, 39(7):1341-1352.
	SHI H, WANG Y, YANG L C, et al. Analysis of codon bias of the cold regulated transcription factor ICE1 in tea plant[J]. Acta Hortic Sin, 2012, 39(7):1341-1352. DOI: 10.16420/j.issn.0513-353x.2012.07.002. doi: 10.16420/j.issn.0513-353x.2012.07.002
[14]	郭秀丽, 王玉, 杨路成, 等. 茶树CBF1基因密码子使用特性分析[J]. 遗传, 2012, 34(12):1614-1623.
	GUO X L, WANG Y, YANG L C, et al. Analysis of codon use features of CBF gene in Camellia sinensis[J]. Hereditas, 2012, 34(12):1614-1623. DOI: 10.3724/SP.J.1005.2012.01614. doi: 10.3724/SP.J.1005.2012.01614
[15]	PAN L L, WANG Y, HU J H, et al. Analysis of codon use features of stearoyl-acyl carrier protein desaturase gene in Camellia sinensis[J]. J Theor Biol, 2013, 334:80-86. DOI: 10.1016/j.jtbi.2013.06.006. doi: 10.1016/j.jtbi.2013.06.006
[16]	ALTSCHUL S F, MADDEN T L, SCHÄFFER A A, et al. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs[J]. Nucleic Acids Res, 1997, 25(17):3389-3402. DOI: 10.1093/nar/25.17.3389. doi: 10.1093/nar/25.17.3389
[17]	TANG F, CHEN N Z, ZHAO M L, et al. Identification and functional divergence analysis of WOX gene family in paper mulberry[J]. Int J Mol Sci, 2017, 18(8):1782. DOI: 10.3390/ijms18081782. doi: 10.3390/ijms18081782
[18]	ARTIMO P, JONNALAGEDDA M, ARNOLD K, et al. ExPASy:SIB bioinformatics resource portal[J]. Nucleic Acids Res, 2012,40(Web Server issue):597-603. DOI: 10.1093/nar/gks400. doi: 10.1093/nar/gks400
[19]	CHOU K C, SHEN H B. Cell-PLoc 2.0:an improved package of web-servers for predicting subcellular localization of proteins in various organisms[J]. Nat Sci, 2010, 2(10):1090-1103. DOI: 10.4236/ns.2010.210136. doi: 10.4236/ns.2010.210136
[20]	SHIELDS D C, SHARP P M. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases[J]. Nucleic Acids Res, 1987, 15(19):8023-8040. DOI: 10.1093/nar/15.19.8023. doi: 10.1093/nar/15.19.8023
[21]	ZHOU M, TONG C F, SHI J S. Analysis of codon usage between different poplar species[J]. J Genet Genomics, 2007, 34(6):555-561. DOI: 10.1016/S1673-8527(07)60061-7. doi: 10.1016/S1673-8527(07)60061-7
[22]	Romero H, Zavala A, Musto H, Bernardi G. The influence of translational selection on codon usage in fishes from the family Cyprinidae[J]. Gene, 2003, 317:141-147. DOI: 10.1016/S0378-1119(03)00701-7. doi: 10.1016/S0378-1119(03)00701-7
[23]	ZHOU M, TONG C F, SHI J S. A preliminary analysis of synonymous codon usage in poplar species[J]. Journal of Plant Physiology & Molecular Biology, 2007, 33(4):285-293. DOI: 10.2471/BLT.13.118778. doi: 10.2471/BLT.13.118778
[24]	MAJEED A, KAUR H, BHARDWAJ P. Selection constraints determine preference for A/U-ending codons in Taxus contorta[J]. Genome, 2020, 63(4):215-224. DOI: 10.1139/gen-2019-0165. doi: 10.1139/gen-2019-0165
[25]	SUEOKA N. Translation-coupled violation of parity rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position[J]. Gene, 1999, 238(1):53-58. DOI: 10.1016/s0378-1119(99)00320-0. doi: 10.1016/s0378-1119(99)00320-0
[26]	FENNOY S L, BAILEY-SERRES J. Synonymous codon usage in Zea mays L.nuclear genes is varied by levels of C and G-ending codons[J]. Nucleic Acids Res, 1993, 21(23):5294-5300. DOI: 10.1093/nar/21.23.5294. doi: 10.1093/nar/21.23.5294
[27]	CHANG Y Y, SONG X B, ZHANG Q X, et al. Genome-wide identification of WOX gene family and expression analysis during rejuvenational rhizogenesis in walnut (Juglans regia L.)[J]. Forests, 2019, 11(1):16. DOI: 10.3390/f11010016. doi: 10.3390/f11010016
[28]	VAN DER GRAAFF E, LAUX T, RENSING S A. The WUS homeobox-containing (WOX) protein family[J]. Genome Biol, 2009, 10(12):248. DOI: 10.1186/gb-2009-10-12-248. doi: 10.1186/gb-2009-10-12-248
[29]	NARDMANN J, WERR W. The shoot stem cell niche in angiosperms:expression patterns of WUS orthologues in rice and maize imply major modifications in the course of mono-and dicot evolution[J]. Mol Biol Evol, 2006, 23(12):2492-2504. DOI: 10.1093/molbev/msl125. doi: 10.1093/molbev/msl125
[30]	LIU B B, WANG L, ZHANG J, et al. WUSCHEL-related homeobox genes in Populus tomentosa:diversified expression patterns and a functional similarity in adventitious root formation[J]. BMC Genomics, 2014, 15:296. DOI: 10.1186/1471-2164-15-296. doi: 10.1186/1471-2164-15-296
[31]	李晓旭, 刘成, 李伟, 等. 番茄WOX转录因子家族的鉴定及其进化、表达分析[J]. 遗传, 2016, 38(5):444-460.
	LI X X, LIU C, LI W, et al. Genome-wide identification,phylogenetic analysis and expression profiling of the WOX family genes in Solanum lycopersicum[J]. Hereditas, 2016, 38(5):444-460. DOI: 10.16288/j.yczz.15-499. doi: 10.16288/j.yczz.15-499
[32]	王占军, 李豹, 姜行舟, 等. 两种茶树全基因组数据的密码子偏好性比较分析[J]. 中国细胞生物学学报, 2018, 40(12):2028-2039.
	WANG Z J, LI B, JIANG X Z, et al. Comparative analysis of the codon preference patterns in two species of Camellia sinensis based on genome data[J]. Chin J Cell Biol, 2018, 40(12):2028-2039.
[33]	WANG Z J, WANG G Y, CAI Q W, et al. Genomewide comparative analysis of codon usage bias in three sequenced Jatropha curcas[J]. J Genet, 2021, 100(1):1-13. DOI: 10.1007/s12041-021-01271-9. doi: 10.1007/s12041-021-01271-9
[34]	LI N, SUN M H, JIANG Z S, et al. Genome-wide analysis of the synonymous codon usage patterns in apple[J]. J Integr Agric, 2016, 15(5):983. DOI: 10.1016/S2095-3119(16)61333-3. doi: 10.1016/S2095-3119(16)61333-3
[35]	SONG H, LIU J, CHEN T, et al. Synonymous codon usage pattern in model legume Medicago truncatula[J]. J Integr Agric, 2018, 17(9):2074-2081. DOI: 10.1016/S2095-3119(18)61961-6. doi: 10.1016/S2095-3119(18)61961-6
[36]	ADITAMA R, TANJUNG Z A, SUDANIA W M, et al. Analysis of codon usage bias reveals optimal codons in Elaeis guineensis[J]. Biodiversitas, 2020, 21(11):5311-5337. DOI: 10.13057/biodiv/d211138. doi: 10.13057/biodiv/d211138
[37]	李晓旭, 郭存, 蒲文宣, 等. 普通烟草WOX转录因子家族的全基因组鉴定及分析[J]. 中国烟草学报, 2021, 27(1):90-100.
	LI X X, GUO C, PU W X, et al. Genome-wide identification and systemic analysis of WOX family genes in tobacco[J]. Acta Tabacaria Sin, 2021, 27(1):90-100. DOI: 10.16472/j.chinatobacco.2020.t0039. doi: 10.16472/j.chinatobacco.2020.t0039

碱基组成 base composition	CSA	CSS	DASZ
GC₁	46.369	46.228	47.543
GC₂	45.577	44.789	45.697
GC₃	46.050	47.303	45.087
平均average	45.999	46.107	46.109

3个茶树品种WOX基因家族的进化及密码子偏好性比较

A comparative study of the evolution and codon usage bias in WOX gene family of three Camellia sinensis cultivars

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[4]	张庆, 魏树和, 代惠萍, 贾根良. 硒对茶树镉毒害的缓解作用研究[J]. 南京林业大学学报（自然科学版）, 2020, 44(1): 200-204.
[5]	袁昌洪,韩冬,杨菲,杨再强. 氮肥对茶树春季光合、抗衰老特性及内源激素含量的影响[J]. 南京林业大学学报（自然科学版）, 2016, 40(05): 67-73.
[6]	吴永刚;姜志林;罗强. 公路边茶园土壤与茶树中重金属的积累与分布[J]. 南京林业大学学报（自然科学版）, 2002, 26(04): 39-42.
[7]	唐荣南;汤兴陆. 湿地松与茶树间作生态效应的研究[J]. 南京林业大学学报（自然科学版）, 1987, 11(02): 35-44.