藜麦CqGAI基因密码子偏好性与进化分析

doi:10.13304/j.nykjdb.2023.0125

摘要/Abstract

摘要：

为了阐明藜麦CqGAI基因密码子使用特性，克隆获得藜麦CqGAI基因序列，运用CodonW、SPSS软件及EMBOSS在线程序分析藜麦CqGAI基因密码子使用偏好性，并与25种植物的GAI基因进行中性绘图、ENC分析和奇偶偏好偏差性分析。结果表明，藜麦CqGAI基因编码序列（coding sequence，CDS）全长1 782 bp，编码593个氨基酸，包含DELLA基因家族特有结构域DELLA、TVHYNP、NLS、VHIID、LHR、RVER；CqGAI基因能够迅速响应赤霉素（gibberellins，GA），在GA信号通路中起关键作用；密码子偏好性分析显示，CqGAI基因的有效密码子数（effective number of codon，ENC）、密码子适应指数（codon adaptation index， CAI）及GC含量分别为54.14、0.21和46.18%，密码子偏好性较弱，偏好以A/T结尾，有27个高频密码子。聚类分析表明，藜麦CqGAI基因与石竹目植物的亲缘关系较近。碱基组成与相关性分析发现，CqGAI基因密码子偏好性受碱基突变和选择效应影响。密码子使用频率表明，大肠杆菌与酵母菌均适用于藜麦CqGAI基因异源表达，拟南芥、烟草、甜菜均可作为藜麦CqGAI基因功能分析的遗传转化受体。以上研究结果为进一步研究藜麦CqGAI基因功能和异源表达提供了重要参考。

关键词: 藜麦, CqGAI基因, 密码子偏好性, 进化分析

Abstract:

To clarify the codon usage characteristics of CqGAI gene， the sequence of CqGAI gene was cloned. The codon usage preference of CqGAI gene was analyzed using CodonW， SPSS software and EMBOSS online program， and neutral mapping， ENC analysis and parity preference bias analysis were performed with GAI genes of 25 plants. The results showed that the length of coding sequence （CDS） of CqGAI gene was 1 782 bp， which encoded 593 amino acids， and contained the unique structural domains of DELLA gene family such as DELLA， TVHYNP， NLS， VHIID， LHR and RVER. The CqGAI gene could rapidly responded to gibberellines （GA），_{which_{played a key role in the GA signaling pathway. Codon bias analysis showed that ENC， CAI and GC content of CqGAI gene were 54.14， 0.21 and 46.18%， respectively， with weak codon bias， preference ending with A/T and 27 high frequency codons. The clustering analyses showed that the CqGAI gene had the closest preference to Caryophyllales. The base composition and correlation analysis revealed that the codon preference of CqGAI gene was influenced by selection effect and base mutation. The frequency of codon usage indicated that both Escherichia coli and yeast were suitable for heterologous expression of CqGAI gene， and Arabidopsis thaliana， Nicotiana tabacum and Beta vulgaris were suitable for genetic transformation recipients for functional analysis of CqGAI gene. Above results provided an important reference for further study the function and heterologous expression of CqGAI gene.}}

Key words: Chenopodium quinoa, CqGAI gene, codon usage bias, evolution analysis

中图分类号:

S516

丰扬, 郭凤根, 王仕玉, 刘正杰, 龙雯虹. 藜麦CqGAI基因密码子偏好性与进化分析[J]. 中国农业科技导报, 2024, 26(4): 27-36.

Yang FENG, Fenggen GUO, Shiyu WANG, Zhengjie LIU, Wenhong LONG. Codon Bias and Evolution Analysis of CqGAI in Chenopodium quinoa[J]. Journal of Agricultural Science and Technology, 2024, 26(4): 27-36.

图/表 12

参考文献 35

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引物名称 Prime name	引物序列 Primer sequence（5’-3’）	用途 Utilization
CqGAI-F	ATGAAGAGGGAACTACCCTTTACG	目的基因 Target gene
CqGAI-R	TCATGTTTCCATTAGACACCCATC	目的基因 Target gene
CqGAI-qF	TGTCGAGGCCGGTTGTTC	qRT-PCR
CqGAI-qR	ACGCCGCTAAAAACCCGA	qRT-PCR
CqActin-F	GAGCACCCTGTTCTTCTGACTG	内参基因 Reference gene
CqActin -R	GAGAAAGAACAGCCTGAATTGC	内参基因 Reference gene

引物名称 Prime name	引物序列 Primer sequence（5’-3’）	用途 Utilization
CqGAI-F	ATGAAGAGGGAACTACCCTTTACG	目的基因 Target gene
CqGAI-R	TCATGTTTCCATTAGACACCCATC	目的基因 Target gene
CqGAI-qF	TGTCGAGGCCGGTTGTTC	qRT-PCR
CqGAI-qR	ACGCCGCTAAAAACCCGA	qRT-PCR
CqActin-F	GAGCACCCTGTTCTTCTGACTG	内参基因 Reference gene
CqActin -R	GAGAAAGAACAGCCTGAATTGC	内参基因 Reference gene

物种 Species	基因登录号 GenBank accession number	G/C含量 G/C content/%				有效密码子数 ENC	密码子适应指数 CAI	最优密码子使用频率 FOC
物种 Species	基因登录号 GenBank accession number	GC1	GC2	GC3	GC	有效密码子数 ENC	密码子适应指数 CAI	最优密码子使用频率 FOC
藜麦 Chenopodium quinoa	OQ067480	52.02	42.76	43.77	46.18	54.14	0.21	0.416
菠菜 Spinacia oleracea	KX026951.1	53.73	44.81	45.45	48.00	54.47	0.20	0.401
甜菜 Beta vulgaris	XM_010683580.3	50.82	42.48	35.95	43.08	50.00	0.19	0.358
苋菜 Amaranthus tricolor	MK049175.1	51.65	41.91	32.18	41.91	50.61	0.20	0.395
陆地棉 Gossypium hirsutum	FJ974045.1	54.94	41.49	49.92	48.78	54.22	0.22	0.441
李 Prunus salicina	KU845589.1	58.99	41.64	63.25	54.63	51.24	0.25	0.480
核桃 Juglans regia	JF766606.2	57.98	42.51	63.68	54.72	52.22	0.26	0.478
牡丹 Paeonia suffruticosa	MH550803.1	58.93	43.51	56.01	52.81	59.03	0.21	0.425
橡胶树 Hevea brasiliensis	KT696440.1	56.85	41.73	43.31	47.30	55.41	0.23	0.424
沙梨 Pyrus pyrifolia	KU311003.1	60.00	42.20	72.60	58.27	47.69	0.26	0.514
杂交玫瑰 Rosa hybrid	KC484652.1	58.32	41.20	72.54	57.35	47.48	0.25	0.501
拟南芥 Arabidopsis thaliana	NM_101361.3	58.80	38.76	47.94	48.50	49.73	0.25	0.472
番茄 Solanum lycopersicum	NM_001247436.1	51.95	42.61	29.54	41.37	44.68	0.21	0.409
毛白杨 Populus tomentosa	JX102471.1	55.79	41.06	45.03	47.30	56.81	0.25	0.458
葡萄 Vitis vinifera	HQ834311.1	60.91	42.64	64.30	55.95	51.67	0.23	0.454
樱桃 Prunus avium	XM_021956293.1	59.73	43.12	59.73	54.19	54.93	0.21	0.415
水蜜桃 Prunus persica	XM_007214894.2	59.43	43.77	60.94	54.71	54.83	0.21	0.412
梅花 Prunus mume	NM_001326504.1	60.37	43.98	61.20	55.18	54.12	0.21	0.415
苹果 Malus domestica	FJ535245.1	60.13	42.70	73.00	58.61	46.64	0.25	0.507
水曲柳 Fraxinus mandshurica	KX905158.1	55.61	39.47	50.00	48.36	55.41	0.20	0.388
马铃薯 Solanum tuberosum	JF834157.1	52.46	42.78	28.18	41.14	43.63	0.22	0.427
高粱 Sorghum bicolor	XM_002450738.2	64.83	50.00	84.78	66.54	38.15	0.26	0.568
小米 Setaria italica	XM_004980464.2	63.79	51.06	86.74	67.20	37.12	0.23	0.514
玉米 Zea mays	XM_008681950.2	64.51	50.39	90.54	68.48	34.68	0.26	0.582
水稻 Oryza sativa	AY464568.1	68.83	52.43	86.64	69.30	37.73	0.26	0.570

物种 Species	基因登录号 GenBank accession number	G/C含量 G/C content/%				有效密码子数 ENC	密码子适应指数 CAI	最优密码子使用频率 FOC
物种 Species	基因登录号 GenBank accession number	GC1	GC2	GC3	GC	有效密码子数 ENC	密码子适应指数 CAI	最优密码子使用频率 FOC
藜麦 Chenopodium quinoa	OQ067480	52.02	42.76	43.77	46.18	54.14	0.21	0.416
菠菜 Spinacia oleracea	KX026951.1	53.73	44.81	45.45	48.00	54.47	0.20	0.401
甜菜 Beta vulgaris	XM_010683580.3	50.82	42.48	35.95	43.08	50.00	0.19	0.358
苋菜 Amaranthus tricolor	MK049175.1	51.65	41.91	32.18	41.91	50.61	0.20	0.395
陆地棉 Gossypium hirsutum	FJ974045.1	54.94	41.49	49.92	48.78	54.22	0.22	0.441
李 Prunus salicina	KU845589.1	58.99	41.64	63.25	54.63	51.24	0.25	0.480
核桃 Juglans regia	JF766606.2	57.98	42.51	63.68	54.72	52.22	0.26	0.478
牡丹 Paeonia suffruticosa	MH550803.1	58.93	43.51	56.01	52.81	59.03	0.21	0.425
橡胶树 Hevea brasiliensis	KT696440.1	56.85	41.73	43.31	47.30	55.41	0.23	0.424
沙梨 Pyrus pyrifolia	KU311003.1	60.00	42.20	72.60	58.27	47.69	0.26	0.514
杂交玫瑰 Rosa hybrid	KC484652.1	58.32	41.20	72.54	57.35	47.48	0.25	0.501
拟南芥 Arabidopsis thaliana	NM_101361.3	58.80	38.76	47.94	48.50	49.73	0.25	0.472
番茄 Solanum lycopersicum	NM_001247436.1	51.95	42.61	29.54	41.37	44.68	0.21	0.409
毛白杨 Populus tomentosa	JX102471.1	55.79	41.06	45.03	47.30	56.81	0.25	0.458
葡萄 Vitis vinifera	HQ834311.1	60.91	42.64	64.30	55.95	51.67	0.23	0.454
樱桃 Prunus avium	XM_021956293.1	59.73	43.12	59.73	54.19	54.93	0.21	0.415
水蜜桃 Prunus persica	XM_007214894.2	59.43	43.77	60.94	54.71	54.83	0.21	0.412
梅花 Prunus mume	NM_001326504.1	60.37	43.98	61.20	55.18	54.12	0.21	0.415
苹果 Malus domestica	FJ535245.1	60.13	42.70	73.00	58.61	46.64	0.25	0.507
水曲柳 Fraxinus mandshurica	KX905158.1	55.61	39.47	50.00	48.36	55.41	0.20	0.388
马铃薯 Solanum tuberosum	JF834157.1	52.46	42.78	28.18	41.14	43.63	0.22	0.427
高粱 Sorghum bicolor	XM_002450738.2	64.83	50.00	84.78	66.54	38.15	0.26	0.568
小米 Setaria italica	XM_004980464.2	63.79	51.06	86.74	67.20	37.12	0.23	0.514
玉米 Zea mays	XM_008681950.2	64.51	50.39	90.54	68.48	34.68	0.26	0.582
水稻 Oryza sativa	AY464568.1	68.83	52.43	86.64	69.30	37.73	0.26	0.570

参数 Parameter	GC1	GC2	GC3	GC
GC2	0.686^**
GC3	0.921^**	0.676^**
GC	0.949^**	0.757^**	0.990^**
ENC	-0.523^**	-0.744^**	-0.555^**	-0.604^**