滇杨TCP基因家族的全基因组鉴定与分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0115

摘要/Abstract

摘要：

【目的】 鉴定滇杨（Populus yunnanensis）TCP基因家族，为滇杨TCP基因功能研究及遗传改良提供理论依据。【方法】 基于滇杨全基因组数据，通过BLAST对滇杨TCP基因家族进行鉴定，利用生物信息学方法分析了该家族成员的理化性质、基因结构、染色体分布、系统进化、启动子分析及密码子特性，并利用RT-qPCR对TCP基因家族的亚族基因CYC/TB1在滇杨不同组织的表达情况进行试验。【结果】 滇杨中共鉴定得到38个TCP基因，可分为PCF、CYC/TB1和CIN三个亚族；TCP基因在滇杨染色体上分布不均，其中4号染色体含有的TCP基因数量最多；同一进化分支的TCP家族成员的Motif及基因结构具有高度的一致性，而不同分支之间呈现一定的多样性；TCP基因家族启动子区域显著富集生长发育、激素及逆境响应的顺式元件；滇杨染色体上分别有 23个、37个与拟南芥和毛果杨具有共线性的TCP基因；密码子偏好性分析显示大多数成员偏好以A和T（U）结尾，且自然选择对该家族成员密码子偏好性影响较大；CYC/TB1亚族中的4个基因在侧芽中的表达量均显著高于其他部位，具有明显的组织特异性。【结论】 鉴定了滇杨TCP家族成员，揭示了CYC/TB1亚族成员在滇杨侧芽的生长中起到重要作用，为滇杨TCP基因功能和调控网络的解析提供了一定的理论基础。

关键词: 滇杨, TCP基因, 侧芽, 密码子, 组织特异性

Abstract:

【Objective】 The identification of the Populus yunnanensis TCP gene family may provide a theoretical basis for the study of TCP gene function and genetic improvement. 【Method】 Based on the whole genome data of P. yunnanensis, the TCP gene family was identified by BLAST, the physical and chemical properties, gene structure, chromosome distribution, phylogeny, promoter analysis and codon characteristics of the members in this family were analyzed by bioinformatics. The expression of the subfamily of TCP gene family, CYC/TB1 gene in different tissues of P. yunnanensis was studied by RT-qPCR. 【Result】 A total of 38 TCP genes were identified in P. yunnanensis, and they were divided into three subfamilies: PCF, CYC/TB1 and CIN. The motif and gene structure of TCP family members of the same evolutionary branch were highly consistent, while there was some diversity among the different branches. The promoter region of TCP gene family was rich in cis-acting elements of growth, hormone and stress response. There were 23 and 37 TCP genes on the chromosomes of P. yunnanensis, respectively, which were found to be collinear with Arabidopsis thaliana and Populus trichocarpa. The codon bias analysis showed that most members ended in A and T（U）, and the natural selection had a strong influence on the codon bias. The expressions of four genes in CYC/TB1 subfamily were significantly higher in lateral buds than in other tissues, these genes may play an important role in the formation and development of lateral buds in P. yunnanensis. 【Conclusion】 The results showed that the TCP family members of P. yunnanensis played an important role in the growth of lateral buds of P. yunnanensis, which provides a theoretical basis for the analysis of TCP gene function and regulation network in P. yunnanensis.

Key words: Populus yunnanensis, TCP gene, lateral bud, codon, tissue specificity

陈智华, 乔振升, 李嘉其, 张晓琳, 马少杰, 何承忠, 纵丹. 滇杨TCP基因家族的全基因组鉴定与分析[J]. 生物技术通报, 2024, 40(11): 214-226.

CHEN Zhi-hua, QIAO Zhen-sheng, LI Jia-qi, ZHANG Xiao-lin, MA Shao-jie, HE Cheng-zhong, ZONG Dan. Genome-wide Identification and Analysis of the TCP Gene Family in Populus yunnanensis[J]. Biotechnology Bulletin, 2024, 40(11): 214-226.

图/表 11

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基因名称Gene name	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
PyTCP12	TGGCCGGTGTTTCTACTGAC	GCTGGTTCAAGCAACTAGGG
PyTCP18	AATCGAAGGCCGGGATCAAG	TCCCCGTTAGTCTCAGGTGT
PyTCP20	CCTCTGAAGTGGGACGTGAC	GGGCTTTCTTCAACATGGGC
PyTCP24	TAACACGGCTCAAGGACCAA	GGGGGAGCCACTGGATAGTT
PyTCP32	GATCTGCAAGACAAGCTACGC	TTCGGACAGCACTTCACACT
PyTCP35	CCATTGAAATCGCGCGTAAGT	GGTCCCCACTTTCGGATACA
PyHIS	TTTAAGACTGATCTGCGTTTCC	GAACAGCCCAACAAGGTATG

基因名称Gene name	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
PyTCP12	TGGCCGGTGTTTCTACTGAC	GCTGGTTCAAGCAACTAGGG
PyTCP18	AATCGAAGGCCGGGATCAAG	TCCCCGTTAGTCTCAGGTGT
PyTCP20	CCTCTGAAGTGGGACGTGAC	GGGCTTTCTTCAACATGGGC
PyTCP24	TAACACGGCTCAAGGACCAA	GGGGGAGCCACTGGATAGTT
PyTCP32	GATCTGCAAGACAAGCTACGC	TTCGGACAGCACTTCACACT
PyTCP35	CCATTGAAATCGCGCGTAAGT	GGTCCCCACTTTCGGATACA
PyHIS	TTTAAGACTGATCTGCGTTTCC	GAACAGCCCAACAAGGTATG

氨基酸Amino acid	密码子Codon	数量Amount	相对同义密码子使用度 Relative synonymous codon usage	氨基酸 Amino acid	密码子Codon	数量Amount	相对同义密码子使用度 Relative synonymous codon usage
Phe 苯丙氨酸	UUU*	316	1.27	Gly 甘氨酸	GGU*	357	1.30
Phe 苯丙氨酸	UUC	183	0.73		GGC	218	0.79
Leu 亮氨酸	UUA	234	1.41		GGA	275	1.00
	UUG*	242	1.45		GGG	252	0.91
	CUU	210	1.26	Pro 脯氨酸	CCU*	322	1.31
	CUC	130	0.78		CCC	148	0.60
	CUA	97	0.58		CCA	401	1.64
	CUG	85	0.51		CCG	109	0.44
Ile 异亮氨酸	AUU*	303	1.53	Thr 苏氨酸	ACU*	334	1.41
	AUC	150	0.76		ACC	203	0.86
	AUA	140	0.71		ACA*	349	1.47
Met 甲硫氨酸	AUG	372	1.00		ACG	62	0.26
Val 缬氨酸	GUU*	253	1.70	Ala 丙氨酸	GCU*	427	1.66
	GUC	91	0.61		GCC	163	0.63
	GUA	102	0.69		GCA*	352	1.37
	GUG	149	1.00		GCG	88	0.34
Tyr 酪氨酸	UAU*	113	1.32	Ter 终止密码子	UAA	7	0.55
Tyr 酪氨酸	UAC	58	0.68		UAG	7	0.55
Cys 半胱氨酸	UGU*	60	1.15		UGA	24	1.89
Cys 半胱氨酸	UGC	44	0.85	Trp 色氨酸	UGG	133	1.00
His 组氨酸	CAU	273	1.15	Arg 精氨酸	CGU	89	0.70
His 组氨酸	CAC	203	0.85		CGC	68	0.54
Gln 谷氨酰胺	CAA*	560	1.23		CGA	81	0.64
Gln 谷氨酰胺	CAG	352	0.77		CGG	68	0.54
Asn 天冬酰胺	AAU	486	1.17		AGA	253	2.00
Asn 天冬酰胺	AAC	347	0.83		AGG*	199	1.58
Lys 赖氨酸	AAA*	318	1.08	Ser 丝氨酸	AGU*	305	1.06
Lys 赖氨酸	AAG	269	0.92		AGC	251	0.87
Asp 天冬氨酸	GAU*	415	1.30		UCU*	452	1.57
Asp 天冬氨酸	GAC	224	0.70		UCC	202	0.70
Glu 谷氨酸	GAA*	394	1.13		UCA*	414	1.43
Glu 谷氨酸	GAG	302	0.87		UCG	108	0.37

氨基酸Amino acid	密码子Codon	数量Amount	相对同义密码子使用度 Relative synonymous codon usage	氨基酸 Amino acid	密码子Codon	数量Amount	相对同义密码子使用度 Relative synonymous codon usage
Phe 苯丙氨酸	UUU*	316	1.27	Gly 甘氨酸	GGU*	357	1.30
Phe 苯丙氨酸	UUC	183	0.73		GGC	218	0.79
Leu 亮氨酸	UUA	234	1.41		GGA	275	1.00
	UUG*	242	1.45		GGG	252	0.91
	CUU	210	1.26	Pro 脯氨酸	CCU*	322	1.31
	CUC	130	0.78		CCC	148	0.60
	CUA	97	0.58		CCA	401	1.64
	CUG	85	0.51		CCG	109	0.44
Ile 异亮氨酸	AUU*	303	1.53	Thr 苏氨酸	ACU*	334	1.41
	AUC	150	0.76		ACC	203	0.86
	AUA	140	0.71		ACA*	349	1.47
Met 甲硫氨酸	AUG	372	1.00		ACG	62	0.26
Val 缬氨酸	GUU*	253	1.70	Ala 丙氨酸	GCU*	427	1.66
	GUC	91	0.61		GCC	163	0.63
	GUA	102	0.69		GCA*	352	1.37
	GUG	149	1.00		GCG	88	0.34
Tyr 酪氨酸	UAU*	113	1.32	Ter 终止密码子	UAA	7	0.55
Tyr 酪氨酸	UAC	58	0.68		UAG	7	0.55
Cys 半胱氨酸	UGU*	60	1.15		UGA	24	1.89
Cys 半胱氨酸	UGC	44	0.85	Trp 色氨酸	UGG	133	1.00
His 组氨酸	CAU	273	1.15	Arg 精氨酸	CGU	89	0.70
His 组氨酸	CAC	203	0.85		CGC	68	0.54
Gln 谷氨酰胺	CAA*	560	1.23		CGA	81	0.64
Gln 谷氨酰胺	CAG	352	0.77		CGG	68	0.54
Asn 天冬酰胺	AAU	486	1.17		AGA	253	2.00
Asn 天冬酰胺	AAC	347	0.83		AGG*	199	1.58
Lys 赖氨酸	AAA*	318	1.08	Ser 丝氨酸	AGU*	305	1.06
Lys 赖氨酸	AAG	269	0.92		AGC	251	0.87
Asp 天冬氨酸	GAU*	415	1.30		UCU*	452	1.57
Asp 天冬氨酸	GAC	224	0.70		UCC	202	0.70
Glu 谷氨酸	GAA*	394	1.13		UCA*	414	1.43
Glu 谷氨酸	GAG	302	0.87		UCG	108	0.37

基因名称Gene name	CDS长度Length of CDS	CAI	CBI/%	Fop/%	ENc/%	GC/%	GC1/%	GC2/%	GC3/%
PyTCP1	909	0.169	-12.4	36.2	45.29	44.8	49.50	43.23	41.58
PyTCP2	1 194	0.194	-5.5	39.3	58.74	49.2	53.02	53.52	40.95
PyTCP3	963	0.182	-7.5	38.7	43.67	45.5	55.76	48.60	32.09
PyTCP4	963	0.180	-8.0	38.4	44.29	45.8	45.79	55.76	48.91
PyTCP5	1 239	0.211	-3.0	42.0	56.06	49.7	56.90	47.46	44.55
PyTCP6	1 047	0.186	-1.9	40.1	58.45	49.4	52.44	52.44	43.27
PyTCP7	1 002	0.191	-1.6	41.0	56.36	48.9	53.59	53.59	39.52
PyTCP8	909	0.165	-12.7	35.8	48.84	44.0	48.51	43.89	39.60
PyTCP9	1 188	0.196	-1.8	42.2	53.49	46.2	48.74	48.99	40.66
PyTCP10	1 425	0.193	-6.5	40.1	53.99	47.0	50.53	47.16	43.16
PyTCP11	1 413	0.191	-7.2	39.8	54.20	47.2	50.74	47.77	43.10
PyTCP12	969	0.183	-0.8	42.2	50.17	41.8	41.49	44.58	39.32
PyTCP13	1 098	0.171	-16.6	32.2	47.83	42.6	47.27	49.50	34.43
PyTCP14	1 716	0.198	-8.1	39.1	50.97	48.9	57.17	53.15	36.19
PyTCP15	816	0.180	3.9	44.8	47.26	52.0	58.46	57.35	40.07
PyTCP16	597	0.272	19.5	53.4	51.98	57.7	56.28	48.74	67.84
PyTCP17	813	0.183	3.3	44.2	46.04	50.4	58.67	56.09	36.16
PyTCP18	1 365	0.199	-10.3	37.7	51.28	43.2	43.96	41.32	44.40
PyTCP19	555	0.216	-8.0	37.6	52.63	45.5	51.89	45.95	38.38
PyTCP20	1 464	0.210	-8.0	38.6	52.48	41.6	44.88	39.75	40.16
PyTCP21	1 152	0.187	-4.2	41.1	57.00	46.8	50.52	47.92	41.93
PyTCP22	1 437	0.199	-5.8	40.7	57.13	47.7	50.31	49.69	43.01
PyTCP23	1 233	0.221	-1.7	42.5	60.03	50.1	56.93	48.91	44.28
PyTCP24	1 185	0.211	-4.0	40.9	50.44	42.2	43.29	41.27	42.03
PyTCP25	1 104	0.219	-4.7	40.4	44.90	44.0	53.26	50.00	28.53
PyTCP26	1 245	0.189	-7.7	39.2	51.85	45.8	52.53	51.33	33.25
PyTCP27	1 248	0.189	-7.5	39.2	52.61	46.3	52.88	51.44	34.13
PyTCP28	1 041	0.209	-5.6	40.1	50.16	45.7	52.45	46.4	38.04
PyTCP29	1 194	0.192	2.6	42.5	57.21	49.5	52.26	53.27	42.96
PyTCP30	1 278	0.208	-4.8	40.2	54.02	42.0	45.77	39.44	40.38
PyTCP31	1 077	0.151	-16.7	32.0	52.85	41.2	45.40	44.57	33.15
PyTCP32	1 080	0.217	-8.6	38.3	44.14	44.1	54.72	49.44	28.06
PyTCP33	969	0.175	-10.3	37.4	44.70	44.4	53.56	48.30	30.96
PyTCP34	1 083	0.173	-18.8	31.1	50.57	42.4	47.09	45.98	34.07
PyTCP35	1 125	0.214	2.4	44.2	56.07	43.0	43.47	42.93	42.40
PyTCP36	1 254	0.205	-5.8	40.6	52.40	45.1	52.63	50.48	31.82
PyTCP37	1 197	0.205	-6.4	40.2	53.22	45.5	54.64	49.37	32.08
PyTCP38	1 041	0.197	-13.4	36.2	49.42	44.6	52.16	47.55	34.01