烟草TCP基因家族的鉴定及表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2022-1141

摘要/Abstract

摘要：

TCP基因是植物特有的转录因子，对植物的生长发育起到重要的作用。鉴定烟草TCP基因家族，为烟草TCP基因功能研究及遗传改良提供理论依据。基于烟草全基因组数据，通过BLAST对烟草TCP基因家族进行鉴定，利用生物信息学的方法分析了该家族成员的理化性质、基因结构、蛋白质结构域、染色体分布、系统进化及启动子分析，并利用RT-qPCR验证了TCP基因家族在烤烟不同品种各个组织的表达情况。烟草中共鉴定了20个TCP基因，将其分为两大类Class I与Class II；已知的TCP基因位于不同的染色体上且分布不均匀，所有TCP基因均具有保守的结构域；TCP基因家族启动子区域显著富集生长发育和激素响应的顺式元件，部分TCP基因还具有低温胁迫的作用元件；20个NtTCPs基因在K326和Ti706不同组织和不同时期叶片内存在不同程度的表达，NtTCPs基因在烟草K326和Ti706中的表达具有组织特异性。其中Class I亚族基因在6个组织和苗期叶片内表达水平较高，而Class II亚族基因在幼苗叶片、上部叶和中部叶表达水平较高。研究结果揭示了烟草TCP基因家族成员在烟草生长发育过程中起到重要作用，为探究烟草TCP基因家族的生物学功能提供了基础。

关键词: 烟草, TCP基因, 全基因组鉴定, 生物信息学, 组织差异, 表达模式分析

Abstract:

TCP gene is a plant-specific transcription factor, and plays an important role in plant growth and development. The identification of tobacco TCP gene family may provide theoretical basis for the study of tobacco TCP gene function and genetic improvement. Based on the whole genome data of tobacco（Nicotiana tabacum L.）, the tobacco TCP gene family was identified by BLAST, and the physicochemical properties, gene structure, protein domain, chromosome distribution, phylogeny evolution and promoter analysis of the family members were analyzed by bioinformatics. The expressions of TCP gene family in various tissues of different flue-cured tobacco varieties were verified via RT-qPCR. A total of 20 TCP genes were identified in tobacco, and they were divided into two categories, Class I and Class II. The known TCP genes were located on different chromosomes and were unevenly distributed, and all TCP genes had conserved domains. The cis-elements of growth, development and hormone response were significantly enriched in the promoter regions of the TCP gene family, and some TCP genes also had low-temperature stress elements; 20 NtTCP genes were expressed to different degrees in different tissues and leaves of K326 and Ti706, and NtTCP genes were expressed in tobacco K326 and Ti706, and the expressions were tissue-specific. The expressions of subfamily Class I genes were higher in 6 tissues and leaves at seedling stage, while the expressions of subfamily Class II genes were higher in seedling leaves, upper leaves and middle leaves. The results revealed that the members of tobacco TCP gene family play an important role in the growth and development of tobacco, which provides a basis for exploring the biological functions of tobacco TCP gene family.

Key words: tobacco, TCP gene, genome-wide identification, bioinformatics, organizational differences, expression pattern analysis

张路阳, 韩文龙, 徐晓雯, 姚健, 李芳芳, 田效园, 张智强. 烟草TCP基因家族的鉴定及表达分析[J]. 生物技术通报, 2023, 39(6): 248-258.

ZHANG Lu-yang, HAN Wen-long, XU Xiao-wen, YAO Jian, LI Fang-fang, TIAN Xiao-yuan, ZHANG Zhi-qiang. Identification and Expression Analysis of the Tobacco TCP Gene Family[J]. Biotechnology Bulletin, 2023, 39(6): 248-258.

图/表 9

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基因Gene	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
NtTCP1	TGTCGACGTCGGTAGAAGCTA	CGTCCATCGACTTTGCTATGA
NtTCP2	CAGCCACTCCCTATGTCATCA	CATGGCCATTAGTTCCCAAAT
NtTCP3	TATGCAGTTCCAGAGCTTCCA	TTTGGTGGTGCAGCAAAATAG
NtTCP4	ATAGCAGCCACTGGAACTGGT	TTGAAACAAACCTCGTCGTTG
NtTCP5	TGGGTCACAAGTCTGAAGGTG	GGGATTGTACCTGTTCCCGTA
NtTCP6	AACCTTCTAAAGACCGCCACA	TTGTGACCCAATTCTCTGGTG
NtTCP7	ACGCGAATTGGGTCATAAATC	GGAATTGTTCCATTGCCTGTT
NtTCP8	GGGCAGTGGGCTCTAGTAATG	CCACAACTGAGGTGGATACGA
NtTCP9	CCATTGCATTTCATGCCTAGA	GACATTCCCAACCCAAGATGT
NtTCP10	TGACGGTAGAGGAAGGCGTAT	TTTGGCCATCAGACTTGTGAC
NtTCP11	ATAGCAGCCACTGGAACTGGT	TGGGAGAGCGAAAAATTAGGA
NtTCP12	GCAATGATAATGCTGGGGAAT	GCATTTGCATTGTCACCACTT
NtTCP13	TTTACCCCACTTGGGTTTGAC	AACAAGTACCCACCACCTTGG
NtTCP14	TGTCGACGTCGGTAGAAGCTA	CCATTATTGCCAGCATCAGAA
NtTCP15	ATTTGCGAGGAGGCACTATGT	TCAACTTTCGTGTGCCTGTCT
NtTCP16	TTGCTTCATCACCAAAACCAG	GACCGAGTTCTACTGGCTGCT
NtTCP17	GTTGAAGGCAGAGGAAGGAGA	TGTTGCAGCAATTATGGAAGG
NtTCP18	CCTCCGAAGAAACAAACCAAG	GTTTCTCCGTCGGACTTATGG
NtTCP19	TCTGGATGTTACCGGTGAGTG	ACCATTGAACCCAACTGAACC
NtTCP20	TGACGGTAGAGGAAGGCGTAT	TTTGACCATCGGACTTGTGAC

基因Gene	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
NtTCP1	TGTCGACGTCGGTAGAAGCTA	CGTCCATCGACTTTGCTATGA
NtTCP2	CAGCCACTCCCTATGTCATCA	CATGGCCATTAGTTCCCAAAT
NtTCP3	TATGCAGTTCCAGAGCTTCCA	TTTGGTGGTGCAGCAAAATAG
NtTCP4	ATAGCAGCCACTGGAACTGGT	TTGAAACAAACCTCGTCGTTG
NtTCP5	TGGGTCACAAGTCTGAAGGTG	GGGATTGTACCTGTTCCCGTA
NtTCP6	AACCTTCTAAAGACCGCCACA	TTGTGACCCAATTCTCTGGTG
NtTCP7	ACGCGAATTGGGTCATAAATC	GGAATTGTTCCATTGCCTGTT
NtTCP8	GGGCAGTGGGCTCTAGTAATG	CCACAACTGAGGTGGATACGA
NtTCP9	CCATTGCATTTCATGCCTAGA	GACATTCCCAACCCAAGATGT
NtTCP10	TGACGGTAGAGGAAGGCGTAT	TTTGGCCATCAGACTTGTGAC
NtTCP11	ATAGCAGCCACTGGAACTGGT	TGGGAGAGCGAAAAATTAGGA
NtTCP12	GCAATGATAATGCTGGGGAAT	GCATTTGCATTGTCACCACTT
NtTCP13	TTTACCCCACTTGGGTTTGAC	AACAAGTACCCACCACCTTGG
NtTCP14	TGTCGACGTCGGTAGAAGCTA	CCATTATTGCCAGCATCAGAA
NtTCP15	ATTTGCGAGGAGGCACTATGT	TCAACTTTCGTGTGCCTGTCT
NtTCP16	TTGCTTCATCACCAAAACCAG	GACCGAGTTCTACTGGCTGCT
NtTCP17	GTTGAAGGCAGAGGAAGGAGA	TGTTGCAGCAATTATGGAAGG
NtTCP18	CCTCCGAAGAAACAAACCAAG	GTTTCTCCGTCGGACTTATGG
NtTCP19	TCTGGATGTTACCGGTGAGTG	ACCATTGAACCCAACTGAACC
NtTCP20	TGACGGTAGAGGAAGGCGTAT	TTTGACCATCGGACTTGTGAC

基因名称 Gene name	基因组登录号 Gene ID	氨基酸数 Number of amino acids	分子量 Molecular weight/kD	等电点 pI	亲水性 GRAVY	亚细胞定位 Subcellular localization
NtTCP1	Nitab4.5_0000069g0220.1	247	25.895	7.93	-0.442	细胞核 Nucleus
NtTCP2	Nitab4.5_0000206g0010.1	442	48.502	8.55	-0.907	细胞核 Nucleus
NtTCP3	Nitab4.5_0000246g0120.1	323	35.413	5.51	-0.822	细胞核 Nucleus
NtTCP4	Nitab4.5_0000269g0060.1	367	39.854	7.37	-0.715	细胞核 Nucleus
NtTCP5	Nitab4.5_0000303g0270.1	326	34.960	6.87	-0.784	细胞核 Nucleus
NtTCP6	Nitab4.5_0000365g0240.1	412	44.290	8.99	-0.746	细胞核 Nucleus
NtTCP7	Nitab4.5_0000519g0050.1	222	24.004	9.82	-0.486	细胞核 Nucleus
NtTCP8	Nitab4.5_0000832g0020.1	357	38.007	5.53	-0.448	细胞核 Nucleus
NtTCP9	Nitab4.5_0000948g0150.1	556	59.693	7.19	-0.758	细胞核 Nucleus
NtTCP10	Nitab4.5_0001089g0050.1	161	16.833	7.33	-0.244	细胞核 Nucleus
NtTCP11	Nitab4.5_0001188g0020.1	399	43.838	6.89	-0.823	细胞核 Nucleus
NtTCP12	Nitab4.5_0003077g0060.1	596	66.701	6.14	-0.808	细胞核 Nucleus
NtTCP13	Nitab4.5_0003202g0050.1	420	46.357	6.57	-0.793	细胞核 Nucleus
NtTCP14	Nitab4.5_0004301g0070.1	300	31.547	8.65	-0.324	细胞核 Nucleus
NtTCP15	Nitab4.5_0005379g0040.1	359	38.206	5.43	-0.444	细胞核 Nucleus
NtTCP16	Nitab4.5_0005709g0020.1	589	65.994	6.65	-0.817	细胞核 Nucleus
NtTCP17	Nitab4.5_0007375g0060.1	295	32.098	7.14	-0.744	细胞核 Nucleus
NtTCP18	Nitab4.5_0007913g0020.1	544	58.332	7.00	-0.761	细胞核 Nucleus
NtTCP19	Nitab4.5_0009198g0010.1	419	44.840	8.04	-0.804	细胞核 Nucleus
NtTCP20	Nitab4.5_0011777g0010.1	261	27.539	9.71	-0.432	细胞核 Nucleus

基因名称 Gene name	基因组登录号 Gene ID	氨基酸数 Number of amino acids	分子量 Molecular weight/kD	等电点 pI	亲水性 GRAVY	亚细胞定位 Subcellular localization
NtTCP1	Nitab4.5_0000069g0220.1	247	25.895	7.93	-0.442	细胞核 Nucleus
NtTCP2	Nitab4.5_0000206g0010.1	442	48.502	8.55	-0.907	细胞核 Nucleus
NtTCP3	Nitab4.5_0000246g0120.1	323	35.413	5.51	-0.822	细胞核 Nucleus
NtTCP4	Nitab4.5_0000269g0060.1	367	39.854	7.37	-0.715	细胞核 Nucleus
NtTCP5	Nitab4.5_0000303g0270.1	326	34.960	6.87	-0.784	细胞核 Nucleus
NtTCP6	Nitab4.5_0000365g0240.1	412	44.290	8.99	-0.746	细胞核 Nucleus
NtTCP7	Nitab4.5_0000519g0050.1	222	24.004	9.82	-0.486	细胞核 Nucleus
NtTCP8	Nitab4.5_0000832g0020.1	357	38.007	5.53	-0.448	细胞核 Nucleus
NtTCP9	Nitab4.5_0000948g0150.1	556	59.693	7.19	-0.758	细胞核 Nucleus
NtTCP10	Nitab4.5_0001089g0050.1	161	16.833	7.33	-0.244	细胞核 Nucleus
NtTCP11	Nitab4.5_0001188g0020.1	399	43.838	6.89	-0.823	细胞核 Nucleus
NtTCP12	Nitab4.5_0003077g0060.1	596	66.701	6.14	-0.808	细胞核 Nucleus
NtTCP13	Nitab4.5_0003202g0050.1	420	46.357	6.57	-0.793	细胞核 Nucleus
NtTCP14	Nitab4.5_0004301g0070.1	300	31.547	8.65	-0.324	细胞核 Nucleus
NtTCP15	Nitab4.5_0005379g0040.1	359	38.206	5.43	-0.444	细胞核 Nucleus
NtTCP16	Nitab4.5_0005709g0020.1	589	65.994	6.65	-0.817	细胞核 Nucleus
NtTCP17	Nitab4.5_0007375g0060.1	295	32.098	7.14	-0.744	细胞核 Nucleus
NtTCP18	Nitab4.5_0007913g0020.1	544	58.332	7.00	-0.761	细胞核 Nucleus
NtTCP19	Nitab4.5_0009198g0010.1	419	44.840	8.04	-0.804	细胞核 Nucleus
NtTCP20	Nitab4.5_0011777g0010.1	261	27.539	9.71	-0.432	细胞核 Nucleus