基于苋菜转录组的<i>TCP</i>基因家族成员鉴定及表达分析

安子贤; 李宜轩; 郑友峰; 肖昉; 王乐; 陈何; 赖钟雄; 牟建梅; 刘生财

doi:10.19303/j.issn.1008-0384.2022.007.007

基于苋菜转录组的TCP基因家族成员鉴定及表达分析

doi: 10.19303/j.issn.1008-0384.2022.007.007

1.
福建农林大学园艺植物生物工程研究所，福建福州 350002
2.
苏州市农业科学院，江苏　苏州 215000

基金项目: 福建省自然科学基金项目（2018J01700）；福建农林大学经济作物种业工程服务队项目（11899170125）

详细信息

作者简介:
安子贤（1998−），女，硕士研究生，研究方向：蔬菜育种与生物技术（E-mail：1010051118@qq.com）

通讯作者:
刘生财（1980−），男，博士，副教授，研究方向：园艺植物生物技术、次生代谢通路（E-mail：1215698900@qq.com）

中图分类号: S 636.4
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出版历程
- 收稿日期: 2022-06-23
- 修回日期: 2022-07-07
- 网络出版日期: 2022-08-07
- 刊出日期: 2022-07-28

Transcriptome-based Identification and Expressions of Amaranth TCP Gene Family

1.
Institute of Horticultural Plant Bioengineering, Fujian Agriculture and Forestry University, Fuzhou, Fujian　350002, China
2.
Suzhou City Academy of Agricultural Sciences, Suzhou, Jiangsu　215000, China

摘要

摘要: 目的基于大红苋菜转录组数据库，对苋菜TCP基因家族成员进行筛选鉴定，为深入探讨苋菜TCP基因家族对苋菜生长发育及非生物胁迫响应提供参考。方法在转录组数据库中，筛选鉴定TCP基因家族成员，并对其进行生物信息学分析；在不同条件处理下培养苋菜幼苗，并利用qRT-PCR技术分析其在不同处理下的表达模式。结果苋菜TCP基因家族有14个成员，全部定位于细胞核；AtrTCP蛋白质长度在230~721 aa区间内，预测相对分子量为25.25~78.57 kD，等电点为6.15~9.45，包含15个保守基序；除AtrTCP11为稳定蛋白外，其余均为不稳定蛋白；miRNA预测到两个AtrTCP家族成员AtrTCP2和AtrTCP6为miR319靶基因。qRT-PCR结果显示：在盐溶液不同浓度（0、50、100 、200 mmol·L^-1）处理下，该基因家族具有不同的表达模式；在蓝光处理下，AtrTCP10基因表达量上调达到了显著水平；AtrTCP2、AtrTCP3、AtrTCP8、AtrTCP9、AtrTCP11和AtrTCP13表达量下调达到了显著水平；在不同铵硝比（0∶0、0∶10、3∶7、5∶5、7∶3、10∶0）处理下，TCP基因家族各成员表达模式不同，其中，AtrTCP3参与整个氮代谢过程；在苋菜各部位进行qRT-PCR分析发现：AtrTCP3、AtrTCP12 在叶片中高表达，其余家族成员均在根部的表达量较高。结论在不同条件处理下，苋菜TCP基因家族各成员表达模式不同，表明苋菜TCP基因家族各成员可能广泛参与非生物胁迫。
- 苋菜 /
- TCP转录因子 /
- 基因家族 /
- 生物信息学分析 /
- 表达
Abstract: Objective Members of the amaranth TCP gene family were identified based on the transcriptome database for an in-depth understanding on the roles they associated with the growth, development, and abiotic stress of the plant. Method Members of the TCP gene family were identified by screening the transcriptome database on Dahong amaranth (Amaranthus tricolor L.) for a bioinformatics analysis. Amaranth seedlings were cultured under different conditions and their expressions under different treatments analyzed by qRT-PCR. Results Amaranth TCP gene family has 14 members, all localized in the nucleus. The length of AtrTCP protein was in the range of 230–721 aa, the predicted relative molecular weight was 25.25–78.57 kD, the isoelectric point was 6.15–9.45, and it contained 15 conserved motifs. Except AtrTCP11, which was stable protein, all the other proteins were unstable. Two AtrTCP family members, AtrTCP2 and AtrTCP6, were predicted as miR319 target genes by miRNA. qRT-PCR showed differentiated expressions of the family members under salt solutions of varied concentrations (i.e., 0, 50, 100, and 200 mmol·L⁻¹). The expression of the upregulated AtrTCP10 reached a significant level under blue light, and so did those of the downregulated AtrTCP2, AtrTCP3, AtrTCP8, AtrTCP9, AtrTCP11, and AtrTCP13. Under different concentrations of ammonium nitrate ratio (0∶0, 0∶10, 3∶7, 5∶5, 7∶3, 10∶0) treatment, the expressions of the TCP genes differed. AtrTCP3 was shown to be involved in the entire nitrogen metabolism process. In tissues of amaranth, AtrTCP3 and AtrTCP12 were highly expressed in leaves, while the others in roots. Conclusion Depending on the treatments, the expressions of the amaranth TCP gene family members differed. It suggested a broad spectrum of involvements by the members associated with abiotic stresses on amaranth.
- Amaranthus tricolor L. /
- transcription factor /
- gene family /
- bioinformatics analysis /
- expression

HTML全文

图 1 苋菜AtrTCP与拟南芥AtTCP基因家族进化树对比

Figure 1. Comparison of AtrTCP family trees of amaranth and Arabidopsis thaliana

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图 2 AtrTCP基因家族保守氨基酸分析

Figure 2. Conserved amino acids in AtrTCP family

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图 3 AtrTCP家族对苋菜盐胁迫处理下的影响

小写字母代表在0.05水平上差异显著。图5、6同。

Figure 3. Effect of AtrTCP family on amaranth under salt stress

Data with lowercase letters represent significant differences at P＜0.05. Same for Figs. 5 and 6.

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图 4 AtrTCP家族在不同光质处理下的表达量

*代表在0.05水平上差异显著。

Figure 4. Expressions of AtrTCP family under light exposures

*represents significant difference at P＜0.05.

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图 5 AtrTCP家族成员在不同铵硝比处理下的表达量

Figure 5. Expression levels of AtrTCP family members treated with different ammonium to nitrate ratios

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图 6 AtrTCP家族在苋菜不同部位的表达趋势

Figure 6. Expressions of AtrTCP family in different tissues of amaranth plant

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表 1 AtrTCP定量引物

Table 1. Quantitative primers of AtrTCP

基因 Gene	正向引物序列（5′-3′） Forward primer sequences （5′-3′）	反向引物序列（5′-3′） Reverse primer sequences（5′-3′）
AtrTCP1	GCTGCTACTGGTGCTTCTATT	ACCCATACCCATACCCATC
AtrTCP2	GATGAGCAGCAACATTCACT	CACCACTTCCACCAACACT
AtrTCP3	TCTTCAACAAGCCGAACC	ATTTCCCACCTCAATCCC
AtrTCP4	GGTTAGTTCAAACGGCAGA	ACTGTCTTCCAAATCGGGT
AtrTCP5	TTATCCATACCCGAACAGC	TTTAGTGTGACGGTCTTTGG
AtrTCP6	TTGCTACTGGTAGAGGTGGT	CCGGACCCATGTAACATTGA
AtrTCP7	AACCTCCACCAAAGACCGT	GTTTCTCCATCTGACTTATGCC
AtrTCP8	GCCTACAGAAACAGTAACCCTC	CCCGTTCAAGAAGCCATT
AtrTCP9	TCCACCAAGGTCATCATCTT	ATCATCGTCTCTCCGTCCA
AtrTCP10	CGCAGAATCAAGAACAAGC	TGACTTTGGTATGGCGGT
AtrTCP11	TGCTACAGGAACCGGGACTATT	GATGGCTTGGATCACTCAACTG
AtrTCP12	TGGAGGCAAAGATAGACATAGC	TAATGGGCAAAGGAGGGA
AtrTCP13	CAACCATCATCGTCCCAA	AGTTCCACTTTGCGGCTGT
AtrTCP14	ACCACAGCCACAACAAAGT	GCGGATACTGAGTCAAAGGA
EF1a	GGGATGCTGGTATGGTGAA	ACGGGTCATTTCTTCTTCTGAG

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表 2 AtrTCP基因家族理化性质分析

Table 2. Physicochemical properties of AtrTCP family

基因 ID Gene ID	基因名称 Gene name	蛋白质长度 Protein length/aa	分子式 Formula	理化性质 Physicochemical properties
基因 ID Gene ID	基因名称 Gene name	蛋白质长度 Protein length/aa	分子式 Formula	相对分子量 Relative molecular weight/kD	等电点 Theoretical pI	不稳定系数 Instability index	平均亲水系数 Grand average of hydropathicity
CL11166.Contig2_All	AtrTCP1	377	C₁₇₄₇H₂₇₇₇N₅₃₅O₅₇₀S₁₄	40.84	6.61	50.76	−0.712
CL1181.Contig4_All	AtrTCP2	423	C₁₉₅₀H₃₀₀₈N₆₀₈O₆₃₆S₆	45.34	6.64	54.40	−0.805
CL4511.Contig1_All	AtrTCP3	326	C₁₅₂₀H₂₄₃₂N₄₆₂O₄₉₅S₆	35.29	9.17	50.51	−0.540
CL531.Contig1_All	AtrTCP4	514	C₂₃₀₉H₃₆₄₀N₇₃₆O₇₉₅S₁₄	54.88	8.57	43.25	−0.823
CL7519.Contig2_All	AtrTCP5	231	C₁₀₉₆H₁₇₁₁N₃₄₁O₃₄₂S₉	25.43	9.00	49.08	−0.764
CL7919.Contig2_All	AtrTCP6	355	C₁₆₇₁H₂₅₇₅N₅₁₉O₅₄₃S₉	38.91	6.79	40.47	−0.860
CL9396.Contig1_All	AtrTCP7	430	C₁₉₅₁H₃₀₃₆N₆₁₆O₆₅₄S₉	45.87	6.66	47.14	−0.747
Unigene1202_All	AtrTCP8	345	C₁₅₄₄H₂₅₂₂N₄₆₂O₅₁₈S₉	36.13	9.30	47.05	−0.408
Unigene22459_All	AtrTCP9	299	C₁₃₇₃H₂₂₁₄N₄₂₂O₄₄₄S₄	31.87	9.45	56.13	−0.563
Unigene27038_All	AtrTCP10	231	C₁₁₁₅H₁₇₇₁N₃₁₇O₃₄₀S₆	25.25	9.23	63.06	−0.492
Unigene27184_All	AtrTCP11	347	C₁₆₀₆H₂₄₈₃N₄₈₅O₅₂₃S₁₀	37.27	8.49	38.62	−0.743
Unigene35431_All	AtrTCP12	230	C₁₁₁₈H₁₇₈₇N₃₂₉O₃₆₄S₄	25.79	8.56	44.38	−0.820
Unigene6554_All	AtrTCP13	431	C₁₉₅₅H₃₀₄₂N₆₁₈O₆₅₆S₉	45.99	6.66	47.05	−0.754
Unigene73441_All	AtrTCP14	721	C₃₃₉₅H₅₄₃₄N₁₀₀₆O₁₁₀₅S₁₇	78.57	6.15	58.04	−0.602

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表 3 AtrTCP基因家族蛋白质二级结构及亚细胞定位分析

Table 3. Protein secondary structures and subcellular localizations of AtrTCP family

转录因子 Transcription factor	TCP结构域 TCP domain	蛋白质二级结构 Secondary protein structure				亚细胞定位 Subcellulav localization
转录因子 Transcription factor	TCP结构域 TCP domain	α-螺旋 Alpha helix/%	β-转角 Beta turn/%	延伸链 Extended strand/%	无规卷曲 Random coil/%	亚细胞定位 Subcellulav localization
AtrTCP1	111-377	19.36	5.04	13.79	61.80	Nucleus.
AtrTCP2	43-178	14.42	2.36	11.58	71.63	Nucleus.
AtrTCP3	86-326	24.23	5.52	15.34	54.91	Nucleus.
AtrTCP4	95-253	14.20	2.53	15.18	68.09	Nucleus.
AtrTCP5	57-228	13.85	9.52	16.45	60.17	Nucleus.
AtrTCP6	55-223	14.08	1.69	14.65	69.58	Nucleus.
AtrTCP7	88-290	20.70	4.19	10.23	64.88	Nucleus.
AtrTCP8	65-176	15.65	5.22	10.43	68.70	Nucleus.
AtrTCP9	51-258	19.73	6.02	18.06	56.19	Nucleus.
AtrTCP10	91-231	19.05	4.76	13.42	62.77	Nucleus.
AtrTCP11	69-256	11.82	10.95	21.33	55.91	Nucleus.
AtrTCP12	54-215	22.61	5.22	13.48	58.70	Nucleus.
AtrTCP13	88-291	14.39	5.10	11.37	69.14	Nucleus.
AtrTCP14	51-332	20.11	5.83	16.37	57.70	Nucleus.

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表 4 苋菜AtrTCP基因家族miRNA的预测及差异表达分析

Table 4. Prediction and differential expressions of AtrTCP family miRNA

基因名称 Gene name	对应 miRNA	期望值 Expectation	抑制 Inhibition	多样性 Multiplicity	表达量 Expression quantity	表达趋势 Express trend
AtrTCP6	miR319_1	1.5	切割 Cleavage	1	0.764797327	上调 Up
	miR319_2	1.5	切割 Cleavage	1	−0.396055889	下调 Down
	miR319a-3p	1.5	切割 Cleavage	1	−0.134714289	下调 Down
	miR319a_1	1.5	切割 Cleavage	1	0.179984679	上调 Up
	miR319a	2.5	切割 Cleavage	1	−0.06725778	下调 Down
	miR319c_3	2.5	切割 Cleavage	1	0.137854295	上调 Up
	miR159a_1	3.0	切割 Cleavage	1	0.073891584	上调 Up
	Total miRNA	—	—	―	0.558499927	上调 Up
AtrTCP2	miR319_1	3.0	切割 Cleavage	1	0.764797327	上调 Up
	miR319_2	3.0	切割 Cleavage	1	−0.396055889	下调 Down
	miR319a-3p	3.0	切割 Cleavage	1	−0.134714289	下调 Down
	miR319a_1	3.0	切割 Cleavage	1	0.179984679	上调 Up
	Total miRNA	—	—	—	0.414011828	上调 Up
AtrTCP11	miR5658	3.0	切割 Cleavage	1	−0.227576991	下调 Down
AtrTCP13	miR5658	3.0	切割 Cleavage	1	−0.227576991	下调 Down
“Total miRNA”表示基因对应miRNA的总表达趋势；“—”表示无结果。 "Total miRNA" represents the Total expression trend of miRNA corresponding to the gene. "—" indicates no result.

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