山金柑GATA基因家族全基因组鉴定及在果实发育中的表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0880

摘要/Abstract

摘要：

目的探究GATA转录因子基因家族在山金柑果实发育中的调控作用。方法采用生物信息学方法，对其山金柑GATA转录因子基因家族进行全基因组鉴定，并结合转录组数据和RT-qPCR，对其理化性质、基因结构、系统发育树和表达模式进行分析。结果在山金柑中共鉴定到26个FhGATAs，不均匀分布在9条染色体上；理化性质分析表明，该家族蛋白都位于细胞核中，分子量在18 019.89-60 342.13 Da范围，属于亲水性蛋白，pI介于4.62-10.33；与拟南芥同源基因进行聚类分析，FhGATA基因家族可分为4个亚家族，同一个亚家族的基序组成和分布模式相似，其中Subfamily Ⅲ亚家族的一些基因在进化过程中缺失；共线性分析表明，山金柑中存在7个共线FhGATAs基因，拟南芥中有24个AtGATAs基因与FhGATAs基因同源，甜橙中有33个CsGATAs基因与FhGATAs基因同源；FhGATA基因的转录调控机制包含光响应和光的反应性元件，以及各种激素反应、胁迫反应和生长发育相关元件；组织表达分析显示，FhGATA基因家族的4个亚家族在根、茎、叶、花、果实和种子中表现不同程度的特异性表达，其中FhGATA24、FhGATA22、FhGATA26、FhGATA18、FhGATA12和FhGATA5在果实中高表达；进一步RT-qPCR分析表明，FhGATA基因与山金柑的单果重和横纵径密切相关，其中FhGATA22和FhGATA18在大果和小果山金柑的果实发育全过程均存在显著差异。结论山金柑含有26个FhGATAs基因，其中FhGATA22和FhGATA18可能是介导山金柑果实大小的调控因子。

关键词: 山金柑, GATA, 转录因子, 基因家族, 果实发育, 表达分析

Abstract:

Objective To explore the regulation of GATA transcription factor gene family in the development of Jindou Kumquat (Fortunella hindsii). Method Bioinformatics was used to identify its GATA transcription factor gene family, and analyze its physicochemical properties, gene structure, phylogenetic tree and expression patterns via combining transcriptome data with RT-qPCR. Result A total of 26 FhGATAs transcription factors were identified in Jindou Kumquat, unevenly distributed on the nine chromosomes. Analysis of the physicochemical properties showed that, this family of proteins were all located in the nucleus, molecular weight in the range from 18 019.89 to 60 342.13 Da, belonging to the hydrophilic proteins, and the pI were 4.62 to 10.33. Cluster analysis with orthologous genes in Arabidopsis thaliana, FhGATA gene family can be divided into four subfamilies, the motif composition and distribution patterns were similar in the same subfamily, and some genes in the Subfamily Ⅲ were missing during evolution. Collinearity analysis showed that, 7 collinear FhGATAs genes in Jindou Kumquat, 24 AtGATAs gene pairs were homologous to the FhGATA gene in A. thaliana, 33 CsGATAs gene were homologous to FhGATA gene in Citrus sinensis. The mechanism of transcriptional regulation of FhGATA genes contained reactive elements that were light-responsive and light, and various hormone responses, stress responses, and growth and development-related. Tissue expression analysis revealed that, the four subfamilies of the FhGATAs gene family showed varying degrees of specific expression in the root, stem, leaf, flower, fruit and seed; moreover, FhGATA24, FhGATA22, FhGATA26, FhGATA18, FhGATA12 and FhGATA5 were highly expressed in the fruit. Further qRT-PCR analysis indicated that, the FhGATA gene was closely related to the single fruit weight, horizontal diameter and vertical diameter of Jindou Kumquat, among them, FhGATA22 and FhGATA18 showed significant differences in the whole fruit development of Jindou kumquat. Conclusion The Jindou kumquat contains 26 FhGATAs genes, of which FhGATA22 and FhGATA18 may be regulators mediating the fruit size.

Key words: Fortunella hindsii, GATA, transcription factor, gene family, fruit development, expression analysis

罗嗣芳, 张祖铭, 谢丽芳, 郭紫晶, 陈兆星, 杨月华, 严翔, 张洪铭. 山金柑GATA基因家族全基因组鉴定及在果实发育中的表达分析[J]. 生物技术通报, 2025, 41(5): 218-230.

LUO Si-fang, ZHANG Zu-ming, XIE Li-fang, GUO Zi-jing, CHEN Zhao-xing, YANG Yue-hua, YAN Xiang, ZHANG Hong-ming. Genome-wide Identification of GATA Gene Family of Jindou Kumquat （Fortunella hindsii） and Their Expression Analysis in Fruit Development[J]. Biotechnology Bulletin, 2025, 41(5): 218-230.

图/表 10

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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′）
UBQ10	GATCCCACCAGACCAGCAA	ACCAAATGAAGGGTTGATTCCTT
FhGATA24	AACATTGTGGCGTTAGTG	GATTGACAGCCTTAGCAG
FhGATA22	GGCCTCAAGTTATCCATG	AGGTCCACTCCTCCAAAG
FhGATA26	TTCTCAAGCGAAAGTCAA	TGCTATGGAACTGGGATG
FhGATA18	TATCCAAGCCAAAGCAAT	CTCCAAAGCGGTGTAGAA
FhGATA12	GCGGAGACCATTTCATTG	GTTGGGATTAGCGTTCGT
FhGATA5	CATACCCACCAGCGAACT	GGATGACGAAGATGAGGC

基因名称Gene name	上游引物Forward primer （5′-3′）	下游引物Reverse primer （5′-3′）
UBQ10	GATCCCACCAGACCAGCAA	ACCAAATGAAGGGTTGATTCCTT
FhGATA24	AACATTGTGGCGTTAGTG	GATTGACAGCCTTAGCAG
FhGATA22	GGCCTCAAGTTATCCATG	AGGTCCACTCCTCCAAAG
FhGATA26	TTCTCAAGCGAAAGTCAA	TGCTATGGAACTGGGATG
FhGATA18	TATCCAAGCCAAAGCAAT	CTCCAAAGCGGTGTAGAA
FhGATA12	GCGGAGACCATTTCATTG	GTTGGGATTAGCGTTCGT
FhGATA5	CATACCCACCAGCGAACT	GGATGACGAAGATGAGGC

基因名称 Gene name	序列ID Sequence ID	氨基酸数 Number of amino acids （aa）	分子量Molecular weight （Da）	等电点 pI	不稳定指数 Instability index	脂肪族指数 Aliphatic index	亲水性 Hydropathicity	亚细胞定位预测 Subcellular localization prediction
FhGATA1	Fh1g02150.1	383	42 038.44	7.6	63.22	63.71	-0.564	细胞核Nucleus
FhGATA2	Fh1g02950.1	255	28 400.27	8.5	69.86	41.37	-0.832	细胞核Nucleus
FhGATA3	Fh1g12080.1	334	36 707.68	5.72	48.19	54.91	-0.618	细胞核Nucleus
FhGATA4	Fh1g20200.1	293	32 046.49	6.21	33.41	65.9	-0.787	细胞核Nucleus
FhGATA5	Fh1g24810.1	174	19 850.51	8.45	48.8	52.13	-0.718	细胞核Nucleus
FhGATA6	Fh1g24830.1	187	21 125.25	9.27	52.56	63.16	-0.663	细胞核Nucleus
FhGATA7	Fh2g01760.1	194	21 244.52	8.36	61.05	49.9	-0.962	细胞核Nucleus
FhGATA8	Fh2g01770.1	235	25 833.13	8.32	43.61	49.15	-1.065	细胞核Nucleus
FhGATA9	Fh3g10640.1	215	24 043.04	8.38	87.62	75.72	-0.713	细胞核Nucleus
FhGATA10	Fh3g25040.1	167	18 019.89	10.01	58.03	61.44	-0.513	细胞核Nucleus
FhGATA11	Fh3g27480.1	376	41 093.1	4.62	47.51	66.14	-0.798	细胞核Nucleus
FhGATA12	Fh3g27490.1	303	32 672.03	5.2	48.69	62.81	-0.637	细胞核Nucleus
FhGATA13	Fh4g04580.1	372	41 136.38	6.13	48.93	53.76	-0.817	细胞核Nucleus
FhGATA14	Fh4g05470.1	319	35 477.63	9.24	50.02	60.28	-0.829	细胞核Nucleus
FhGATA15	Fh4g05480.1	314	35 084.39	9.58	51.19	60.32	-0.8	细胞核Nucleus
FhGATA16	Fh4g10680.1	323	35 563.4	9.6	65.28	63.5	-0.733	细胞核Nucleus
FhGATA17	Fh5g07350.1	542	60 342.13	6.08	57.42	69.23	-0.656	细胞核Nucleus
FhGATA18	Fh5g35260.1	323	35 397.56	7.03	64.95	63.16	-0.733	细胞核Nucleus
FhGATA19	Fh5g42420.1	146	16 120.58	10.33	40.91	60.89	-0.696	细胞核Nucleus
FhGATA20	Fh5g48920.1	263	29 379.13	6.17	59.82	55.29	-0.89	细胞核Nucleus
FhGATA21	Fh7g06080.1	341	37 419.93	6.27	56.8	62.29	-0.61	细胞核Nucleus
FhGATA22	Fh8g08720.1	321	35 679.5	5.41	57.96	50.34	-0.681	细胞核Nucleus
FhGATA23	Fh8g12210.1	401	44 617.78	5.43	51.58	62.82	-0.694	细胞核Nucleus
FhGATA24	Fh8g25310.1	370	42 072.87	9.06	60.54	61.38	-0.663	细胞核Nucleus
FhGATA25	Fh9g01800.1	181	19 719.64	9.26	54.8	85.69	-0.387	细胞核Nucleus
FhGATA26	Fh9g11500.1	262	29 032.8	8.44	46.74	68.02	-0.599	细胞核Nucleus

基因名称 Gene name	序列ID Sequence ID	氨基酸数 Number of amino acids （aa）	分子量Molecular weight （Da）	等电点 pI	不稳定指数 Instability index	脂肪族指数 Aliphatic index	亲水性 Hydropathicity	亚细胞定位预测 Subcellular localization prediction
FhGATA1	Fh1g02150.1	383	42 038.44	7.6	63.22	63.71	-0.564	细胞核Nucleus
FhGATA2	Fh1g02950.1	255	28 400.27	8.5	69.86	41.37	-0.832	细胞核Nucleus
FhGATA3	Fh1g12080.1	334	36 707.68	5.72	48.19	54.91	-0.618	细胞核Nucleus
FhGATA4	Fh1g20200.1	293	32 046.49	6.21	33.41	65.9	-0.787	细胞核Nucleus
FhGATA5	Fh1g24810.1	174	19 850.51	8.45	48.8	52.13	-0.718	细胞核Nucleus
FhGATA6	Fh1g24830.1	187	21 125.25	9.27	52.56	63.16	-0.663	细胞核Nucleus
FhGATA7	Fh2g01760.1	194	21 244.52	8.36	61.05	49.9	-0.962	细胞核Nucleus
FhGATA8	Fh2g01770.1	235	25 833.13	8.32	43.61	49.15	-1.065	细胞核Nucleus
FhGATA9	Fh3g10640.1	215	24 043.04	8.38	87.62	75.72	-0.713	细胞核Nucleus
FhGATA10	Fh3g25040.1	167	18 019.89	10.01	58.03	61.44	-0.513	细胞核Nucleus
FhGATA11	Fh3g27480.1	376	41 093.1	4.62	47.51	66.14	-0.798	细胞核Nucleus
FhGATA12	Fh3g27490.1	303	32 672.03	5.2	48.69	62.81	-0.637	细胞核Nucleus
FhGATA13	Fh4g04580.1	372	41 136.38	6.13	48.93	53.76	-0.817	细胞核Nucleus
FhGATA14	Fh4g05470.1	319	35 477.63	9.24	50.02	60.28	-0.829	细胞核Nucleus
FhGATA15	Fh4g05480.1	314	35 084.39	9.58	51.19	60.32	-0.8	细胞核Nucleus
FhGATA16	Fh4g10680.1	323	35 563.4	9.6	65.28	63.5	-0.733	细胞核Nucleus
FhGATA17	Fh5g07350.1	542	60 342.13	6.08	57.42	69.23	-0.656	细胞核Nucleus
FhGATA18	Fh5g35260.1	323	35 397.56	7.03	64.95	63.16	-0.733	细胞核Nucleus
FhGATA19	Fh5g42420.1	146	16 120.58	10.33	40.91	60.89	-0.696	细胞核Nucleus
FhGATA20	Fh5g48920.1	263	29 379.13	6.17	59.82	55.29	-0.89	细胞核Nucleus
FhGATA21	Fh7g06080.1	341	37 419.93	6.27	56.8	62.29	-0.61	细胞核Nucleus
FhGATA22	Fh8g08720.1	321	35 679.5	5.41	57.96	50.34	-0.681	细胞核Nucleus
FhGATA23	Fh8g12210.1	401	44 617.78	5.43	51.58	62.82	-0.694	细胞核Nucleus
FhGATA24	Fh8g25310.1	370	42 072.87	9.06	60.54	61.38	-0.663	细胞核Nucleus
FhGATA25	Fh9g01800.1	181	19 719.64	9.26	54.8	85.69	-0.387	细胞核Nucleus
FhGATA26	Fh9g11500.1	262	29 032.8	8.44	46.74	68.02	-0.599	细胞核Nucleus

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