Identification and Bioinformatics Analysis of Coconut ZF-HD GeneFamily

doi:10.3969/j.issn.1000-2561.2020.02.011

Abstract

Abstract:

ZF-HD protein is a family of transcription factors that contain zinc finger domains and only exist in plants. It not only regulates the growth and development of plants, but also plays an important role in floristic response to stress. In this study, 20 ZF-HD proteins of coconut were identified by comparison with the developed coconut genome database. Bioinformatics methods were used to analyze its genic structure, protein physicochemical properties, protein conserved domains, motifs, phylogenetic trees and expression profiles. The analysis showed that the coconut ZF-HD proteins are mostly basic protein. And they are mainly located in the nucleus, chloroplast and mitochondria. The coconut ZF-HD gene family could be divided into 6 subfamilies, each of which had similar structural domains and super secondary structures. The motif search analysis showed that the CoMIF subfamily only contained the zinc finger domain conserved sequence, and the other subfamilies contained the zinc finger domain sequence and the homeobox domain sequence. And expression profiling revealed that CoZHD18 and CoZHD20 were not detected in the sequenced tissues, and the expression levels of other family members in each tissue were different.

Key words: ZF-HD gene family, coconut, bioinformatics

CLC Number:

S667.4
Q786

SUN Xiwei,FAN Haikuo,Gong Shufang,LIU Rui,JIU Fengfeng,XIAO Yong. Identification and Bioinformatics Analysis of Coconut ZF-HD GeneFamily[J]. Chinese Journal of Tropical Crops, 2020, 41(2): 284-291.

Figures/Tables 10

References 19

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基因名 Gene Name	基因号 Gene ID	氨基酸数量 Amino acid/aa	分子量 Molecular mass/Da	等电点 Isoelectric point	亚细胞定位Subcellular localization
基因名 Gene Name	基因号 Gene ID	氨基酸数量 Amino acid/aa	分子量 Molecular mass/Da	等电点 Isoelectric point	nucl	cyto	plas	chlo	mito	cyto_nucl
CoZHD1	lcl\|CCG003285.1	238	25712.16	8.64	7	4		1	1
CoZHD2	lcl\|CCG005276.1	91	10012.12	8.85	2	1		10
CoZHD3	lcl\|CCG005440.1	274	30030.29	9.16	12	2
CoZHD4	lcl\|CCG005549.1	339	35822.11	8.64	14
CoZHD5	lcl\|CCG007468.1	300	32047.29	8.43	14
CoZHD6	lcl\|CCG007917.1	252	27800.2	9.30	13.5					7.5
CoZHD7	lcl\|CCG009609.1	266	28833.93	7.25	14
CoZHD8	lcl\|CCG012613.1	670	75156.63	6.35	7.5	4.5				6.5
CoZHD9	lcl\|CCG013720.1	280	28805.92	7.72	4	2			7
CoZHD10	lcl\|CCG014342.1	287	29589.81	7.32	3	2		1	7
CoZHD11	lcl\|CCG014499.1	314	33697.67	8.89	12			1
CoZHD12	lcl\|CCG014663.1	211	22848.11	9.66	2	3		7	2
CoZHD13	lcl\|CCG015462.1	186	20300.82	8.53	6	2			6
CoZHD14	lcl\|CCG015634.1	253	27585.59	9.06	10			3
CoZHD15	lcl\|CCG020271.1	291	31226.47	8.62	14
CoZHD16	lcl\|CCG020520.1	254	27337.28	9.32		3			11
CoZHD17	lcl\|CCG024320.1	277	30453.79	8.38	12		1
CoZHD18	lcl\|CCG025566.1	270	29806.72	8.59	13
CoZHD19	lcl\|CCG025946.1	308	32154.39	6.78	13
CoZHD20	lcl\|CCG025947.1	101	11148.78	8.82		3		10

基因名 Gene Name	基因号 Gene ID	氨基酸数量 Amino acid/aa	分子量 Molecular mass/Da	等电点 Isoelectric point	亚细胞定位Subcellular localization
基因名 Gene Name	基因号 Gene ID	氨基酸数量 Amino acid/aa	分子量 Molecular mass/Da	等电点 Isoelectric point	nucl	cyto	plas	chlo	mito	cyto_nucl
CoZHD1	lcl\|CCG003285.1	238	25712.16	8.64	7	4		1	1
CoZHD2	lcl\|CCG005276.1	91	10012.12	8.85	2	1		10
CoZHD3	lcl\|CCG005440.1	274	30030.29	9.16	12	2
CoZHD4	lcl\|CCG005549.1	339	35822.11	8.64	14
CoZHD5	lcl\|CCG007468.1	300	32047.29	8.43	14
CoZHD6	lcl\|CCG007917.1	252	27800.2	9.30	13.5					7.5
CoZHD7	lcl\|CCG009609.1	266	28833.93	7.25	14
CoZHD8	lcl\|CCG012613.1	670	75156.63	6.35	7.5	4.5				6.5
CoZHD9	lcl\|CCG013720.1	280	28805.92	7.72	4	2			7
CoZHD10	lcl\|CCG014342.1	287	29589.81	7.32	3	2		1	7
CoZHD11	lcl\|CCG014499.1	314	33697.67	8.89	12			1
CoZHD12	lcl\|CCG014663.1	211	22848.11	9.66	2	3		7	2
CoZHD13	lcl\|CCG015462.1	186	20300.82	8.53	6	2			6
CoZHD14	lcl\|CCG015634.1	253	27585.59	9.06	10			3
CoZHD15	lcl\|CCG020271.1	291	31226.47	8.62	14
CoZHD16	lcl\|CCG020520.1	254	27337.28	9.32		3			11
CoZHD17	lcl\|CCG024320.1	277	30453.79	8.38	12		1
CoZHD18	lcl\|CCG025566.1	270	29806.72	8.59	13
CoZHD19	lcl\|CCG025946.1	308	32154.39	6.78	13
CoZHD20	lcl\|CCG025947.1	101	11148.78	8.82		3		10

亚家族Subfamily	家族成员 Family Members
ZHDⅠ	CoZHD9、CoZHD10、AtZHD1、AtZHD2
ZHDⅡ	AtZHD3、AtZHD4、AtZHD5、CoZHD3、CoZHD14、CoZHD17、CoZHD18
ZHDⅢ	AtZHD6、AtZHD7
ZHDⅣ	AtZHD8、AtZHD9、AtZHD10、AtZHD11、AtZHD12、CoZHD1、CoZHD5、CoZHD15、CoZHD19
ZHDⅤ	AtZHD13、AtZHD14、CoZHD12、CoZHD13、CoZHD16
MIF	AtMIF1、AtMIF2、AtMIF3、CoZHD2、CoZHD8、CoZHD20
UK	CoZHD4、CoZHD5、CoZHD6、CoZHD7、CoZHD11、CoZHD15

亚家族Subfamily	家族成员 Family Members
ZHDⅠ	CoZHD9、CoZHD10、AtZHD1、AtZHD2
ZHDⅡ	AtZHD3、AtZHD4、AtZHD5、CoZHD3、CoZHD14、CoZHD17、CoZHD18
ZHDⅢ	AtZHD6、AtZHD7
ZHDⅣ	AtZHD8、AtZHD9、AtZHD10、AtZHD11、AtZHD12、CoZHD1、CoZHD5、CoZHD15、CoZHD19
ZHDⅤ	AtZHD13、AtZHD14、CoZHD12、CoZHD13、CoZHD16
MIF	AtMIF1、AtMIF2、AtMIF3、CoZHD2、CoZHD8、CoZHD20
UK	CoZHD4、CoZHD5、CoZHD6、CoZHD7、CoZHD11、CoZHD15

亚家族Subfamily	家族成员 Family Members
CoZHDⅠ	CoZHD9、CoZHD10
CoZHDⅡ	CoZHD3、CoZHD14、CoZHD17、CoZHD18
CoZHDⅢ	CoZHD1、CoZHD5、CoZHD15、CoZHD19
CoZHDⅣ	CoZHD12、CoZHD13、CoZHD14、CoZHD16
CoMIF	CoZHD2、CoZHD8、CoZHD20
UK	CoZHD4、CoZHD5、CoZHD6、CoZHD7、 CoZHD11、CoZHD15