Genome-wide Identification and Expression Analysis of Prunus avium Gretchen Hagen 3（GH3）Gene Family

doi:10.16420/j.issn.0513-353x.2020-0911

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (12): 2360-2374.doi: 10.16420/j.issn.0513-353x.2020-0911

Genome-wide Identification and Expression Analysis of Prunus avium Gretchen Hagen 3（GH3）Gene Family

HOU Qiandong¹, SHEN Tianjiao¹, YU Huanhuan¹, QIU Zhilang¹, WEN Zhuang¹, ZHANG Huimin¹^,², WU Yawei³, WEN Xiaopeng¹^,^*()

¹Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region（Ministry of Education）,Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering（CICMEAB）,Institute of Agro-bioengineering,College of Life Sciences,Guizhou University,Guiyang 550025,China
²Institute for Forest Resources & Environment of Guizhou,College of Forestry,Guizhou University,Guiyang 550025,China
³Institute of Fruit Tree Research,Guizhou Provincial Academy of Agricultural Sciences,Guiyang 550006,China

Received:2021-01-06 Revised:2021-05-06 Published:2022-01-04
Contact: WEN Xiaopeng E-mail:xpwensc@hotmail.com

Abstract

Abstract:

Auxin plays a crucial role in regulating the growth and development of plants. The acyl acid amido synthetase Gretchen Hagen 3（GH3）may modulate auxin levels via conjugting both indole-3-acetic acid（IAA）and salicylic acid（SA）in response to environment changes. In the current investigation,genome-wide identification and comprehensive analysis of the GH3 gene family in sweet cherry（Prunus avium）were conducted using the genomic sequence. Totally,eight members of PavGH3 genes were identified from the whole genome of sweet cherry,which are not evenly distributed on the chromosomes,with the coding sequence of 1 683-1 851 bp,most of which were forecasted in chloroplast. The analysis of gene structure and domain revealed that PavGH3 demonstrated high similarity among the members,and the number of exons was three or four. A total of 16 conserved domains were obtained,and the number of the conserved domains varied among the members. These gene members were clustered into two major groups（I and II）,based on phylogenetic analysis. Sequence analysis of promoters showed many cis-regulatory elements which presumably responsed to phytohormones such as abscisic acid,methyl jasmonate etc. Synteny block indicated that PavGH3.5 and PavGH3.6 showed collinearity with GH3 in Arabidopsis thaliana,suggesting that they were evolutionarily conserved. Multiple sequence alignment demonstrated that these members are highly similar and conserved. As detected by qRT-PCR in 17 tissues. PavGH3.2,PavGH3.3 and PavGH3.6 were highy expressed in these tissues. PavGH3.4 and PavGH3.5 were up-regulated in the dropped-fruit of the second physiological abscission in comparison with that of the first one. Compared with retention fruits,surprisingly,PavGH3.5 and PavGH3.7 were significantly down-regulated in the first physiological fruit drops,PavGH3.4 and PavGH3.6 were up-regulated. IAA,GA₃,ABA and MeJA were used to foliar application,and PavGH3.2,PavGH3.3,PavGH3.6 and PavGH3.7 were differentially expressed in response to the type and application stage of the phytohormones,however,no responses were observed in the others. Therefore,it is speculated that the PavGH3 gene family is considerably involved in the regulation of the growth and development of sweet cherry,and probably in the fruit abscission.

Key words: Prunus avium, Gretchen Hagen 3, gene family, auxin response, expression analysis

CLC Number:

S662.5

HOU Qiandong, SHEN Tianjiao, YU Huanhuan, QIU Zhilang, WEN Zhuang, ZHANG Huimin, WU Yawei, WEN Xiaopeng. Genome-wide Identification and Expression Analysis of Prunus avium Gretchen Hagen 3（GH3）Gene Family[J]. Acta Horticulturae Sinica, 2021, 48(12): 2360-2374.

Figures/Tables 9

References 58

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基因 Gene	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer	扩增产物/bp PCR product	退火温度/℃ T_m
PavGH3.1	CAGTTGCAGAAATGCTGTGTCC	TCATGTGGCTTGCTTAGTGGGT	276	61
PavGH3.2	GGTCCTCAGCAGCCGAATCAC	CCACCCTTCAGAAGCGCCATA	265	64
PavGH3.3	ACTTCTTTGGTGCCCCTTGCTTC	GTGGTCTGTGCGCTATGGTGTGT	179	65
PavGH3.4	CTCTTACACCCTCATTCCCTCCAT	CGACTCTCAGCACATCTCCAACT	224	59
PavGH3.5	CATAGAGGAGACGACCAGGAACA	GGAACTCAGAGATGGGATGAGAGCT	239	62
PavGH3.6	CTCCCATCTTGTCAGCTCACCCA	GCTCACGAACAGAAAGTACAGGCCC	197	62
PavGH3.7	CTGTTGAGGTTCTTGGTGGGC	AGTTTTCTCGGGGGGTTGCA	263	60
PavGH3.8	CTCCCTTGCTTTCTCTGCCTAAT	GACCACAGCCTCAATGTACTTG	125	60
PavEF1-α2	ATCCAGAGTAGCAGAACCAATCAC	GTTAGGCATCCAGTCCCAGAAT	127	58
PavRSP3	TCAAGGTCAGGTAAGGGGGTC	GTGAGGTGATTGTTAGTGGAAAGC	223	56.5

基因 Gene	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer	扩增产物/bp PCR product	退火温度/℃ T_m
PavGH3.1	CAGTTGCAGAAATGCTGTGTCC	TCATGTGGCTTGCTTAGTGGGT	276	61
PavGH3.2	GGTCCTCAGCAGCCGAATCAC	CCACCCTTCAGAAGCGCCATA	265	64
PavGH3.3	ACTTCTTTGGTGCCCCTTGCTTC	GTGGTCTGTGCGCTATGGTGTGT	179	65
PavGH3.4	CTCTTACACCCTCATTCCCTCCAT	CGACTCTCAGCACATCTCCAACT	224	59
PavGH3.5	CATAGAGGAGACGACCAGGAACA	GGAACTCAGAGATGGGATGAGAGCT	239	62
PavGH3.6	CTCCCATCTTGTCAGCTCACCCA	GCTCACGAACAGAAAGTACAGGCCC	197	62
PavGH3.7	CTGTTGAGGTTCTTGGTGGGC	AGTTTTCTCGGGGGGTTGCA	263	60
PavGH3.8	CTCCCTTGCTTTCTCTGCCTAAT	GACCACAGCCTCAATGTACTTG	125	60
PavEF1-α2	ATCCAGAGTAGCAGAACCAATCAC	GTTAGGCATCCAGTCCCAGAAT	127	58
PavRSP3	TCAAGGTCAGGTAAGGGGGTC	GTGAGGTGATTGTTAGTGGAAAGC	223	56.5

基因 Gene	基因ID Gene ID	染色体 chromosome	CDS/bp	氨基酸长度/aa Length	蛋白分子量 Molecular weight	理论等电点 Theoretical pI	亲水性 GRAVY	亚细胞定位预测 Subcellular localization
PavGH3.1	Pav_sc0001540.1_g090.1.mk	PAV_r1.0chr1	1 851	616	70 875.15	5.68	-0.295	细胞质,细胞核 Cytoplasm,nucleus
PavGH3.2	Pav_sc0000254.1_g140.1.mk	PAV_r1.0chr2	1 683	560	62 622.79	5.80	-0.136	叶绿体 Chloroplast
PavGH3.3	Pav_sc0002360.1_g300.1.mk	PAV_r1.0chr3	1 794	597	67 453.09	6.45	-0.212	叶绿体 Chloroplast
PavGH3.4	Pav_sc0000269.1_g440.1.mk	PAV_r1.0chr4	1 845	614	69 182.12	5.91	-0.272	叶绿体 Chloroplast
PavGH3.5	Pav_sc0000049.1_g070.1.mk	PAV_r1.0chr6	1 800	599	67 477.05	5.81	-0.265	叶绿体 Chloroplast
PavGH3.6	Pav_sc0001422.1_g120.1.mk	PAV_r1.0chr8	1 803	600	67 636.32	5.56	-0.258	叶绿体 Chloroplast
PavGH3.7	Pav_sc0003065.1_g090.1.mk	PAV_r1.0chr8	1 725	574	64 563.26	5.92	-0.096	叶绿体 Chloroplast
PavGH3.8	Pav_sc0000848.1_g820.1.mk	PAV_r1.0chr8	1 806	601	68 250.59	5.87	-0.196	叶绿体 Chloroplast

基因 Gene	基因ID Gene ID	染色体 chromosome	CDS/bp	氨基酸长度/aa Length	蛋白分子量 Molecular weight	理论等电点 Theoretical pI	亲水性 GRAVY	亚细胞定位预测 Subcellular localization
PavGH3.1	Pav_sc0001540.1_g090.1.mk	PAV_r1.0chr1	1 851	616	70 875.15	5.68	-0.295	细胞质,细胞核 Cytoplasm,nucleus
PavGH3.2	Pav_sc0000254.1_g140.1.mk	PAV_r1.0chr2	1 683	560	62 622.79	5.80	-0.136	叶绿体 Chloroplast
PavGH3.3	Pav_sc0002360.1_g300.1.mk	PAV_r1.0chr3	1 794	597	67 453.09	6.45	-0.212	叶绿体 Chloroplast
PavGH3.4	Pav_sc0000269.1_g440.1.mk	PAV_r1.0chr4	1 845	614	69 182.12	5.91	-0.272	叶绿体 Chloroplast
PavGH3.5	Pav_sc0000049.1_g070.1.mk	PAV_r1.0chr6	1 800	599	67 477.05	5.81	-0.265	叶绿体 Chloroplast
PavGH3.6	Pav_sc0001422.1_g120.1.mk	PAV_r1.0chr8	1 803	600	67 636.32	5.56	-0.258	叶绿体 Chloroplast
PavGH3.7	Pav_sc0003065.1_g090.1.mk	PAV_r1.0chr8	1 725	574	64 563.26	5.92	-0.096	叶绿体 Chloroplast
PavGH3.8	Pav_sc0000848.1_g820.1.mk	PAV_r1.0chr8	1 806	601	68 250.59	5.87	-0.196	叶绿体 Chloroplast

Genome-wide Identification and Expression Analysis of Prunus avium Gretchen Hagen 3（GH3）Gene Family

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[3]	ZHAO Xueyan, WANG Qi, WANG Li, WANG Fangyuan, WANG Qing, LI Yan. Comparative Transcriptome Analysis of Differential Expression in Different Tissues of Corydalis yanhusuo [J]. Acta Horticulturae Sinica, 2023, 50(1): 177-187.
[4]	GAO Yanlong, WU Yuxia, ZHANG Zhongxing, WANG Shuangcheng, ZHANG Rui, ZHANG De, WANG Yanxiu. Bioinformatics Analysis of Apple ELO Gene Family and Its Expression Analysis Under Low Temperature Stress [J]. Acta Horticulturae Sinica, 2022, 49(8): 1621-1636.
[5]	LIU Jinming, GUO Caihua, YUAN Xing, KANG Chao, QUAN Shaowen, NIU Jianxin. Genome-wide Identification of Dof Family Genes and Expression Analysis Sepal Persistent and Abscission in Pear [J]. Acta Horticulturae Sinica, 2022, 49(8): 1637-1649.
[6]	QIU Ziwen, LIU Linmin, LIN Yongsheng, LIN Xiaojie, LI Yongyu, WU Shaohua, YANG Chao. Cloning and Functional Analysis of the MbEGS Gene from Melaleuca bracteata [J]. Acta Horticulturae Sinica, 2022, 49(8): 1747-1760.
[7]	ZHENG Lin, WANG Shuai, LIU Yunuo, DU Meixia, PENG Aihong, HE Yongrui, CHEN Shanchun, ZOU Xiuping. Gene Cloning and Expression Analysis of NAC Gene in Citrus in Response to Huanglongbing [J]. Acta Horticulturae Sinica, 2022, 49(7): 1441-1457.
[8]	MA Weifeng, LI Yanmei, MA Zonghuan, CHEN Baihong, MAO Juan. Identification of Apple POD Gene Family and Functional Analysis of MdPOD15 Gene [J]. Acta Horticulturae Sinica, 2022, 49(6): 1181-1199.
[9]	ZHANG Kai, MA Mingying, WANG Ping, LI Yi, JIN Yan, SHENG Ling, DENG Ziniu, MA Xianfeng. Identification of HSP20 Family Genes in Citrus and Their Expression in Pathogen Infection Responses Citrus Canker [J]. Acta Horticulturae Sinica, 2022, 49(6): 1213-1232.
[10]	LIANG Chen, SUN Ruyi, XIANG Rui, SUN Yimeng, SHI Xiaoxin, DU Guoqiang, WANG Li. Genome-wide Identification of Grape GRF Family and Expression Analysis [J]. Acta Horticulturae Sinica, 2022, 49(5): 995-1007.
[11]	XIAO Xuechen, LIU Mengyu, JIANG Mengqi, CHEN Yan, XUE Xiaodong, ZHOU Chengzhe, WU Xingjian, WU Junnan, GUO Yinsheng, YEH Kaiwen, LAI Zhongxiong, LIN Yuling. Whole-genome Identification and Expression Analysis of SNAT,ASMT and COMT Families of Melatonin Synthesis Pathway in Dimocarpus longan [J]. Acta Horticulturae Sinica, 2022, 49(5): 1031-1046.
[12]	GAO Weilin, ZHANG Liman, XUE Chaoling, ZHANG Yao, LIU Mengjun, ZHAO Jin. Expression of E-type MADS-box Genes in Flower and Fruits and Protein Interaction Analysis in Chinese Jujube [J]. Acta Horticulturae Sinica, 2022, 49(4): 739-748.
[13]	LIU Mengyu, JIANG Mengqi, CHEN Yan, ZHANG Shuting, XUE Xiaodong, XIAO Xuechen, LAI Zhongxiong, LIN Yuling. Genome-wide Identification and Expression Analysis of GDSL Esterase/Lipase Genes in Dimocarpus longan [J]. Acta Horticulturae Sinica, 2022, 49(3): 597-612.
[14]	JIANG Cuicui, FANG Zhizhen, ZHOU Danrong, LIN Yanjuan, YE Xinfu. Identification and Expression Analysis of Sugar Transporter Family Genes in‘Furongli’（Prunus salicina） [J]. Acta Horticulturae Sinica, 2022, 49(2): 252-264.
[15]	WANG Guangpeng, LIU Tongkun, XU Xinfeng, LI Zhubo, GAO Zhanyuan, HOU Xilin. Identification of LEA Family and Expression Analysis of Some Members Under Low-temperature Stress in Chinese Cabbage [J]. Acta Horticulturae Sinica, 2022, 49(2): 304-318.