红树莓E2F/DP基因家族的鉴定及表达分析

doi:10.11924/j.issn.1000-6850.casb2026-0234

中国农学通报 ›› 2026, Vol. 42 ›› Issue (16): 61-70.doi: 10.11924/j.issn.1000-6850.casb2026-0234

红树莓E2F/DP基因家族的鉴定及表达分析

杨明蛟¹(), 赵志磊², 李明¹, 李寒³, 张羽萌¹, 樊小伟⁴, 郑奕宸¹, 张瑞杰¹, 青梦瑶¹, 顾玉红¹()

¹ 河北农业大学生命科学学院，河北保定 071001
² 河北大学质量技术监督学院，河北保定 071002
³ 河北农业大学林学院，河北保定 071001
⁴ 河北农业大学现代科技学院，河北保定 071000

收稿日期:2026-03-26 修回日期:2026-05-15 出版日期:2026-08-25 发布日期:2026-08-20
通讯作者:
顾玉红，女，1977年出生，河北昌黎人，教授，博士，研究方向：植物发育生物学。通信地址：071001 河北保定莲池区乐凯南大街2596号河北农业大学生命科学学院，E-mail：gyhshengwu@163.com。
作者简介:
杨明蛟，男，2001年出生，河北唐山人，研究生，研究方向：植物发育生物学。通信地址：071001 河北保定莲池区乐凯南大街2596号河北农业大学生命科学学院，E-mail：ymj20011123@163.com。
基金资助:
河北省重点研发计划项目“红树莓种质资源收集评价及优异种质创制利用”(20326338D)

Identification and Expression Analysis of E2F/DP Gene Family of Rubus idaeus

YANG Mingjiao¹(), ZHAO Zhilei², LI Ming¹, LI Han³, ZHANG Yumeng¹, FAN Xiaowei⁴, ZHENG Yichen¹, ZHANG Ruijie¹, QING Mengyao¹, GU Yuhong¹()

¹ College of Life Science, Hebei Agricultural University, Baoding, Hebei 071001
² College of Quality and Technical Supervision, Hebei University, Baoding, Hebei 071002
³ College of Forestry, Hebei Agricultural University, Baoding, Hebei 071001
⁴ College of Modern Science and Technology, Hebei Agricultural University, Baoding, Hebei 071000

Received:2026-03-26 Revised:2026-05-15 Published:2026-08-25 Online:2026-08-20

摘要/Abstract

摘要：

E2F/DP基因家族在植物生长发育和逆境胁迫响应中扮演着至关重要的调控角色。本研究旨在通过生物信息学方法对红树莓E2F/DP基因家族进行鉴定，并分析其在不同组织和经褪黑素处理后的表达模式，为深入揭示其功能奠定基础。从‘海尔特兹’红树莓的转录组数据库中筛选出3个E2F/DP基因家族成员，利用生物信息学手段进行分析；之后利用qRT-PCR技术，考察这些基因在不同组织器官、不同发育时期果实和外施褪黑素后果实E2F/DP的表达量。研究结果表明，RuE2F/DPs编码的蛋白质氨基酸数量为243~761 aa，相对分子质量范围为26.88~82.55 kDa，等电点在5.69~9.07之间。RuE2F/DP-1为稳定亲水蛋白质，RuE2F/DP2-3为不稳定亲水蛋白。所有RuE2F/DPs编码的蛋白质均定位于细胞核，不含信号肽，属于非分泌蛋白和非跨膜蛋白、含有E2F_TDP保守结构域，其二级结构均由共4种结构构成，其中包含了α螺旋、β转角、无规则卷曲、折叠延伸链，三级结构预测结果与二级结构一致。RuE2F/DP-1和RuE2F/DP-3之间表现出显著的表达相关性。RuE2F/DP基因家族含有9~14个外显子和4~10个保守基序。系统进化分析表明，RuE2F/DP家族成员分属不同亚组，红树莓与草莓的亲缘关系更密切。启动子顺式作用元件表明，RuE2F/DP基因家族主要参与植物的生长发育，并响应干旱、低温等胁迫环境。qRT-PCR分析表明，RuE2F/DP基因家族的3个成员在嫩根和青果中的表达量高于其他组织。褪黑素处理对RuE2F/DP1-2有正调控功能，对RuE2F/DP-3有负调控功能。研究结果揭示RuE2F/DP基因家族可能在红树莓根系生长、果实的生长发育、生长过程中的逆境胁迫以及对褪黑素的激素响应中发挥作用。

关键词: 红树莓, E2F/DP基因, 生物信息学, 表达分析, 荧光定量PCR, 褪黑素, 组织特异性

Abstract:

The E2F/DP gene family plays a significant regulatory role in the growth, development and stress response of plants. The bioinformatics analysis of the E2F/DP gene family in red raspberry (Rubus idaeus) and the expression pattern analysis in different tissues and after exogenous spraying of melatonin lay the foundation for in-depth exploration of the function of E2F/DP genes in red raspberry. In this study, three members of the E2F/DP gene family were obtained from the transcriptome database of ‘Heritage’ red raspberry. The E2F/DP gene family of red raspberry was analyzed by bioinformatics methods. Subsequently, the expression levels of E2F/DP in different tissues and organs, fruits at different developmental stages and fruits after exogenous spraying of melatonin were analyzed by qRT-PCR. The proteins encoded by RuE2F/DPs have a minimum of 243 amino acids and a maximum of 761 amino acids, with a minimum relative molecular mass of 26.88 kDa and a maximum of 82.55 kDa. Their isoelectric points range from 5.69 to 9.07. RuE2F/DP-1 is a stable hydrophilic protein, while RuE2F/DP2-3 is unstable hydrophilic protein. All RuE2F/DPs-encoded proteins are located in the cell nucleus, have no signal peptides, are non-secretory proteins, non-transmembrane proteins, and contain the conserved E2F_TDP domain. Their secondary structures are all composed of four types of structures, including α-helices, β-turns, random coils, and extended strands. The prediction results of their tertiary structures are consistent with their secondary structures. RuE2F/DP-1 and RuE2F/DP-3 have expression correlations. The RuE2F/DP gene family contains 9 to 14 exons and 4 to 10 conserved motifs; phylogenetic analysis indicates that the RuE2F/DP family members belong to different subgroups, and red raspberry is more closely related to strawberry; the cis-acting elements in the promoter suggest that the RuE2F/DP gene family mainly participates in plant growth and development and responses to drought, low temperature and other stress environments; qRT-PCR analysis shows that the expression levels of three members of the RuE2F/DP gene family in young roots and green fruits are higher than those in other tissues; melatonin treatment has a positive regulatory function on RuE2F/DP1-2 and a negative regulatory function on RuE2F/DP-3. The research results reveal that the RuE2F/DP gene family may play a role in the growth of red raspberry roots, the growth and development of fruits, the response to adverse stress during the growth process, and the hormone response to melatonin.

Key words: red raspberry (Rubus idaeus), E2F/DP gene, bioinformatics analysis, expression analysis, RT-qPCR, melatonin, tissue specificity

中图分类号:

S663.2

杨明蛟, 赵志磊, 李明, 李寒, 张羽萌, 樊小伟, 郑奕宸, 张瑞杰, 青梦瑶, 顾玉红. 红树莓E2F/DP基因家族的鉴定及表达分析[J]. 中国农学通报, 2026, 42(16): 61-70.

YANG Mingjiao, ZHAO Zhilei, LI Ming, LI Han, ZHANG Yumeng, FAN Xiaowei, ZHENG Yichen, ZHANG Ruijie, QING Mengyao, GU Yuhong. Identification and Expression Analysis of E2F/DP Gene Family of Rubus idaeus[J]. Chinese Agricultural Science Bulletin, 2026, 42(16): 61-70.

图/表 12

参考文献 44

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生物信息学分析	在线软件	网址
理化性质分析	Protparam	https://web.expasy.org/protparam/
疏水性预测	ExPASy-ProtScale	https://web.expasy.org/protscale/
磷酸化位点预测	NetPhos 3.1 Serve	https://services.healthtech.dtu.dk/service.php?NetPhos-3.1
信号肽预测	SignalP 5.0	https://services.healthtech.dtu.dk/service.php?SignalP-5.0
亚细胞定位	Cell Ploc 2.0	http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc-2/
跨膜结构预测	TMHMM 2.0	https://services.healthtech.dtu.dk/service.php?TMHMM-2.0
保守结构域	SMART	http://smart.embl-heidelberg.de/smart/job_status.pl?jobid
二级结构预测	Prabi	https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html#top
三级结构预测	SWISS-MODEL	https://swissmodel.expasy.org/

生物信息学分析	在线软件	网址
理化性质分析	Protparam	https://web.expasy.org/protparam/
疏水性预测	ExPASy-ProtScale	https://web.expasy.org/protscale/
磷酸化位点预测	NetPhos 3.1 Serve	https://services.healthtech.dtu.dk/service.php?NetPhos-3.1
信号肽预测	SignalP 5.0	https://services.healthtech.dtu.dk/service.php?SignalP-5.0
亚细胞定位	Cell Ploc 2.0	http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc-2/
跨膜结构预测	TMHMM 2.0	https://services.healthtech.dtu.dk/service.php?TMHMM-2.0
保守结构域	SMART	http://smart.embl-heidelberg.de/smart/job_status.pl?jobid
二级结构预测	Prabi	https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html#top
三级结构预测	SWISS-MODEL	https://swissmodel.expasy.org/

引物名称	引物序列5’-3’
E2F/DP-1-F	ACATTAACGGCGACGATGC
E2F/DP-1-R	GTTCTGCCCTTGCTTTCCAC
E2F/DP-2-F	TTGAAAAGACCCACACAGCAGATAC
E2F/DP-2-R	CTACTTTGCCCCTCTTACAACTGAC
E2F/DP-3-F	TCCCAACCACCCACAATAGG
E2F/DP-3-R	GCATTTGAAGCGAGCTTATCG
GAPDH-F	CCAATGAAGTCAGTAGACAC
GAPDH-R	GAAAGGTTCTTCCCTCTCTC

引物名称	引物序列5’-3’
E2F/DP-1-F	ACATTAACGGCGACGATGC
E2F/DP-1-R	GTTCTGCCCTTGCTTTCCAC
E2F/DP-2-F	TTGAAAAGACCCACACAGCAGATAC
E2F/DP-2-R	CTACTTTGCCCCTCTTACAACTGAC
E2F/DP-3-F	TCCCAACCACCCACAATAGG
E2F/DP-3-R	GCATTTGAAGCGAGCTTATCG
GAPDH-F	CCAATGAAGTCAGTAGACAC
GAPDH-R	GAAAGGTTCTTCCCTCTCTC

基因名称	基因号	氨基酸数量/个	分子量/ kDa	等电点	不稳定指数	亲水性	磷酸化位点				信号肽	亚细胞定位	跨膜结构
基因名称	基因号	氨基酸数量/个	分子量/ kDa	等电点	不稳定指数	亲水性	丝氨酸	苏氨酸	酪氨酸	总计	信号肽	亚细胞定位	跨膜结构
RuE2F/DP-1	TRINITY_DN4246_c0_g1	375	41.49	9.07	39.90	-0.732	33	8	3	44	无	细胞核	无
RuE2F/DP-2	TRINITY_DN5065_c0_g2	243	26.88	5.69	61.40	-0.649	21	5	4	30	无	细胞核	无
RuE2F/DP-3	TRINITY_DN14014_c0_g1	761	82.55	5.98	51.92	-0.683	61	28	11	100	无	细胞核	无

红树莓E2F/DP基因家族的鉴定及表达分析

Identification and Expression Analysis of E2F/DP Gene Family of Rubus idaeus

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基因名称	占比/%				二级结构图	三级结构图
基因名称	α螺旋	β转角	无规则卷曲	折叠延伸链	二级结构图	三级结构图
RuE2F/DP-1	35.20	2.40	55.73	6.67
RuE2F/DP-2	43.21	3.29	42.80	10.70
RuE2F/DP-3	34.69	5.39	46.12	13.80

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