黄瓜ERF基因家族鉴定及其在雌花芽分化中的表达分析

doi:10.3864/j.issn.0578-1752.2020.01.013

摘要/Abstract

摘要：

【目的】通过以黄瓜9930_V2版本基因组为参照进行生物信息学分析,对ERF基因家族在基因组中的数量、结构以及表达特征进行分析,为研究ERF转录因子在黄瓜雌花分化与发育中的作用提供数据支持。【方法】根据已报道的拟南芥ERF,利用黄瓜基因组数据库中9930_V2版本基因组进行BLAST比对,通过MEGA、MEME、TBtools、ExPASy等工具进行生物信息学分析。采用qRT-PCR方法检测不同性型黄瓜材料、雌花发育初期不同阶段中ERF基因家族成员的表达水平。采用酵母单杂交方法验证家族成员与乙烯响应元件GCC-box的互作。【结果】从黄瓜材料9930基因组中鉴定得到138个ERF基因家族成员,共分为10个亚族,编码氨基酸长度介于126—745。按照基因家族成员在染色体上的位置分布,将其命名为CsERF1-CsERF138。多序列比对和motif分析结果表明,黄瓜ERF基因家族均具有AP2/ERF结构域,其中4个成员具有B3结构域。表达分析结果显示,在不同性型材料中共有19个ERF家族成员差异表达,其中9个在FFMMAA基因型中高表达,10个在ffMMAA基因型中高表达。通过雌花芽发育初期ERF家族成员的表达趋势分析,发现31个ERF随子房发育表达上调,30个表达下调。初步证明CsERF9和CsERF31具有结合GCC-box元件的功能。【结论】从黄瓜基因组中鉴定出138个ERF基因家族成员,均拥有1个或多个AP2/ERF结构域;其中部分成员在不同性型材料中差异表达,并可能参与雌花分化初期的基因表达调控;部分成员具有结合保守元件GCC-box调控下游基因表达的功能。

关键词: 黄瓜, 乙烯信号, 雌花发育, ERF基因, 性别决定

Abstract:

【Objective】The objectives of this research were to identify the Ethylene Response Factor (ERF) family genes from cucumber (Cucumis sativus L.) genome and to know the profile of ERF family such as gene number, gene structure and expression characters in cucumber, so as to provide a theoretical basis for exploring what roles the ERF transcription factors played in female flowers development. 【Method】 The ERF genes in cucumber genome were identified by BLAST software in the 9930_V2 genome database based on Arabidopsis ERF genes. EMBOSS, MEME, TBtools, ExPASy and MEGA 7.0 software were used for carrying out various bioinformatics analysis of ERF. The qRT-PCR was used to detect the expression of cucumber ERF gene family in female buds’ differentiation. 【Result】 Total of 138 ERF genes were identified from cucumber genome, which could be divided into 10 classes. These 138 ERF genes were named from CsERF1 to CsERF138, and the number of amino acids of these ERF genes was between 126 and 745. Multiple sequence alignments and Motif analysis showed that the CsERF gene family had two conserved domains, namely AP2/ERF domain and B3 domain. There were 19 ERF genes showed different expression between FFMMAA and ffMMAA genotype, 9 of them up-regulated in FFMMAA genotype and the other 10 up-regulated in ffMMAA genotype. The expression trend analysis showed 31 ERF genes up-regulated and 30 genes down-regulated in the initial-phase of female buds’ differentiation. Furthermore, it was demonstrated that CsERF9 and CsERF31 could bind the GCC-box. 【Conclusion】 138 ERF gene family members were identified from the cucumber 9930_V2 genome. These entire ERF gene shared AP2/ERF domain. Some of the ERF family members were related to sex determination and female flower development and could bind GCC-box to regulate downstream genes expression.

Key words: cucumber, ethylene signal, female flower development, ERF, sex determination

潘健,温海帆,何欢乐,连红莉,王刚,潘俊松,蔡润. 黄瓜ERF基因家族鉴定及其在雌花芽分化中的表达分析[J]. 中国农业科学, 2020, 53(1): 133-147.

Jian PAN,HaiFan WEN,HuanLe HE,HongLi LIAN,Gang WANG,JunSong PAN,Run CAI. Genome-Wide Identification of Cucumber ERF Gene Family and Expression Analysis in Female Bud Differentiation[J]. Scientia Agricultura Sinica, 2020, 53(1): 133-147.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2020.01.013

https://www.chinaagrisci.com/CN/Y2020/V53/I1/133

图/表 8

图1

表1

CsERF基因家族相关信息"

名称 Name	黄瓜基因组基因编号 ID in cucumber (9930_V2)	注释到拟南芥成员 Annotated to Arabidopsis	成员名称 Name in Arabidopsis	所属亚族 Class	氨基酸个数 Number of amino acids
CsERF1*	Csa1G000550	AT5G61890	ERF114	2	216
CsERF2	Csa1G042290	AT1G68550	ERF118	2	336
CsERF3	Csa1G075030	AT1G28360	ERF12	4	164
CsERF4	Csa1G075060	AT5G44210	ERF9	4	211
CsERF5	Csa1G269870	AT1G50680	-	5	339
CsERF6	Csa1G275920	AT1G16060	ADAP	6	363
CsERF7	Csa1G340430	AT1G15360	WIN1	7	223
CsERF8	Csa1G364460	AT5G11590	DREB3	9	250
CsERF9	Csa2G177210	AT3G23240	ERF1B	1	228
CsERF10	Csa1G597730	AT1G19210	ERF017	9	203
CsERF11*	Csa1G605670	AT2G05990	MOD1	5	745
CsERF12*	Csa2G001000	AT5G11590	DREB3	9	252
CsERF13	Csa2G006270	AT1G15360	WIN1	7	246
CsERF14*	Csa2G092800	AT5G17430	BBM	6	650
CsERF15	Csa2G138780	AT4G13620	ERF062	10	400
CsERF16	Csa1G423190	AT5G57390	AIL5	6	466
CsERF17	Csa2G177220	AT3G23230	ERF098	1	126
CsERF18	Csa2G279250	AT4G36920	AP2	6	483
CsERF19*	Csa2G279260	AT2G23340	ERF008	9	159
CsERF20*	Csa2G297760	AT2G33710	ERF112	2	285
CsERF21*	Csa2G307850	AT1G78080	RAP2-4	10	362
CsERF22	Csa2G349090	AT1G12980	ESR1	4	358
CsERF23*	Csa2G354000	AT4G37750	ANT	6	696
CsERF24	Csa2G356600	AT1G46768	RAP2-1	9	142
CsERF25*	Csa2G363010	AT1G75490	DREB2D	8	212
CsERF26	Csa2G374590	AT5G11590	DREB3	9	231
CsERF27	Csa2G382540	AT5G25190	ERF003	7	175
CsERF28*	Csa2G382550	AT5G25190	ERF003	7	164
CsERF29*	Csa2G401240	AT1G22810	ERF019	9	148
CsERF30*	Csa3G017320	AT4G17500	ERF1A	1	279
CsERF31	Csa3G135120	AT3G23240	ERF1B	1	228
CsERF32	Csa3G018320	AT4G17490	ERF6	1	344
CsERF33	Csa3G019400	AT2G44940	ERF034	9	214
CsERF34	Csa3G042390	AT5G52020	ERF025	9	170
CsERF35	Csa3G073900	AT3G20310	ERF7	4	214
CsERF36*	Csa3G114470	AT5G65510	AIL7	6	283
CsERF37	Csa3G116720	AT2G44840	ERF13	1	144
CsERF38	Csa3G116730	AT2G44840	ERF13	1	157
CsERF39	Csa3G389850	AT3G23240	ERF1B	1	224
CsERF40*	Csa3G120390	AT4G27950	CRF4	3	283
CsERF41	Csa3G124760	AT5G19790	RAP2-11	3	243
CsERF42	Csa3G133130	AT1G68550	ERF118	2	213
CsERF43	Csa3G135620	AT3G23230	ERF098	1	158
CsERF44	Csa3G135630	AT3G23230	ERF098	1	133
CsERF45	Csa3G152130	AT5G18560	ERF086	4	326
CsERF46*	Csa3G164580	AT3G16770	RAP2-3	2	225
CsERF47	Csa3G180260	AT4G25470	DREB1C	9	213
CsERF48*	Csa3G207390	AT4G34410	ERF109	2	274
CsERF49	Csa3G357110	AT4G27950	CRF4	3	326
CsERF50*	Csa3G118010	AT2G44940	ERF034	9	230
CsERF51	Csa3G630280	AT4G13040	-	10	234
CsERF52	Csa3G646560	AT3G14230	RAP2-2	2	370
CsERF53*	Csa3G652380	AT1G72570	AIL1	6	490
CsERF54	Csa3G736760	AT2G28550	RAP2-7	6	527
CsERF55#*	Csa3G751430	AT2G36450	ERF024	9	183
CsERF56*	Csa3G751440	AT4G25490	DREB1B	9	204
CsERF57	Csa3G812170	AT3G57600	DREB2F	8	333
CsERF58*	Csa3G822440	AT2G41710	-	6	432
CsERF59	Csa3G827310	AT3G54320	WRI1	6	337
CsERF60	Csa3G865380	AT1G75490	DREB2D	8	184
CsERF61	Csa3G878210	AT5G25390	SHN3	7	194
CsERF62	Csa3G895680	AT4G32800	ERF043	9	227
CsERF63	Csa4G001970	AT3G16770	RAP2-3	2	272
CsERF64	Csa4G004960	AT1G15360	WIN1	7	190
CsERF65	Csa4G006210	AT5G25190	ERF003	7	180
CsERF66	Csa4G007070	AT1G28160	ERF087	4	227
CsERF67	Csa4G007650	AT1G71450	ERF021	9	179
CsERF68	Csa4G023020	AT5G61600	ERF104	1	194
CsERF69	Csa4G051360	AT4G23750	CRF2	3	319
CsERF70	Csa4G192030	AT5G19790	RAP2-11	3	225
CsERF71	Csa4G268100	AT5G19790	RAP2-11	3	211
CsERF72*	Csa4G290800	AT1G51190	PLT2	6	615
CsERF73	Csa4G292470	AT2G28550	RAP2-7	6	456
CsERF74	Csa4G314390	AT2G40340	DREB2C	8	372
CsERF75	Csa4G370550	AT1G21910	ERF012	9	232
CsERF76	Csa4G630010	AT3G15210	ERF4	4	193
CsERF77	Csa4G641590	AT3G50260	ERF011	9	149
CsERF78*	Csa4G644740	AT4G37750	ANT	6	573
CsERF79	Csa4G649620	AT1G74930	ERF018	9	186
CsERF80	Csa4G652640	AT5G25190	ERF003	7	203
CsERF81	Csa5G139630	AT4G27950	CRF4	3	268
CsERF82	Csa5G146300	AT5G19790	RAP2-11	3	210
CsERF83	Csa5G150420	AT1G64380	ERF061	10	304
CsERF84	Csa5G151530	AT4G23750	CRF2	3	318
CsERF85	Csa5G155560	AT5G52020	ERF025	9	252
CsERF86*	Csa5G155570	AT4G25470	DREB1C	9	225
CsERF87	Csa5G165850	AT4G17500	ERF1A	1	250
CsERF88	Csa5G167110	AT5G07580	ERF106	1	160
CsERF89*	Csa5G167120	AT5G51190	ERF105	1	235
CsERF90	Csa5G174570	AT5G51990	DREB1D	9	200
CsERF91	Csa5G175970	AT2G28550	RAP2-7	6	441
CsERF92	Csa5G598600	AT1G24590	ESR2	4	341
CsERF93	Csa5G608380	AT1G68840	RAV2	5	344
CsERF94	Csa5G609620	AT1G68550	ERF118	2	309
CsERF95*	Csa5G612310	AT3G54320	WRI1	6	439
CsERF96*	Csa5G637750	AT5G19790	RAP2-11	3	395
CsERF97	Csa5G647260	AT5G25810	TINY	9	163
CsERF98	Csa5G649870	AT1G33760	ERF022	9	163
CsERF99	Csa5G649890	AT1G71450	ERF021	9	192
CsERF100*	Csa6G011730	AT2G40220	ABI4	8	305
CsERF101	Csa6G012810	AT2G40340	DREB2C	8	410
CsERF102	Csa6G167230	AT1G50640	ERF3	4	219
CsERF103*	Csa6G040610	AT1G21910	ERF012	9	201
CsERF104	Csa6G042450	AT2G46310	CRF5	3	243
CsERF105*	Csa6G055940	AT5G61890	ERF114	2	404
CsERF106	Csa6G091830	AT5G13330	ERF113	2	191
CsERF107	Csa6G104640	AT4G32800	ERF043	9	213
CsERF108*	Csa6G124180	AT2G40340	DREB2C	8	179
CsERF109	Csa6G133770	AT4G27950	CRF4	3	281
CsERF110*	Csa6G017030	AT5G61890	ERF114	2	310
CsERF111*	Csa6G296960	AT2G28550	RAP2-7	6	497
CsERF112	Csa6G318160	AT3G16770	RAP2-3	2	231
CsERF113	Csa6G361330	AT1G19210	ERF017	9	213
CsERF114	Csa6G404260	AT3G54320	WRI1	6	366
CsERF115	Csa6G421660	AT1G50640	ERF3	4	214
CsERF116#*	Csa6G450420	AT2G36450	ERF024	9	224
CsERF117*	Csa6G486790	AT5G61890	ERF114	2	338
CsERF118	Csa6G490860	AT4G34410	ERF109	2	193
CsERF119	Csa6G491020	AT4G36920	AP2	6	537
CsERF120*	Csa6G491030	AT5G67190	ERF010	9	173
CsERF121*	Csa6G496390	AT4G37750	ANT	6	629
CsERF122	Csa6G500550	AT1G78080	RAP2-4	10	271
CsERF123	Csa6G518040	AT3G15210	ERF4	4	246
CsERF124	Csa6G518290	AT5G47220	ERF2	1	177
CsERF125	Csa6G518300	AT4G18450	ERF091	1	277
CsERF126	Csa7G047400	AT2G20880	ERF053	10	397
CsERF127	Csa7G049230	AT5G44210	ERF9	4	209
CsERF128*	Csa7G073700	AT4G34410	ERF109	2	256
CsERF129	Csa7G352440	AT4G13040	-	10	231
CsERF130	Csa7G375820	AT3G23240	ERF1B	1	231
CsERF131	Csa7G375830	AT3G23230	ERF098	1	148
CsERF132*	Csa7G431330	AT1G16060	ADAP	6	367
CsERF133	Csa7G432080	AT5G25190	ERF003	7	196
CsERF134	Csa7G432130	AT1G80580	ERF084	3	183
CsERF135	Csa7G447150	AT5G11590	DREB3	9	201
CsERF136*	Csa7G448110	AT1G53910	RAP2-12	2	389
CsERF137	CsaUNG003730	AT5G13910	LEP	4	228
CsERF138*	CsaUNG031640	AT1G13260	RAV1	5	317

表1

图2

图3

图4

图5

图6

图7

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