Scientia Agricultura Sinica ›› 2020, Vol. 53 ›› Issue (1): 133-147.doi: 10.3864/j.issn.0578-1752.2020.01.013

• SPECIAL FOCUS: MOLECULAR BIOLOGY OF CUCUMBER • Previous Articles     Next Articles

Genome-Wide Identification of Cucumber ERF Gene Family and Expression Analysis in Female Bud Differentiation

Jian PAN,HaiFan WEN,HuanLe HE,HongLi LIAN,Gang WANG,JunSong PAN,Run CAI()   

  1. School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240
  • Received:2019-05-28 Accepted:2019-10-29 Online:2020-01-01 Published:2020-01-19
  • Contact: Run CAI E-mail:cairun@sjtu.edu.cn

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

Fig. 1

The AP2/ERF conserved domain in ERF members of cucumber"

Table 1

Information of CsERF gene family members"

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

Fig. 2

The chromosome location of the ERF gene family in cucumber"

Fig. 3

The phylogenetic tree of ERF family in cucumber (Roman numerals I-X indicate 10 sub-families)"

Fig. 4

Gene structure analysis of ERF family members in cucumber Genes in red indicate highly express in FFMMAA genotype line, genes in blue indicate highly express in ffMMAA genotype line, red and blue triangles indicate genes show an up- and down-regulated trend in female bud development, respectively"

Fig. 5

The significant differential expression CsERF in FFMMAA (A) and ffMMAA (B) cucumber lines shoot apical (t test, P value<0.05)"

Fig. 6

The significant differences in the expression of CsERF in early stages of female bud development"

Fig. 7

Yeast one-hybrid assay of interaction between CsERF31, CsERF39 and GCC-box (A), the two sets of down-regulated and GCC-box in promoter genes analyzed using the VENN method (B), and GO enrichment analysis of down-regulated (left) and up-regulated (right) genes with GCC-box in promoters (C)"

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