Genome-Wide Identified MADS-Box Genes in Prunus campanulata ‘Plena’ and Theirs Roles in Double-Flower Development
Abstract
:1. Introduction
2. Results
2.1. MADS-Box Gene Family Identification
2.2. Phylogenetic Analysis of the MADS-Box Gene Family
2.3. Chromosome Localization and Synteny Analysis of the MADS-Box Gene Family
2.4. MADS-Box Gene Structure and Conserved Motif Analysis
2.5. Prediction of Cis-Acting Elements of the Promoter Region
2.6. Phenotypic Identification of Double Flowers in PCP
2.7. MIKCc-Type MADS-Box Gene Expression Analysis
2.8. Expression Analysis of ABCE Class Genes in PCP by qRT–PCR
3. Discussion
4. Materials and Methods
4.1. MADS-Box Gene Family Identification
4.2. Phylogenetic Analysis of the MADS-Box Gene Family
4.3. Chromosome Location and Synteny Analysis of the MADS-Box Gene family
4.4. MADS-Box Gene Structure and Motif Analysis
4.5. Prediction of Cis-Regulatory Elements in the Promoter Region
4.6. MADS-Box Gene Family Expression Analysis
4.7. ABCE Class Gene Expression Analysis in PCP by qRT–PCR
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | Gene Id | CDS (bp) | Exon Count | Protein Length (aa) | MW | PI | Type | Subfamily |
---|---|---|---|---|---|---|---|---|
PcMADS01 | evm.TU.LG01.1677 | 1116 | 1 | 371 | 40,923 | 6.43 | Type I | Mγ |
PcMADS02 | evm.TU.LG01.1680 | 1086 | 1 | 361 | 39,386 | 4.91 | Type I | Mγ |
PcMADS03 | evm.TU.LG01.2444 | 3849 | 8 | 240 | 27,570 | 8.79 | Type II | MIKC |
PcMADS04 | evm.TU.LG01.3136 | 3183 | 8 | 250 | 28,746 | 8.24 | Type II | MIKC |
PcMADS05 | evm.TU.LG01.3137 | 2657 | 8 | 238 | 27,871 | 8.45 | Type II | MIKC |
PcMADS06 | evm.TU.LG01.3902 | 2179 | 8 | 236 | 27,631 | 10.11 | Type II | MIKC |
PcMADS07 | evm.TU.LG01.462 | 609 | 1 | 202 | 21,822 | 4.74 | Type I | Mα |
PcMADS08 | evm.TU.LG01.464 | 1345 | 2 | 261 | 28,905 | 7.73 | Type I | Mα |
PcMADS09 | evm.TU.LG01.465 | 621 | 1 | 206 | 22,364 | 4.16 | Type I | Mα |
PcMADS10 | evm.TU.LG01.4975 | 2325 | 7 | 210 | 24,310 | 8.4 | Type II | MIKC |
PcMADS11 | evm.TU.LG01.5169 | 3670 | 12 | 347 | 39,188 | 5.31 | Type I | Mα |
PcMADS12 | evm.TU.LG01.5349 | 6915 | 8 | 235 | 26,615 | 5.31 | Type II | MIKC |
PcMADS13 | evm.TU.LG01.5368 | 690 | 1 | 229 | 26,436 | 9.28 | Type I | Mγ |
PcMADS14 | evm.TU.LG01.5407 | 17,349 | 8 | 239 | 27,368 | 9.47 | Type II | MIKC |
PcMADS15 | evm.TU.LG01.5499 | 3775 | 7 | 204 | 23,253 | 7.74 | Type II | MIKC |
PcMADS16 | evm.TU.LG01.5511 | 186 | 1 | 61 | 7096 | 9.93 | Type I | Mα |
PcMADS17 | evm.TU.LG01.5564 | 534 | 1 | 177 | 20,236 | 6.76 | Type I | Mγ |
PcMADS18 | evm.TU.LG01.785 | 645 | 1 | 214 | 23,580 | 9.08 | Type I | Mα |
PcMADS19 | evm.TU.LG02.1730 | 5045 | 7 | 215 | 24,830 | 9.24 | Type II | MIKC |
PcMADS20 | evm.TU.LG02.1732 | 4340 | 8 | 244 | 27,946 | 9.2 | Type II | MIKC |
PcMADS21 | evm.TU.LG02.2071 | 705 | 1 | 234 | 26,130 | 8.97 | Type I | Mα |
PcMADS22 | evm.TU.LG02.2165 | 1107 | 1 | 368 | 42,473 | 8.15 | Type I | Mβ |
PcMADS23 | evm.TU.LG02.2176 | 480 | 1 | 159 | 18,298 | 9.1 | Type I | Mγ |
PcMADS24 | evm.TU.LG02.2988 | 591 | 1 | 196 | 22,129 | 9.07 | Type I | Mα |
PcMADS25 | evm.TU.LG02.3371 | 2785 | 7 | 193 | 22,092 | 5.1 | Type II | MIKC |
PcMADS26 | evm.TU.LG02.426 | 4661 | 7 | 213 | 24,431 | 8.36 | Type II | MIKC |
PcMADS27 | evm.TU.LG02.430 | 2588 | 8 | 240 | 27,638 | 6.86 | Type II | MIKC |
PcMADS28 | evm.TU.LG02.905 | 417 | 1 | 138 | 16,228 | 9.15 | Type I | Mβ |
PcMADS29 | evm.TU.LG03.1170 | 897 | 1 | 298 | 33,021 | 4.64 | Type I | Mβ |
PcMADS30 | evm.TU.LG03.1188 | 519 | 1 | 172 | 19,651 | 4.54 | Type I | Mα |
PcMADS31 | evm.TU.LG03.1189 | 627 | 1 | 208 | 23,207 | 4.54 | Type I | Mα |
PcMADS32 | evm.TU.LG03.1235 | 630 | 1 | 209 | 23,355 | 4.56 | Type I | Mα |
PcMADS33 | evm.TU.LG03.2185 | 3887 | 8 | 228 | 25,828 | 6.26 | Type II | MIKC |
PcMADS34 | evm.TU.LG03.2269 | 5928 | 6 | 210 | 24,224 | 9.52 | Type II | MIKC |
PcMADS35 | evm.TU.LG03.2316 | 498 | 1 | 165 | 18,708 | 9.43 | Type I | Mα |
PcMADS36 | evm.TU.LG03.3240 | 732 | 1 | 243 | 27,584 | 9.32 | Type I | Mγ |
PcMADS37 | evm.TU.LG03.3242 | 744 | 1 | 247 | 28,263 | 9.52 | Type I | Mβ |
PcMADS38 | evm.TU.LG04.2508 | 564 | 1 | 187 | 20,858 | 9.47 | Type I | Mα |
PcMADS39 | evm.TU.LG04.2509 | 630 | 1 | 209 | 23,872 | 9.16 | Type I | Mα |
PcMADS40 | evm.TU.LG04.2573 | 6284 | 8 | 243 | 27,992 | 4.00 | Type II | MIKC |
PcMADS41 | evm.TU.LG04.594 | 567 | 1 | 188 | 21,250 | 5.52 | Type I | Mα |
PcMADS42 | evm.TU.LG05.1117 | 849 | 1 | 282 | 31,473 | 9.56 | Type I | Mβ |
PcMADS43 | evm.TU.LG05.1150 | 201 | 1 | 66 | 7606 | 9.56 | Type I | Mα |
PcMADS44 | evm.TU.LG05.1670 | 1173 | 1 | 390 | 45,056 | 8.61 | Type I | Mβ |
PcMADS45 | evm.TU.LG05.2530 | 950 | 4 | 168 | 19,381 | 6.51 | Type I | Mβ |
PcMADS46 | evm.TU.LG05.2661 | 5046 | 8 | 269 | 30,703 | 8.45 | Type II | MIKC |
PcMADS47 | evm.TU.LG05.2662 | 3855 | 8 | 246 | 28,156 | 9.08 | Type II | MIKC |
PcMADS48 | evm.TU.LG05.313 | 672 | 1 | 223 | 25,373 | 8.76 | Type I | Mα |
PcMADS49 | evm.TU.LG05.3202 | 1252 | 2 | 367 | 42,008 | 5.92 | Type I | Mβ |
PcMADS50 | evm.TU.LG05.3221 | 8940 | 7 | 215 | 24,330 | 8.82 | Type II | MIKC |
PcMADS51 | evm.TU.LG05.347 | 693 | 1 | 230 | 25,864 | 9.34 | Type I | Mα |
PcMADS52 | evm.TU.LG06.1294 | 651 | 1 | 216 | 23,904 | 9.32 | Type I | Mα |
PcMADS53 | evm.TU.LG06.1306 | 635 | 2 | 190 | 21,197 | 8.85 | Type I | Mγ |
PcMADS54 | evm.TU.LG06.1307 | 681 | 1 | 226 | 26,016 | 8.90 | Type I | Mγ |
PcMADS55 | evm.TU.LG06.1308 | 1068 | 1 | 355 | 39,738 | 8.78 | Type I | Mγ |
PcMADS56 | evm.TU.LG06.2017 | 1572 | 7 | 235 | 27,154 | 9.34 | Type II | MIKC |
PcMADS57 | evm.TU.LG06.458 | 465 | 2 | 137 | 16,243 | 7.64 | Type I | Mβ |
PcMADS58 | evm.TU.LG06.495 | 705 | 1 | 234 | 27,455 | 8.29 | Type I | Mβ |
PcMADS59 | evm.TU.LG06.907 | 2469 | 8 | 262 | 29,850 | 9.34 | Type II | MIKC |
PcMADS60 | evm.TU.LG07.1086 | 828 | 1 | 275 | 30,057 | 6.32 | Type I | Mα |
PcMADS61 | evm.TU.LG07.1087 | 1068 | 1 | 355 | 38,629 | 5.53 | Type I | Mα |
PcMADS62 | evm.TU.LG07.1144 | 723 | 1 | 240 | 26,943 | 9.06 | Type I | Mα |
PcMADS63 | evm.TU.LG07.1145 | 657 | 1 | 218 | 24,761 | 9.46 | Type I | Mα |
PcMADS64 | evm.TU.LG07.1998 | 15,428 | 8 | 245 | 28,108 | 9.52 | Type II | MIKC |
PcMADS65 | evm.TU.LG07.2059 | 5798 | 8 | 219 | 24,627 | 6.93 | Type II | MIKC |
PcMADS66 | evm.TU.LG08.1574 | 4634 | 7 | 218 | 25,041 | 9.04 | Type II | MIKC |
PcMADS67 | evm.TU.LG08.27 | 669 | 1 | 222 | 25,391 | 9.15 | Type I | Mα |
PcMADS68 | evm.TU.LG08.341 | 2436 | 8 | 255 | 29,194 | 8.64 | Type II | MIKC |
PcMADS69 | evm.TU.LG08.342 | 4013 | 8 | 251 | 28,613 | 8.82 | Type II | MIKC |
PcMADS70 | evm.TU.LG08.479 | 2939 | 11 | 373 | 41,912 | 5.77 | Type I | Mα |
PcMADS71 | evm.TU.LG08.917 | 2323 | 7 | 200 | 23,175 | 9.9 | Type II | MIKC |
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Nie, C.; Xu, X.; Zhang, X.; Xia, W.; Sun, H.; Li, N.; Ding, Z.; Lv, Y. Genome-Wide Identified MADS-Box Genes in Prunus campanulata ‘Plena’ and Theirs Roles in Double-Flower Development. Plants 2023, 12, 3171. https://doi.org/10.3390/plants12173171
Nie C, Xu X, Zhang X, Xia W, Sun H, Li N, Ding Z, Lv Y. Genome-Wide Identified MADS-Box Genes in Prunus campanulata ‘Plena’ and Theirs Roles in Double-Flower Development. Plants. 2023; 12(17):3171. https://doi.org/10.3390/plants12173171
Chicago/Turabian StyleNie, Chaoren, Xiaoguo Xu, Xiaoqin Zhang, Wensheng Xia, Hongbing Sun, Na Li, Zhaoquan Ding, and Yingmin Lv. 2023. "Genome-Wide Identified MADS-Box Genes in Prunus campanulata ‘Plena’ and Theirs Roles in Double-Flower Development" Plants 12, no. 17: 3171. https://doi.org/10.3390/plants12173171