Genome-Wide Identification and Analysis of the VQ Motif-Containing Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)
Abstract
:1. Introduction
2. Results
2.1. Identification and Sequence Analysis of VQ Genes in Chinese Cabbage
Gene Name | Gene Locus | Chr. No. | Strand Direction | Location | CDS | Protein | ||
---|---|---|---|---|---|---|---|---|
Length (aa) | Mol.Wt. (KDa) | pI | ||||||
BrVQ1-1 | Bra025998 | A06 | − | 6,588,703–6,588,999 | 297 | 98 | 10.81 | 4.75 |
BrVQ1-2 | Bra016616 | A08 | + | 19,301,503–19,301,796 | 294 | 97 | 10.92 | 5.13 |
BrVQ3-1 | Bra025892 | A06 | − | 8,759,573–8,760,265 | 693 | 230 | 25.07 | 8.67 |
BrVQ3-2 | Bra012276 | A07 | + | 8,889,633–8,890,172 | 540 | 179 | 19.29 | 5.1 |
BrVQ4 | Bra030082 | A07 | + | 6,712,561–6,713,295 | 735 | 244 | 26.74 | 9.66 |
BrVQ5 | Bra035492 | A08 | − | 7,791,236–7,791,901 | 666 | 221 | 25.40 | 6.58 |
BrVQ8 | Bra033934 | A02 | − | 108,00,121–10,800,534 | 414 | 137 | 15.36 | 10.19 |
BrVQ9-1 | Bra035028 | A07 | − | 21,850,607–21,851,491 | 885 | 294 | 31.58 | 10.12 |
BrVQ9-2 | Bra008356 | A02 | − | 14,998,946–14,999,815 | 870 | 289 | 31.19 | 10.39 |
BrVQ10-1 | Bra008359 | A02 | + | 15,035,463–15,035,777 | 315 | 104 | 11.61 | 5.83 |
BrVQ10-2 | Bra003642 | A07 | − | 14,203,152–14,203,469 | 318 | 105 | 11.69 | 5.01 |
BrVQ10-3 | Bra035035 | A07 | + | 21,882,989–21,883,270 | 282 | 93 | 10.44 | 4.67 |
BrVQ11-1 | Bra035182 | A07 | + | 22,479,008–22,479,511 | 504 | 167 | 18.96 | 7.96 |
BrVQ11-2 | Bra003566 | A07 | − | 13,824,994–13,825,515 | 522 | 173 | 19.66 | 9.69 |
BrVQ11-3 | Bra008473 | A02 | + | 15,858,716–15,859,210 | 495 | 164 | 18.79 | 8.74 |
BrVQ12 | Bra039937 | A09 | + | 31,714,821–31,715,237 | 417 | 138 | 16.09 | 9.66 |
BrVQ14-1 | Bra023004 | A03 | + | 8,183,495–8,184,808 | 1314 | 437 | 48.10 | 8.58 |
BrVQ14-2 | Bra017329 | A04 | + | 15,346,657–15,347,685 | 1029 | 342 | 37.24 | 10.53 |
BrVQ14-3 | Bra005358 | A05 | − | 5,012,814–5,014,478 | 1185 | 394 | 43.13 | 10.09 |
BrVQ15 | Bra016956 | A04 | − | 17,404,492–17,405,181 | 690 | 229 | 24.84 | 7.87 |
BrVQ16-1 | Bra000216 | A03 | + | 9,940,673–9,941,098 | 426 | 141 | 15.57 | 8.91 |
BrVQ16-2 | Bra004604 | A05 | + | 1,001,763–1,002,185 | 423 | 140 | 15.29 | 4.89 |
BrVQ18-1 | Bra004825 | A05 | + | 1,984,033–1,984,575 | 543 | 180 | 20.11 | 9.24 |
BrVQ18-2 | Bra037658 | A04 | + | 18,293,805–18,294,347 | 543 | 180 | 19.98 | 9.33 |
BrVQ19-1 | Bra027262 | A05 | + | 20,006,387–20,007,064 | 678 | 225 | 24.21 | 9.44 |
BrVQ19-2 | Bra021096 | A01 | + | 23,997,911–23,998,561 | 651 | 216 | 23.49 | 9.33 |
BrVQ20 | Bra037588 | A01 | + | 22,145,216–22,146,079 | 864 | 287 | 30.28 | 6.54 |
BrVQ21-1 | Bra037569 | A01 | + | 22,005,523–22,006,176 | 654 | 217 | 22.73 | 6.05 |
BrVQ21-2 | Bra022345 | A05 | + | 182,87,618–18,288,268 | 651 | 216 | 23.06 | 6.29 |
BrVQ21-3 | Bra001716 | A03 | − | 18,018,055–18,018,699 | 645 | 214 | 22.95 | 6.22 |
BrVQ22-1 | Bra023849 | A01 | + | 2,0411,389–20,411,979 | 591 | 196 | 20.61 | 9.69 |
BrVQ22-2 | Bra041035 | Scaffold000402 | − | 11,806–12,390 | 585 | 194 | 20.40 | 9.89 |
BrVQ23-1 | Bra007265 | A09 | − | 28,278,350–28,278,799 | 450 | 149 | 16.52 | 4.88 |
BrVQ23-2 | Bra014675 | A04 | + | 2,158,610–2,159,095 | 486 | 161 | 18.10 | 5.1 |
BrVQ23-3 | Bra014674 | A04 | + | 2,155,783–2,156,247 | 465 | 154 | 17.35 | 5.17 |
BrVQ24-1 | Bra007279 | A09 | + | 28,339,520–28,340,206 | 687 | 228 | 23.79 | 6.59 |
BrVQ24-2 | Bra014665 | A04 | − | 2,098,440–2,099,141 | 702 | 233 | 24.57 | 8.05 |
BrVQ25-1 | Bra007373 | A09 | + | 28,879,454–28,879,999 | 546 | 181 | 20.12 | 6.19 |
BrVQ25-2 | Bra014594 | A04 | − | 1,651,117–1,651,650 | 534 | 177 | 19.56 | 6.7 |
BrVQ26-1 | Bra007505 | A09 | + | 29,533,410–29,533,874 | 465 | 154 | 17.58 | 7.02 |
BrVQ26-2 | Bra014514 | A04 | − | 1,142,901–1,143,341 | 441 | 146 | 16.68 | 8 |
BrVQ26-3 | Bra003400 | A07 | + | 13,026,327–13,029,056 | 846 | 281 | 32.87 | 7.16 |
BrVQ27 | Bra039565 | A01 | − | 11,929,165–11,929,719 | 555 | 184 | 19.83 | 9.76 |
BrVQ28 | Bra013438 | A01 | + | 5,666,359–5,666,979 | 621 | 206 | 23.15 | 5.37 |
BrVQ29-1 | Bra010608 | A08 | + | 15,506,771–15,507,115 | 345 | 114 | 12.72 | 9.05 |
BrVQ29-2 | Bra017849 | A03 | + | 30,916,676–30,917,020 | 345 | 114 | 12.84 | 9.05 |
BrVQ30-1 | Bra010666 | A08 | + | 15,875,832–15,876,719 | 888 | 295 | 32.18 | 6.18 |
BrVQ30-2 | Bra011838 | A01 | − | 282,249–283,121 | 873 | 290 | 31.74 | 7.94 |
BrVQ31 | Bra005995 | A03 | + | 1,534,982–153,5506 | 525 | 174 | 19.11 | 9.37 |
BrVQ32-1 | Bra022063 | A02 | + | 18,984,720–18,985,412 | 693 | 230 | 25.41 | 10.26 |
BrVQ32-2 | Bra024996 | A06 | − | 24,596,158–24,596,844 | 687 | 228 | 25.12 | 9.99 |
BrVQ33-1 | Bra003032 | A10 | + | 5,893,364–5,894,047 | 684 | 227 | 25.28 | 9.99 |
BrVQ33-2 | Bra022675 | A02 | − | 8,093,063–8,093,788 | 726 | 241 | 26.93 | 9.75 |
BrVQ34-1 | Bra024362 | A06 | + | 15,221,647–15,222,738 | 1092 | 363 | 39.11 | 5.76 |
BrVQ34-2 | Bra037806 | A09 | + | 3,657,352–3,658,311 | 960 | 319 | 34.26 | 5.94 |
BrVQ34-3 | Bra031876 | A02 | + | 27,356,488–27,357,465 | 978 | 325 | 35.03 | 6.65 |
BrVQ35 | Bra006328 | A03 | − | 3,034,196–3,038,533 | 1707 | 568 | 62.99 | 8.89 |
2.2. Phylogenetic Tree, Gene Structure, and Conserved Domains Analysis in Chinese Cabbage
2.3. Multiple Sequence Alignment and Motif Analysis
2.4. Chromosome Mapping and Syntenic Analysis of VQ Genes in B. rapa
tPCK Chr a | Block | Arabidopsis Gene | Chinese Cabbage Gene | ||
---|---|---|---|---|---|
LF b | MF1 c | MF2 c | |||
tPCK1 | A | AtVQ1(AT1G17147) | BrVQ1-1 | BrVQ1-2 | – |
– | – | – | BrVQ3-1 | – | – |
– | – | – | – | – | BrVQ3-2 |
tPCK1 | B | AtVQ4(AT1G28280) | – | – | BrVQ4 |
tPCK1 | B | AtVQ5(AT1G32585) | – | BrVQ5 | – |
tPCK6 | E | AtVQ8(AT1G68450) | – | BrVQ8 | – |
tPCK6 | E | AtVQ9(AT1G78310) | BrVQ9-1 | BrVQ9-2 | – |
tPCK6 | E | AtVQ10(AT1G78410) | BrVQ10-3 | BrVQ10-1 | BrVQ10-2 |
tPCK6 | E | AtVQ11(AT1G80450) | BrVQ11-1 | BrVQ11-3 | BrVQ11-2 |
tPCK3 | I | AtVQ12(AT2G22880) | BrVQ12 | – | – |
tPCK3 | J | AtVQ14(AT2G35230) | BrVQ14-3 | BrVQ14-2 | BrVQ14-1 |
tPCK3 | J | AtVQ15(AT2G41010) | – | BrVQ15 | – |
tPCK3 | J | AtVQ16(AT2G41180) | BrVQ16-2 | – | BrVQ16-1 |
tPCK3 | J | AtVQ18(AT2G44340) | BrVQ18-1 | BrVQ18-2 | – |
tPCK2 | F | AtVQ19(AT3G15300) | BrVQ19-1 | BrVQ19-2 | – |
tPCK2 | F | AtVQ20(AT3G18360) | – | BrVQ20 | – |
tPCK2 | F | AtVQ21(AT3G18690) | BrVQ21-2 | BrVQ21-1 | BrVQ21-3 |
tPCK2 | F | AtVQ22(AT3G22160) | – | BrVQ22-1 | – |
tPCK6 | N | AtVQ23(AT3G56710) | BrVQ23-1 | BrVQ23-2/BrVQ23-3 | – |
tPCK6 | N | AtVQ24(AT3G56880) | BrVQ24-1 | BrVQ24-2 | – |
tPCK6 | N | AtVQ25(AT3G58000) | BrVQ25-1 | BrVQ25-2 | – |
tPCK6 | N | AtVQ26(AT3G60090) | BrVQ26-1 | BrVQ26-2 | BrVQ26-3 |
tPCK4 | T | AtVQ27(AT4G15120) | BrVQ27 | – | – |
tPCK4 | U | AtVQ28(AT4G20000) | BrVQ28 | – | – |
tPCK4 | U | AtVQ29(AT4G37710) | – | BrVQ29-2 | BrVQ29-1 |
tPCK4 | U | AtVQ30(AT4G39720) | BrVQ30-2 | – | BrVQ30-1 |
tPCK5 | R | AtVQ31(AT5G08480) | – | BrVQ31 | – |
tPCK7 | V | AtVQ32(AT5G46780) | BrVQ32-2 | BrVQ32-1 | – |
tPCK5 | Wb | AtVQ33(AT5G53830) | BrVQ33-1 | – | BrVQ33-2 |
tPCK7 | X | AtVQ34(AT5G65170) | BrVQ34-1 | BrVQ34-3 | BrVQ34-2 |
– | – | – | – | BrVQ35 | – |
2.5. Phylogenetic Tree of the VQ Domains in Arabidopsis, Rice and Chinese Cabbage
2.6. Expression Pattern of the BrVQ Genes in Different Tissues
2.7. Expression Analysis of the BrVQ Genes under Abiotic Stresses
2.8. Expression Analysis of the BrVQ Genes under Phytohormone Treatment
2.9. Comparison of the Expression Patterns of BrVQ Genes and Their Orthologs in Arabidopsis
3. Discussion
3.1. VQ Gene Duplication in Chinese Cabbage
3.2. Function of the VQ Proteins in Plant Growth and Development
3.3. Function of the VQ Proteins in Abiotic and Biotic Resistance
4. Experimental Section
4.1. Plant Materials, Growth Conditions, and Stress Treatments
4.2. Sequence Retrieval
4.3. Identification and Analysis of the VQ Genes and Proteins in Chinese Cabbage
4.4. RNA Isolation and qRT-PCR
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Zhang, G.; Wang, F.; Li, J.; Ding, Q.; Zhang, Y.; Li, H.; Zhang, J.; Gao, J. Genome-Wide Identification and Analysis of the VQ Motif-Containing Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis). Int. J. Mol. Sci. 2015, 16, 28683-28704. https://doi.org/10.3390/ijms161226127
Zhang G, Wang F, Li J, Ding Q, Zhang Y, Li H, Zhang J, Gao J. Genome-Wide Identification and Analysis of the VQ Motif-Containing Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis). International Journal of Molecular Sciences. 2015; 16(12):28683-28704. https://doi.org/10.3390/ijms161226127
Chicago/Turabian StyleZhang, Gaoyuan, Fengde Wang, Jingjuan Li, Qian Ding, Yihui Zhang, Huayin Li, Jiannong Zhang, and Jianwei Gao. 2015. "Genome-Wide Identification and Analysis of the VQ Motif-Containing Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)" International Journal of Molecular Sciences 16, no. 12: 28683-28704. https://doi.org/10.3390/ijms161226127