Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L.
Abstract
:1. Introduction
2. Results
2.1. Identification and Chromosomal Location of the Rice PHD Family Genes
2.2. Phylogenetic Analyses and Gene Architecture of the Rice PHD Family
2.3. Investigation of the Conserved Functional Domains in OsPHD Proteins
2.4. Expression Profiles of OsPHD Genes in Rice Tissues
2.5. Expression Responses of OsPHD Genes to Environmental Stresses
2.6. Quantitative Real-Time PCR Analyses of OsPHDs Expression in Response to Environmental Stresses
3. Discussion
4. Materials and Methods
4.1. Identification of the PHD-Finger Family Genes in Rice
4.2. Multiple Alignment, Phylogenetic Analysis and Chromosomal Location of the Rice PHD Family Genes
4.3. Analyses of Gene Structure, Functional Domains and Conserved Motifs of the Rice PHD Family
4.4. Expression Analysis of the Rice PHD Family Genes in Diverse Tissues and Under Different Stress Treatments
4.5. Quantitative Real-Time PCR Analyses of the Rice PHD Family Genes in Response to Environmental Stresses
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Name | TIGR Locus ID | Chr. | Location | Open Reading Frame Length (bp) | Protein | Alias | ||
---|---|---|---|---|---|---|---|---|
Amino Acids (aa) | Molecular Weight (KD) | Isoelectric Point | ||||||
OsPHD1 | LOC_Os01g08820 | 1 | 4431532–4433679 (R) | 1824 | 607 | 63.23 | 8.01 | OsPhd3 [18] |
OsPHD2 | LOC_Os01g11952 | 1 | 6507356–6514891 (R) | 2976 | 991 | 110.89 | 8.18 | |
OsPHD3 | LOC_Os01g11960 | 1 | 6518127–6521046 (R) | 1218 | 405 | 44.46 | 5.30 | |
OsPHD4 | LOC_Os01g46700 | 1 | 26591955–26599634 (F) | 3048 | 1015 | 115.46 | 6.40 | |
OsPHD5 | LOC_Os01g65600 | 1 | 38081608–38085548 (F) | 2151 | 716 | 79.23 | 7.44 | OsPhd4 [18] |
OsPHD6 | LOC_Os01g66070 | 1 | 38344410–38344937 (F) | 528 | 175 | 19.75 | 4.84 | OsPhd5 [18] |
OsPHD7 | LOC_Os01g66420 | 1 | 38566147–38570861(R) | 819 | 272 | 29.57 | 5.32 | OsPhd7 [18] |
OsPHD8 | LOC_Os01g73460 | 1 | 42567843–42573082 (F) | 1158 | 385 | 43.48 | 8.92 | OsPhd2 [18] |
OsPHD9 | LOC_Os01g73480 | 1 | 42579342–42583645 (F) | 2694 | 897 | 95.02 | 9.65 | |
OsPHD10 | LOC_Os02g03030 | 2 | 1190846–1192461 (F) | 1086 | 361 | 39.59 | 9.16 | OsPhd11 [18] |
OsPHD11 | LOC_Os02g09910 | 2 | 5131380–5132629 (F) | 780 | 259 | 26.93 | 5.78 | |
OsPHD12 | LOC_Os02g09920 | 2 | 5145548–5151131 (F) | 2940 | 979 | 110.22 | 4.85 | |
OsPHD13 | LOC_Os02g35600 | 2 | 21413884–21417221 (F) | 804 | 267 | 29.20 | 6.00 | OsPhd12 [18] |
OsPHD14 | LOC_Os02g48810 | 2 | 29871368–29875355 (F) | 2064 | 687 | 71.93 | 5.25 | OsPhd14 [18] |
OsPHD15 | LOC_Os02g52960 | 2 | 32384631–32396094 (F) | 4461 | 1486 | 164.12 | 7.48 | |
OsPHD16 | LOC_Os03g04980 | 3 | 2409861–2413432 (F) | 762 | 253 | 27.61 | 5.65 | OsPhd18 [18] |
OsPHD17 | LOC_Os03g19020 | 3 | 10651192–10655656 (F) | 2400 | 799 | 90.27 | 4.54 | |
OsPHD18 | LOC_Os03g19190 | 3 | 10752594–10759931 (F) | 4389 | 1462 | 158.32 | 7.95 | |
OsPHD19 | LOC_Os03g50780 | 3 | 28988380–28991862 (F) | 2094 | 697 | 76.64 | 5.86 | |
OsPHD20 | LOC_Os03g53630 | 3 | 30747354–30755128 (F) | 4038 | 1345 | 146.86 | 6.70 | OsPhd17 [18] |
OsPHD21 | LOC_Os03g53700 | 3 | 30791616–30797021 (F) | 762 | 253 | 28.77 | 4.66 | |
OsPHD22 | LOC_Os03g58530 | 3 | 33328214–33333421 (F) | 657 | 218 | 25.02 | 8.34 | |
OsPHD23 | LOC_Os03g60390 | 3 | 34342899–34346745 (R) | 744 | 247 | 27.75 | 5.64 | OsPhd16 [18] |
OsPHD24 | LOC_Os04g34720 | 4 | 21001722–21010737 (F) | 1314 | 437 | 48.44 | 5.41 | OsPhd21 [18] |
OsPHD25 | LOC_Os04g35430 | 4 | 21559229–21565988 (R) | 4308 | 1435 | 160.19 | 8.03 | OsPhd20 [18] |
OsPHD26 | LOC_Os04g36730 | 4 | 22189014–22191831 (F) | 771 | 256 | 28.24 | 5.98 | |
OsPHD27 | LOC_Os04g52020 | 4 | 30888156–30903920 (R) | 2439 | 812 | 90.94 | 6.60 | |
OsPHD28 | LOC_Os04g59510 | 4 | 35382882–35390423 (R) | 1158 | 385 | 43.00 | 5.13 | |
OsPHD29 | LOC_Os05g03430 | 5 | 1426929–1438465 (F) | 2631 | 876 | 97.00 | 4.81 | |
OsPHD30 | LOC_Os05g07040 | 5 | 3697729–3702359 (R) | 777 | 258 | 28.84 | 5.39 | |
OsPHD31 | LOC_Os05g34640 | 5 | 20542370–20547114 (F) | 777 | 258 | 29.07 | 5.28 | OsPhd22 [18] |
OsPHD32 | LOC_Os06g01170 | 6 | 131089–138360 (F) | 3078 | 1025 | 111.11 | 6.70 | OsPhd24 [18] |
OsPHD33 | LOC_Os06g08790 | 6 | 4393376–4401129 (F) | 2445 | 814 | 91.95 | 8.67 | |
OsPHD34 | LOC_Os06g10690 | 6 | 5575867–5584373 (F) | 3420 | 1139 | 125.22 | 7.20 | |
OsPHD35 | LOC_Os06g12400 | 6 | 6725306–6734446 (F) | 2379 | 792 | 87.21 | 4.95 | OsHAZ1 [27] |
OsPHD36 | LOC_Os06g17280 | 6 | 10003546–10007033 (F) | 2292 | 763 | 83.42 | 7.58 | |
OsPHD37 | LOC_Os06g20410 | 6 | 11725804–11734594 (R) | 1989 | 662 | 71.45 | 9.02 | OsPhd28 [18] |
OsPHD38 | LOC_Os06g51450 | 6 | 31161699–31169513 (R) | 2400 | 799 | 87.56 | 9.87 | |
OsPHD39 | LOC_Os06g51490 | 6 | 31184911–31187612 (R) | 864 | 287 | 32.52 | 7.39 | |
OsPHD40 | LOC_Os07g07690 | 7 | 3859755–3868364 (F) | 4329 | 1442 | 156.86 | 8.46 | |
OsPHD41 | LOC_Os07g08880 | 7 | 4606679–4614599 (F) | 657 | 218 | 24.89 | 7.94 | |
OsPHD42 | LOC_Os07g12910 | 7 | 7414568–7418059 (R) | 735 | 244 | 27.37 | 6.39 | OsPhd34 [18] |
OsPHD43 | LOC_Os07g31450 | 7 | 18625785–18638679 (R) | 6579 | 2192 | 243.66 | 6.37 | |
OsPHD44 | LOC_Os07g41740 | 7 | 25013506–25017814 (F) | 837 | 278 | 30.38 | 5.56 | OsPhd32 [18] |
OsPHD45 | LOC_Os07g46690 | 7 | 27902966–27912209 (R) | 5022 | 1673 | 186.85 | 6.80 | OsPhd30 [18] |
OsPHD46 | LOC_Os07g49030 | 7 | 29353044–29356917 (R) | 2361 | 786 | 88.01 | 4.46 | OsPhd29 [18] |
OsPHD47 | LOC_Os07g49290 | 7 | 29519451–29522145 (R) | 2235 | 744 | 83.32 | 8.32 | OsPhd31 [18] |
OsPHD48 | LOC_Os08g01420 | 8 | 272854–276978 (R) | 1692 | 563 | 62.13 | 6.07 | OsPhd35 [18] OsEhd3 [28] |
OsPHD49 | LOC_Os08g32620 | 8 | 20204623–20208055 (F) | 651 | 216 | 24.82 | 8.41 | |
OsPHD50 | LOC_Os09g04890 | 9 | 2601650–2615934 (R) | 3069 | 1022 | 115.53 | 7.48 | |
OsPHD51 | LOC_Os09g21770 | 9 | 13181330–13184741 (F) | 651 | 216 | 24.64 | 8.84 | |
OsPHD52 | LOC_Os09g27620 | 9 | 16786041–16788255 (F) | 2040 | 679 | 73.76 | 7.60 | OsMS1 [29] |
OsPHD53 | LOC_Os09g38440 | 9 | 22130437–22135245 (F) | 2133 | 710 | 79.43 | 9.16 | |
OsPHD54 | LOC_Os11g05130 | 11 | 2247706–2256169 (R) | 5667 | 1888 | 206.55 | 5.70 | OsPhd37 [18] |
OsPHD55 | LOC_Os11g12650 | 11 | 7125124–7128857 (R) | 2148 | 715 | 79.80 | 8.29 | |
OsPHD56 | LOC_Os11g14010 | 11 | 7776646–7784194 (R) | 765 | 254 | 28.51 | 5.16 | OsPhd40 [18] |
OsPHD57 | LOC_Os11g18770 | 11 | 10648362–10657255 (R) | 3171 | 1056 | 113.99 | 7.91 | |
OsPHD58 | LOC_Os12g24540 | 12 | 14012791–14020313 (R) | 3807 | 1268 | 138.94 | 5.39 | |
OsPHD59 | LOC_Os12g34330 | 12 | 20806080–20813363 (R) | 2067 | 688 | 76.07 | 9.22 |
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Sun, M.; Jia, B.; Yang, J.; Cui, N.; Zhu, Y.; Sun, X. Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L. Int. J. Mol. Sci. 2017, 18, 2005. https://doi.org/10.3390/ijms18092005
Sun M, Jia B, Yang J, Cui N, Zhu Y, Sun X. Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L. International Journal of Molecular Sciences. 2017; 18(9):2005. https://doi.org/10.3390/ijms18092005
Chicago/Turabian StyleSun, Mingzhe, Bowei Jia, Junkai Yang, Na Cui, Yanming Zhu, and Xiaoli Sun. 2017. "Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L." International Journal of Molecular Sciences 18, no. 9: 2005. https://doi.org/10.3390/ijms18092005