Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification and Characterization of Cell Cycle Genes in B. pendula
2.2. Chromosome Distribution of the B. pendula Cell Cycle Genes
2.3. Phylogenetic, Gene Structure and Conserved Sequence and Specific Motif Analyses of B. pendula Cell Cycle Genes
2.4. RNA-Seq Expression Analysis of Betula pendula Cell Cycle Genes
3. Results
3.1. Identification of Betula pendula Cell Cycle Genes and Physical and Chemical Properties Analysis
3.2. Chromosome Distribution of Cell Cycle Genes in B. pendula
3.3. Identification and Analysis of Cyclin Dependent Kinases (CDK) Gene Family Members of Betula platyphylla
3.4. Identification and Analysis of Cyclins (CYC) Gene Family Members of in Birch
3.5. Identification and Analysis of Cyclin Dependent Kinases Subunit (CKS) Gene Family Members in Birch
3.6. Identification and Analysis of Rb and Ubiquitin-Conjugating Enzyme Factor and DP (E2F/DP) Gene Family Members in Birch
3.7. Identification and Analysis of KIP-Related Proteins (KRP) and WEE Gene Family Members of Betula pendula
3.8. RNA-Seq Expression Analysis of Betula pendula Cell Cycle Genes
4. Discussion
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Gene Family | Gene Name | Gene ID | Deduced Number of Amino Acids | Molecular Weight (Da) | Isoelectric Point (pI) | Instability Index | Grand Average of Hydropathicity |
---|---|---|---|---|---|---|---|
CDK | CDKA.1 | Bpev01.c0957.g0013 | 295 | 33,777.93 | 6.42 | 39.45 | −0.247 |
CDKB1.1 | Bpev01.c0224.g0013 | 305 | 34,519.94 | 8.16 | 30.49 | −0.272 | |
CDKB2.1 | Bpev01.c0480.g0058 | 319 | 36,190.12 | 9.04 | 30.26 | −0.297 | |
CDKC1.1 | Bpev01.c0000.g0179 | 515 | 57,319.57 | 9.22 | 44.26 | −0.810 | |
CDKC1.2 | Bpev01.c0275.g0056 | 649 | 71,959.85 | 9.11 | 47.61 | −0.579 | |
CDKC1.3 | Bpev01.c0344.g0012 | 721 | 80,003.75 | 9.28 | 47.51 | −0.657 | |
CDKC1.4 | Bpev01.c0349.g0031 | 698 | 77,679.08 | 9.30 | 43.51 | −0.563 | |
CDKC1.5 | Bpev01.c0420.g0019 | 563 | 62,760.24 | 9.36 | 54.61 | −0.681 | |
CDKC1.6 | Bpev01.c0745.g0005 | 711 | 79,499.18 | 9.30 | 51.47 | −0.664 | |
CDKC1.7 | Bpev01.c1061.g0010 | 711 | 79,560.55 | 9.69 | 48.78 | −0.634 | |
CDKC1.8 | Bpev01.c1202.g0053 | 568 | 63,441.50 | 9.63 | 51.02 | −0.575 | |
CDKD.1 | Bpev01.c1443.g0002 | 415 | 46,691.88 | 9.36 | 36.70 | −0.391 | |
CDKE1.1 | Bpev01.c0263.g0012 | 111 | 12,348.09 | 6.03 | 34.85 | −0.374 | |
CDKE1.2 | Bpev01.c0390.g0015 | 478 | 53,271.81 | 9.30 | 41.51 | −0.461 | |
CDKF.1 | Bpev01.c0389.g0056 | 474 | 53,297.39 | 4.51 | 53.09 | −0.434 | |
Cyclins | CYCA1.1 | Bpev01.c0118.g0029 | 498 | 56,182.49 | 8.17 | 49.57 | −0.364 |
CYCA1.2 | Bpev01.c0706.g0005 | 238 | 27,110.95 | 5.35 | 52.20 | −0.202 | |
CYCA1.3 | Bpev01.c1588.g0004 | 493 | 54,391.90 | 6.43 | 56.98 | −0.220 | |
CYCA2.1 | Bpev01.c0167.g0006 | 521 | 59,705.00 | 8.99 | 48.34 | −0.263 | |
CYCA2.2 | Bpev01.c0207.g0010 | 491 | 55,055.52 | 8.63 | 46.18 | −0.243 | |
CYCA2.3 | Bpev01.c1398.g0012 | 365 | 41,875.90 | 5.20 | 61.96 | −0.336 | |
CYCA2.4 | Bpev01.c1588.g0005 | 514 | 56,762.03 | 8.19 | 46.44 | −0.234 | |
CYCA3.1 | Bpev01.c1764.g0001 | 361 | 40,479.12 | 9.29 | 39.11 | −0.247 | |
CYCA3.2 | Bpev01.c1028.g0001 | 381 | 43,109.82 | 8.83 | 43.20 | −0.355 | |
CYCB1.1 | Bpev01.c1009.g0008 | 459 | 50,545.59 | 9.00 | 38.21 | −0.207 | |
CYCB1.2 | Bpev01.c0645.g0033 | 427 | 47,430.69 | 8.73 | 50.72 | −0.264 | |
CYCB2.1 | Bpev01.c0022.g0129 | 435 | 49,791.13 | 5.39 | 50.14 | −0.365 | |
CYCB2.2 | Bpev01.c0455.g0011 | 394 | 45,186.84 | 4.82 | 46.83 | −0.117 | |
CYCB2.3 | Bpev01.c0134.g0104 | 435 | 49,391.85 | 5.63 | 48.64 | −0.269 | |
CYCB3.1 | Bpev01.c1259.g0013 | 221 | 26,057.57 | 6.39 | 32.87 | 0.011 | |
CYCD1.1 | Bpev01.c0848.g0042 | 325 | 36,316.28 | 5.31 | 61.70 | −0.215 | |
CYCD3.1 | Bpev01.c0157.g0019 | 382 | 43,607.70 | 5.19 | 62.70 | −0.238 | |
CYCD3.2 | Bpev01.c0506.g0013 | 128 | 13,598.62 | 9.30 | 71.59 | 0.009 | |
CYCD3.3 | Bpev01.c0106.g0013 | 141 | 14,557.40 | 9.10 | 89.39 | −0.343 | |
CYCD3.4 | Bpev01.c0229.g0031 | 140 | 14,728.15 | 7.89 | 58.46 | 0.184 | |
CYCD3.5 | Bpev01.c0015.g0054 | 374 | 42,291.38 | 5.08 | 64.20 | −0.111 | |
CYCD3.6 | Bpev01.c0640.g0020 | 374 | 42,444.17 | 5.22 | 52.89 | −0.295 | |
CYCD4.1 | Bpev01.c0018.g0055 | 352 | 39,061.57 | 5.26 | 48.70 | −0.080 | |
CYCD4.2 | Bpev01.c0645.g0025 | 290 | 32,331.38 | 6.66 | 49.71 | −0.004 | |
CYCD6.1 | Bpev01.c0469.g0009 | 309 | 35,275.72 | 6.03 | 44.03 | −0.081 | |
CYCD6.2 | Bpev01.c1653.g0004 | 352 | 40,349.92 | 9.27 | 53.39 | 0.023 | |
CYCH.1 | Bpev01.c1947.g0006 | 520 | 59,565.08 | 8.40 | 40.98 | −0.418 | |
CKS | CKS1.1 | Bpev01.c1113.g0001 | 1316 | 148,157.79 | 6.70 | 47.53 | −0.523 |
CKS1.2 | Bpev01.c1602.g0008 | 86 | 10,264.60 | 9.05 | 63.75 | −0.981 | |
Rb | Rb1 | Bpev01.c0457.g0045 | 1019 | 112,457.11 | 7.28 | 51.61 | −0.232 |
Rb2 | Bpev01.c2803.g0002 | 69 | 7110.27 | 5.05 | 25.09 | 0.375 | |
E2F/DP | E2Fa | Bpev01.c0105.g0012 | 473 | 51,575.73 | 5.10 | 49.59 | −0.595 |
E2Fb | Bpev01.c2596.g0002 | 475 | 52,376.33 | 4.84 | 50.61 | −0.692 | |
E2Fc | Bpev01.c0214.g0033 | 456 | 51,109.76 | 5.61 | 55.05 | −0.807 | |
DPa1 | Bpev01.c0423.g0003 | 346 | 38,243.67 | 5.62 | 60.94 | −0.758 | |
Dpa2 | Bpev01.c0427.g0013 | 748 | 84,137.36 | 9.26 | 40.81 | −0.288 | |
DEL | DEL1 | Bpev01.c0813.g0011 | 377 | 42,243.32 | 8.80 | 41.91 | −0.693 |
DEL2 | Bpev01.c0094.g0053 | 351 | 39,730.68 | 8.64 | 47.44 | −0.721 | |
RP | KRP1 | Bpev01.c0000.g0097 | 245 | 27,423.72 | 6.76 | 60.33 | −0.822 |
KRP2 | Bpev01.c0016.g0069 | 242 | 26,897.62 | 7.84 | 53.03 | −1.146 | |
KRP3 | Bpev01.c2423.g0003 | 183 | 20,002.40 | 5.55 | 53.69 | −0.507 | |
KRP4 | Bpev01.c0027.g0181 | 209 | 23,217.59 | 5.36 | 78.83 | −0.880 | |
WEE | WEE1 | Bpev01.c0579.g0004 | 498 | 55,758.40 | 6.74 | 52.91 | −0.446 |
WEE2 | Bpev01.c0579.g0010 | 97 | 10,666.77 | 4.42 | 52.08 | −0.464 |
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Li, Y.; Chen, S.; Liu, Y.; Huang, H. Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch. Forests 2022, 13, 120. https://doi.org/10.3390/f13010120
Li Y, Chen S, Liu Y, Huang H. Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch. Forests. 2022; 13(1):120. https://doi.org/10.3390/f13010120
Chicago/Turabian StyleLi, Yijie, Song Chen, Yuhang Liu, and Haijiao Huang. 2022. "Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch" Forests 13, no. 1: 120. https://doi.org/10.3390/f13010120
APA StyleLi, Y., Chen, S., Liu, Y., & Huang, H. (2022). Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch. Forests, 13(1), 120. https://doi.org/10.3390/f13010120