Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L.
Abstract
:1. Introduction
2. Results
2.1. Identification of ZHD Family Genes and Sequence Analysis of Their Proteins
2.2. Sequence Alignment and Phylogenetic Tree Construction
2.3. Chromosomal Location, Gene Structure, and Motif Composition Analysis
2.4. Analysis of Cis-Elements in ZmZHD Promoters
2.5. Synteny and Evolutionary Analysis of ZmZHDGenes
2.6. Construction of a PPI Network and Expression Profiling of ZmZHD Genes in Various Tissues
2.7. MiRNA Target Site Prediction and Validation
3. Discussion
4. Materials and Methods
4.1. Gene Retrieval and Sequence Analysis of the ZHD Gene Family in Maize
4.2. Sequence Alignment and Phylogenetic Tree Construction
4.3. Chromosomal Locations, Motif Compositions, and Exon and Intron Distributions
4.4. Cis-Acting Elements and Functional Prediction
4.5. Synteny Analysis of ZHD Proteins and ks/ka Ratios
4.6. Protein–Protein Interaction and Z. mays L. RNA-Sequencing Data Analysis
4.7. MiRNA Target Site Prediction
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Gene ID | Chromosome Location | Protein Length (aa) | Mol. Wt. 1KDA | pI 1 | GRAVY 1 | Exon | Intron | Subcellular Location | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Number | Start | End | Length | |||||||||
ZmZHD1 | GRMZM2G068330 | 4 | 11278503 | 112881332 | 250330460 | 382 | 39,774.87 | 8.13 | −0.58 | 2 | 1 | Nucleus |
ZmZHD2 | GRMZM2G161315 | 7 | 112902252 | 1129906963 | 185808916 | 370 | 38,611.45 | 8.21 | −0.524 | 1 | Cell wall, nucleus | |
ZmZHD3 | GRMZM2G346920 | 1 | 200895999 | 200900836 | 308452471 | 361 | 37,825.61 | 7.03 | −0.515 | 1 | Chloroplast, nucleus | |
ZmZHD4 | GRMZM2G425236 | 5 | 10221783 | 10225985 | 226353449 | 240 | 24,975.74 | 7.16 | −0.629 | 1 | Nucleus | |
ZmZHD5 | GRMZM2G438438 | 1 | 212576317 | 212581228 | 308452471 | 373 | 38,662.73 | 7.21 | −0.31 | 1 | Nucleus | |
ZmZHD6 | GRMZM2G414844 | 6 | 166374440 | 166378910 | 181357234 | 242 | 26,692.75 | 8.8 | −0.985 | 1 | Nucleus | |
ZmZHD7 | GRMZM2G353734 | 4 | 85319366 | 85325092 | 250330460 | 526 | 55,497.21 | 9.02 | −0.575 | 3 | 2 | Nucleus |
ZmZHD8 | GRMZM2G423423 | 1 | 269145949 | 269149835 | 308452471 | 231 | 24,075.72 | 8.35 | −0.687 | 1 | Nucleus | |
ZmZHD9 | GRMZM2G353076 | 3 | 230480803 | 230481862 | 238017767 | 100 | 10,401.41 | 8.93 | −0.608 | 1 | Nucleus | |
ZmZHD10 | GRMZM2G470974 | 10 | 2632775 | 2633842 | 152435371 | 98 | 10,100.06 | 6.87 | −0.628 | 1 | Nucleus | |
ZmZHD11 | GRMZM2G328438 | 8 | 73654879 | 73656447 | 182411202 | 254 | 27,689.12 | 8.51 | −0.805 | 1 | Nucleus | |
ZmZHD12 | GRMZM2G417229 | 5 | 201282254 | 201284278 | 226353449 | 302 | 32,353.12 | 6.95 | −0.746 | 1 | Nucleus | |
ZmZHD13 | GRMZM2G071112 | 7 | 112658777 | 112661470 | 185808916 | 89 | 9802.04 | 8.16 | −0.361 | 5 | 4 | Nucleus |
ZmZHD14 | GRMZM2G172586 | 10 | 2639262 | 2640147 | 152435371 | 98 | 10,113.1 | 7.59 | −0.628 | 1 | Nucleus | |
ZmZHD15 | GRMZM2G089619 | 2 | 50140925 | 50142374 | 243,675,191 | 300 | 31,130.79 | 6.72 | −0.437 | 1 | Nucleus | |
ZmZHD16 | GRMZM2G389379 | 2 | 188271896 | 188273136 | 243,675,191 | 286 | 29,912.64 | 6.96 | −0.485 | 1 | Nucleus | |
ZmZHD17 | GRMZM2G069365 | 4 | 160153804 | 160155930 | 250330460 | 446 | 48,227.78 | 6.64 | −0.793 | 1 | Nucleus | |
ZmZHD18 | GRMZM2G462417 | 4 | 185816491 | 185819532 | 250330460 | 655 | 71,591.15 | 9.01 | −0.046 | 3 | 2 | Nucleus |
ZmZHD19 | GRMZM2G370863 | 4 | 85758755 | 85759432 | 250330460 | 127 | 13,351.19 | 7.53 | −0.138 | 1 | Nucleus | |
ZmZHD20 | GRMZM2G051955 | 2 | 181822882 | 181824556 | 243675191 | 361 | 37,714.29 | 7.73 | −0.578 | 1 | Cell wall, nucleus | |
ZmZHD21 | GRMZM5G821755 | 3 | 136934215 | 136936196 | 238017767 | 331 | 35,115.48 | 8.57 | −0.593 | 2 | 1 | Nucleus |
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Islam, M.A.U.; Nupur, J.A.; Khalid, M.H.B.; Din, A.M.U.; Shafiq, M.; Alshegaihi, R.M.; Ali, Q.; Ali, Q.; Kamran, Z.; Manzoor, M.; et al. Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L. Genes 2022, 13, 2112. https://doi.org/10.3390/genes13112112
Islam MAU, Nupur JA, Khalid MHB, Din AMU, Shafiq M, Alshegaihi RM, Ali Q, Ali Q, Kamran Z, Manzoor M, et al. Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L. Genes. 2022; 13(11):2112. https://doi.org/10.3390/genes13112112
Chicago/Turabian StyleIslam, Md. Abir Ul, Juthy Abedin Nupur, Muhammad Hayder Bin Khalid, Atta Mohi Ud Din, Muhammad Shafiq, Rana M. Alshegaihi, Qurban Ali, Qurban Ali, Zuha Kamran, Mujahid Manzoor, and et al. 2022. "Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L." Genes 13, no. 11: 2112. https://doi.org/10.3390/genes13112112
APA StyleIslam, M. A. U., Nupur, J. A., Khalid, M. H. B., Din, A. M. U., Shafiq, M., Alshegaihi, R. M., Ali, Q., Ali, Q., Kamran, Z., Manzoor, M., Haider, M. S., Shahid, M. A., & Manghwar, H. (2022). Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L. Genes, 13(11), 2112. https://doi.org/10.3390/genes13112112