Codon Bias of the DDR1 Gene and Transcription Factor EHF in Multiple Species
Abstract
:1. Introduction
2. Results
2.1. Construction of DDR1 Gene and EHF Phylogenetic Trees
2.2. Codon Usage Patterns for the DDR1 Gene and EHF
2.3. Relative Synonymous Codon Usage (RSCU) Values Analysis and Determination of Putative Optimal Codons for DDR1 and EHF across 24 Species
2.4. Hierarchical Clustering Analysis of RSCU for DDR1 and EHF
2.5. PCA Analysis of 24 Species and Codons Separately Using RSCU Values
2.6. Correlation Analysis of Codon Usage Preference between DDR1 Gene and EHF
2.7. Analysis of DDR1 Gene and EHF Third Codon Bias
2.8. Multidimensional Clustering Analysis of CAI for DDR1–EHF Based on K-Means
3. Discussion
4. Materials and Methods
4.1. DDR1 Gene Data and EHF TF Data Collection
4.2. Phylogenetic Trees and Hierarchical Cluster Analysis
4.3. Parametric Statistical Methods for Codons
4.4. Codon Correlation and Third Codon Analysis
4.5. PCA and K-Means Cluster Analyses
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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Species | T3s/% | C3s/% | A3s/% | G3s/% | CAI | CBI | Fop | Nc | GC3s/% | GC/% | Gravy | Aromo |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Bos taurus | 17.23 | 47.39 | 11.21 | 44.48 | 0.197 | 0.071 | 0.442 | 41.49 | 75.90 | 63.30 | −0.23 | 0.09 |
Bos indicus × Bos taurus | 17.49 | 46.58 | 11.30 | 45.61 | 0.199 | 0.066 | 0.441 | 41.59 | 75.70 | 62.90 | −0.22 | 0.09 |
Bos javanicus | 17.23 | 47.39 | 11.21 | 44.48 | 0.198 | 0.072 | 0.443 | 41.67 | 75.90 | 63.30 | −0.22 | 0.09 |
Bos indicus | 16.73 | 47.94 | 11.22 | 44.39 | 0.198 | 0.082 | 0.448 | 41.72 | 76.30 | 63.40 | −0.20 | 0.09 |
Bos mutus | 17.04 | 47.72 | 11.02 | 44.43 | 0.199 | 0.082 | 0.449 | 41.78 | 76.20 | 63.30 | −0.20 | 0.09 |
Bubalus carabanensis | 16.82 | 47.85 | 11.27 | 44.44 | 0.202 | 0.083 | 0.449 | 41.80 | 76.20 | 63.40 | −0.22 | 0.09 |
Bubalus bubalis | 17.08 | 47.13 | 11.23 | 45.81 | 0.205 | 0.081 | 0.450 | 41.82 | 76.10 | 63.00 | −0.21 | 0.09 |
Capra hircus | 17.21 | 47.40 | 10.41 | 46.00 | 0.207 | 0.087 | 0.453 | 41.85 | 76.60 | 63.30 | −0.22 | 0.09 |
Ovis aries | 17.98 | 46.59 | 10.59 | 45.8 | 0.208 | 0.088 | 0.454 | 41.94 | 75.80 | 63.00 | −0.21 | 0.09 |
Cervus elaphus | 18.77 | 46.28 | 11.11 | 44.23 | 0.204 | 0.083 | 0.450 | 41.96 | 74.60 | 62.90 | −0.22 | 0.09 |
Dama dama | 18.41 | 46.87 | 11.24 | 43.86 | 0.205 | 0.087 | 0.452 | 42.00 | 74.90 | 63.00 | −0.22 | 0.09 |
Moschus berezovskii | 18.12 | 46.68 | 10.92 | 44.48 | 0.203 | 0.074 | 0.444 | 42.00 | 75.30 | 63.20 | −0.21 | 0.09 |
Cervus canadensis | 18.90 | 46.15 | 10.82 | 44.53 | 0.204 | 0.083 | 0.450 | 42.01 | 74.70 | 63.00 | −0.22 | 0.09 |
Globicephala melas | 18.35 | 47.23 | 10.12 | 45.13 | 0.210 | 0.094 | 0.456 | 42.02 | 75.90 | 63.20 | −0.27 | 0.09 |
Phocoena sinus | 18.28 | 46.74 | 10.53 | 45.13 | 0.214 | 0.101 | 0.460 | 42.02 | 75.60 | 63.20 | −0.22 | 0.09 |
Mesoplodon densirostris | 18.54 | 46.08 | 11.37 | 44.76 | 0.208 | 0.083 | 0.449 | 42.14 | 74.70 | 62.90 | −0.22 | 0.09 |
Lagenorhynchus albirostri | 18.12 | 46.68 | 10.66 | 45.21 | 0.210 | 0.097 | 0.457 | 42.16 | 75.60 | 63.10 | −0.22 | 0.09 |
Delphinus delphis | 18.38 | 46.41 | 10.66 | 45.21 | 0.210 | 0.091 | 0.454 | 42.19 | 75.40 | 63.00 | −0.22 | 0.09 |
Tursiops truncatus | 18.12 | 46.81 | 10.66 | 45.06 | 0.211 | 0.095 | 0.456 | 42.19 | 75.60 | 63.10 | −0.22 | 0.09 |
Neophocaena asiaeoriental asiaeoriental | 18.54 | 46.48 | 10.53 | 45.13 | 0.214 | 0.101 | 0.460 | 42.21 | 75.30 | 63.10 | −0.22 | 0.09 |
Balaenoptera ricei | 19.35 | 45.75 | 10.56 | 45.05 | 0.206 | 0.076 | 0.445 | 42.32 | 74.60 | 62.80 | −0.23 | 0.09 |
Monodon monoceros | 18.64 | 46.28 | 11.24 | 44.46 | 0.211 | 0.096 | 0.456 | 42.52 | 74.70 | 62.80 | −0.22 | 0.09 |
Orcinus orca | 18.38 | 46.28 | 10.81 | 45.21 | 0.209 | 0.090 | 0.452 | 42.57 | 75.30 | 63.00 | −0.22 | 0.09 |
Physeter catodon | 19.17 | 45.63 | 10.55 | 45.28 | 0.208 | 0.089 | 0.452 | 42.66 | 74.80 | 63.00 | −0.22 | 0.09 |
Species | T3s/% | C3s/% | A3s/% | G3s/% | CAI | CBI | Fop | Nc | GC3s/% | GC% | Gravy | Aromo |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Bos taurus | 21.38 | 46.54 | 30.92 | 32.87 | 0.277 | 0.215 | 0.554 | 57.52 | 59.90 | 49.10 | −0.95 | 0.10 |
Bos indicus × Bos taurus | 22.67 | 49.78 | 25.73 | 34.02 | 0.292 | 0.226 | 0.56 | 54.01 | 63.10 | 50.70 | −0.81 | 0.11 |
Bos javanicus | 21.38 | 46.54 | 30.92 | 32.87 | 0.277 | 0.215 | 0.554 | 57.52 | 59.90 | 49.10 | −0.95 | 0.10 |
Bos indicus | 27.37 | 47.37 | 21.71 | 33.54 | 0.304 | 0.187 | 0.536 | 50.46 | 61.70 | 50.80 | −0.47 | 0.10 |
Bos mutus | 21.95 | 49.76 | 28.04 | 33.52 | 0.287 | 0.206 | 0.55 | 53.46 | 62.30 | 50.40 | −0.87 | 0.12 |
Bubalus carabanensis | 25.57 | 47.03 | 25.00 | 33.16 | 0.276 | 0.199 | 0.542 | 54.68 | 60.90 | 50.00 | −0.64 | 0.12 |
Bubalus bubalis | 24.22 | 48.88 | 26.34 | 33.16 | 0.29 | 0.204 | 0.548 | 54.06 | 61.60 | 50.10 | −0.79 | 0.11 |
Capra hircus | 23.21 | 48.66 | 27.80 | 32.81 | 0.284 | 0.218 | 0.555 | 55.03 | 61.20 | 50.20 | −0.80 | 0.11 |
Ovis aries | 34.60 | 37.26 | 23.67 | 31.90 | 0.249 | 0.108 | 0.483 | 54.81 | 53.60 | 49.40 | −0.28 | 0.12 |
Cervus elaphus | 23.21 | 49.11 | 25.73 | 34.02 | 0.274 | 0.187 | 0.537 | 53.93 | 62.60 | 50.80 | −0.79 | 0.11 |
Dama dama | 22.64 | 50.00 | 24.74 | 33.71 | 0.284 | 0.242 | 0.567 | 53.56 | 63.60 | 51.00 | −0.68 | 0.12 |
Moschus berezovskii | 21.88 | 50.00 | 25.73 | 34.72 | 0.288 | 0.23 | 0.562 | 53.42 | 63.70 | 51.20 | −0.78 | 0.11 |
Cervus canadensis | 23.21 | 49.11 | 25.24 | 34.54 | 0.274 | 0.187 | 0.537 | 54.31 | 63.00 | 50.90 | −0.79 | 0.11 |
Globicephala melas | 21.17 | 50.45 | 26.79 | 33.67 | 0.272 | 0.198 | 0.544 | 52.53 | 63.30 | 50.90 | −0.77 | 0.11 |
Phocoena sinus | 21.17 | 49.55 | 28.23 | 33.33 | 0.269 | 0.185 | 0.537 | 53.24 | 62.30 | 50.60 | −0.76 | 0.11 |
Mesoplodon densirostris | 22.97 | 49.55 | 26.96 | 33.51 | 0.272 | 0.175 | 0.532 | 52.32 | 62.10 | 50.20 | −0.80 | 0.12 |
Lagenorhynchus albirostri | 19.23 | 48.08 | 32.03 | 32.64 | 0.251 | 0.175 | 0.532 | 56.16 | 60.70 | 49.10 | −0.92 | 0.10 |
Delphinus delphis | 21.72 | 50.23 | 26.44 | 33.85 | 0.271 | 0.202 | 0.546 | 53.08 | 63.20 | 50.70 | −0.78 | 0.11 |
Tursiops truncatus | 19.87 | 46.79 | 32.68 | 32.64 | 0.253 | 0.175 | 0.532 | 57.44 | 59.70 | 48.80 | −0.92 | 0.10 |
Neophocaena asiaeoriental asiaeoriental | 21.17 | 49.55 | 28.23 | 33.33 | 0.269 | 0.185 | 0.537 | 53.24 | 62.30 | 50.60 | −0.76 | 0.11 |
Balaenoptera ricei | 20.27 | 51.35 | 27.05 | 34.02 | 0.266 | 0.198 | 0.544 | 53.15 | 64.10 | 50.80 | −0.80 | 0.11 |
Monodon monoceros | 20.72 | 50.90 | 27.40 | 33.51 | 0.272 | 0.199 | 0.544 | 53.05 | 63.30 | 50.70 | −0.76 | 0.11 |
Orcinus orca | 19.23 | 47.44 | 32.68 | 32.64 | 0.253 | 0.175 | 0.532 | 56.58 | 60.20 | 49.00 | −0.92 | 0.10 |
Physeter catodon | 21.62 | 50.45 | 27.05 | 33.51 | 0.27 | 0.198 | 0.544 | 52.62 | 63.00 | 50.60 | −0.79 | 0.11 |
Amino Acid | Codon | Number | RSCU | Amino Acid | Codon | Number | RSCU |
---|---|---|---|---|---|---|---|
Phe | UUU | 318 | 0.77 | Ala | GCU | 253 | 0.60 |
UUC * | 506 | 1.23 | GCC * | 1005 | 2.38 | ||
Leu | UUA | 105 | 0.24 | GCA | 177 | 0.42 | |
UUG | 155 | 0.36 | GCG | 252 | 0.60 | ||
CUU | 182 | 0.42 | Tyr | UAU | 281 | 0.87 | |
CUC * | 664 | 1.52 | UAC * | 366 | 1.13 | ||
CUA | 141 | 0.33 | His | CAU | 150 | 0.58 | |
CUG * | 1368 | 3.14 | CAC * | 369 | 1.42 | ||
Ile | AUU | 74 | 0.36 | Gln | CAA | 74 | 0.19 |
AUC * | 522 | 2.52 | CAG * | 682 | 1.81 | ||
AUA | 26 | 0.13 | Asn | AAU | 212 | 0.66 | |
Val | GUU | 118 | 0.32 | AAC * | 427 | 1.34 | |
GUC | 301 | 0.83 | Lys | AAA | 45 | 0.16 | |
GUA | 75 | 0.21 | AAG * | 513 | 1.84 | ||
GUG * | 958 | 2.63 | Asp | GAU | 475 | 0.79 | |
Ser | UCU | 157 | 0.75 | GAC * | 726 | 1.21 | |
UCC * | 289 | 1.38 | Glu | GAA | 150 | 0.25 | |
UCA | 77 | 0.37 | GAG * | 1049 | 1.75 | ||
UCG | 79 | 0.38 | Cys | UGU | 127 | 0.62 | |
AGU | 148 | 0.71 | UGC * | 282 | 1.38 | ||
AGC * | 505 | 2.41 | Arg | CGU | 95 | 0.35 | |
Pro | CCU | 423 | 0.89 | CGC * | 428 | 1.59 | |
CCC * | 864 | 1.82 | CGA | 127 | 0.47 | ||
CCA | 343 | 0.72 | CGG * | 630 | 2.33 | ||
CCG | 268 | 0.56 | AGA | 62 | 0.23 | ||
Thr | ACU | 124 | 0.60 | AGG * | 277 | 1.03 | |
ACC * | 443 | 2.15 | Gly | GGU | 151 | 0.30 | |
ACA | 126 | 0.61 | GGC * | 825 | 1.64 | ||
ACG | 133 | 0.65 | GGA | 268 | 0.53 | ||
GGG * | 767 | 1.53 |
Amino Acid | Codon | Number | RSCU | Amino Acid | Codon | Number | RSCU |
---|---|---|---|---|---|---|---|
Phe | UUU | 87 | 0.64 | Ala | GCU | 37 | 0.54 |
UUC * | 164 | 1.36 | GCC * | 116 | 1.76 | ||
Leu | UUA | 71 | 0.70 | GCA | 63 | 0.97 | |
UUG | 74 | 0.73 | GCG | 49 | 0.72 | ||
CUU | 66 | 0.61 | Tyr | UAU | 110 | 0.83 | |
CUC * | 187 | 1.74 | UAC * | 156 | 1.17 | ||
CUA | 33 | 0.32 | His | CAU | 81 | 0.63 | |
CUG * | 201 | 1.91 | CAC * | 165 | 1.37 | ||
Ile | AUU | 85 | 0.89 | Gln | CAA | 67 | 0.35 |
AUC * | 197 | 2.07 | CAG * | 327 | 1.65 | ||
AUA | 3 | 0.03 | Asn | AAU | 189 | 0.85 | |
Val | GUU | 23 | 0.36 | AAC * | 253 | 1.15 | |
GUC * | 56 | 1.08 | Lys | AAA * | 242 | 1.06 | |
GUA * | 67 | 1.27 | AAG | 214 | 0.94 | ||
GUG * | 69 | 1.29 | Asp | GAU | 73 | 0.46 | |
Ser | UCU | 32 | 0.36 | GAC * | 243 | 1.54 | |
UCC * | 109 | 1.24 | Glu | GAA * | 276 | 1.24 | |
UCA | 35 | 0.41 | GAG | 168 | 0.76 | ||
UCG | 10 | 0.12 | Cys | UGU | 3 | 0.04 | |
AGU | 81 | 0.91 | UGC * | 107 | 1.96 | ||
AGC* | 259 | 2.95 | Arg | CGU | 34 | 0.62 | |
Pro | CCU* | 95 | 1.35 | CGC | 33 | 0.59 | |
CCC | 66 | 0.96 | CGA * | 61 | 1.10 | ||
CCA* | 64 | 1.00 | CGG * | 68 | 1.36 | ||
CCG | 45 | 0.69 | AGA | 77 | 1.47 | ||
Thr | ACU | 74 | 0.66 | AGG * | 48 | 0.88 | |
ACC* | 211 | 1.90 | Gly | GGU | 70 | 0.70 | |
ACA | 110 | 1.00 | GGC | 101 | 0.99 | ||
ACG | 51 | 0.44 | GGA | 95 | 0.94 | ||
GGG * | 137 | 1.38 |
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Zhang, Z.; Li, W.; Wang, Z.; Ma, S.; Zheng, F.; Liu, H.; Zhang, X.; Ding, Y.; Yin, Z.; Zheng, X. Codon Bias of the DDR1 Gene and Transcription Factor EHF in Multiple Species. Int. J. Mol. Sci. 2024, 25, 10696. https://doi.org/10.3390/ijms251910696
Zhang Z, Li W, Wang Z, Ma S, Zheng F, Liu H, Zhang X, Ding Y, Yin Z, Zheng X. Codon Bias of the DDR1 Gene and Transcription Factor EHF in Multiple Species. International Journal of Molecular Sciences. 2024; 25(19):10696. https://doi.org/10.3390/ijms251910696
Chicago/Turabian StyleZhang, Zhiyong, Wenxi Li, Ziyang Wang, Shuya Ma, Fangyuan Zheng, Hongyu Liu, Xiaodong Zhang, Yueyun Ding, Zongjun Yin, and Xianrui Zheng. 2024. "Codon Bias of the DDR1 Gene and Transcription Factor EHF in Multiple Species" International Journal of Molecular Sciences 25, no. 19: 10696. https://doi.org/10.3390/ijms251910696