Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequencing Data Reference
2.2. CNV and CNVR Detection
2.3. CNVR Selection
2.4. Functional Annotation of CNVRs
3. Results
3.1. CNV and CNVR Detection
3.2. PCA and Evolutionary Tree Analysis
3.3. Differential CNVRs Measurement
3.4. Functional Analysis
3.5. QTLs Overlapping with Identified CNVRs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Chr | Length | All | AQ | SS | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Total | DUP | DEL | Total | DUP | DEL | Total | DUP | DEL | ||
1 | 274.33 | 1175 | 641 | 446 | 1157 | 639 | 431 | 457 | 117 | 287 |
2 | 151.94 | 1031 | 557 | 369 | 1016 | 556 | 357 | 445 | 147 | 225 |
3 | 132.85 | 607 | 316 | 243 | 601 | 315 | 238 | 227 | 47 | 153 |
4 | 130.91 | 574 | 276 | 249 | 566 | 276 | 242 | 261 | 78 | 154 |
5 | 104.53 | 587 | 292 | 235 | 581 | 292 | 230 | 258 | 70 | 155 |
6 | 170.84 | 865 | 475 | 308 | 856 | 473 | 304 | 328 | 93 | 195 |
7 | 121.84 | 561 | 274 | 208 | 548 | 272 | 199 | 257 | 66 | 136 |
8 | 138.97 | 569 | 226 | 302 | 558 | 222 | 296 | 251 | 47 | 186 |
9 | 139.51 | 652 | 320 | 252 | 642 | 320 | 244 | 295 | 81 | 175 |
10 | 69.36 | 290 | 109 | 176 | 286 | 108 | 174 | 153 | 31 | 118 |
11 | 79.17 | 283 | 74 | 198 | 278 | 74 | 193 | 144 | 18 | 120 |
12 | 61.6 | 394 | 210 | 140 | 387 | 209 | 136 | 158 | 42 | 95 |
13 | 208.34 | 874 | 445 | 361 | 861 | 445 | 348 | 363 | 102 | 226 |
14 | 141.76 | 672 | 351 | 259 | 668 | 350 | 257 | 276 | 84 | 154 |
15 | 140.41 | 504 | 262 | 217 | 492 | 261 | 208 | 206 | 56 | 132 |
16 | 79.94 | 287 | 81 | 204 | 283 | 81 | 200 | 157 | 22 | 133 |
17 | 63.49 | 328 | 132 | 167 | 324 | 132 | 163 | 165 | 38 | 108 |
18 | 55.98 | 176 | 70 | 100 | 175 | 70 | 99 | 78 | 8 | 65 |
Total | 2265.77 | 10,429 | 5111 | 4434 | 10,279 | 5095 | 4319 | 4479 | 1147 | 2817 |
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Fan, S.; Kong, C.; Chen, Y.; Zheng, X.; Zhou, R.; Zhang, X.; Wu, X.; Zhang, W.; Ding, Y.; Yin, Z. Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars. Genes 2023, 14, 472. https://doi.org/10.3390/genes14020472
Fan S, Kong C, Chen Y, Zheng X, Zhou R, Zhang X, Wu X, Zhang W, Ding Y, Yin Z. Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars. Genes. 2023; 14(2):472. https://doi.org/10.3390/genes14020472
Chicago/Turabian StyleFan, Shuhao, Chengcheng Kong, Yige Chen, Xianrui Zheng, Ren Zhou, Xiaodong Zhang, Xudong Wu, Wei Zhang, Yueyun Ding, and Zongjun Yin. 2023. "Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars" Genes 14, no. 2: 472. https://doi.org/10.3390/genes14020472
APA StyleFan, S., Kong, C., Chen, Y., Zheng, X., Zhou, R., Zhang, X., Wu, X., Zhang, W., Ding, Y., & Yin, Z. (2023). Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars. Genes, 14(2), 472. https://doi.org/10.3390/genes14020472