Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Interspecies Synteny
3.2. Reference-Assisted Chromosome Assembly
3.3. Assembly of Chromosome-Scale Fragments
3.4. Refinement of Fox-Dog Synteny at Chromosomal Breakpoints
3.5. Assembled Chromosomes
4. Discussion
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
Appendix A
Appendix B
Appendix C
References
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Fox Chromosomes | Dog Chromosome | Previously Unassigned Positions on Dog Chromosome (bp) | Previous Gap Size (Kbp) | Dog Chromosome Positions Still Unassigned (bp) | Updated Gap Size (Kbp) |
---|---|---|---|---|---|
1 & 5 | 1 | 24,600,000–25,700,000 | 1100 | 24,988,836–25,579,247 | 590.4 |
2 & 13 | 13 | 37,800,000–38,600,000 | 800 | 38,258,211–38,277,954 | 19.7 |
5 (2 fragments) | 18 | 24,400,000–26,000,000 | 1600 | 25,259,332–25,332,083 | 72.8 |
4 & 5 | 19 | 18,800,000–22,100,000 | 3300 | 19,878,341–20,333,685 | 455.3 |
Fox Fragment | Dog Chromosome | Dog Positions (Mbp) | Direction | Cat Chromosome | Cat Position (Mbp) |
---|---|---|---|---|---|
4pt | 19 * | 0–19.9 | Forward | B1 | 84.0–144.6 |
4pp | 32 | 0–38.7 | Reverse | ||
4q | 4 | 0–88.3 | Forward | D2 | 8.6–48.2 |
A1 | 172.6–227.4 | ||||
13p | 13 * | 0–38.3 | Reverse | F2 | 0.6–82.8 |
13qp | 29 | 0–41.7 | Reverse | ||
13qt | 7 | 0–80.9 | Reverse | D3 | 33.3–71.5 |
F1 | 0.4–41.3; 65.7–68.7 |
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Rando, H.M.; Farré, M.; Robson, M.P.; Won, N.B.; Johnson, J.L.; Buch, R.; Bastounes, E.R.; Xiang, X.; Feng, S.; Liu, S.; et al. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes 2018, 9, 308. https://doi.org/10.3390/genes9060308
Rando HM, Farré M, Robson MP, Won NB, Johnson JL, Buch R, Bastounes ER, Xiang X, Feng S, Liu S, et al. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes. 2018; 9(6):308. https://doi.org/10.3390/genes9060308
Chicago/Turabian StyleRando, Halie M., Marta Farré, Michael P. Robson, Naomi B. Won, Jennifer L. Johnson, Ronak Buch, Estelle R. Bastounes, Xueyan Xiang, Shaohong Feng, Shiping Liu, and et al. 2018. "Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly" Genes 9, no. 6: 308. https://doi.org/10.3390/genes9060308