A Satellite-Free Centromere in Equus przewalskii Chromosome 10
Abstract
:1. Introduction
2. Results
2.1. Characterization of a Fibroblasts Cell Line from Equus przewalskii
2.2. Chromosomal Distribution of Satellite DNA Families in Equus przewalskii
2.3. ChIP-Seq Analysis of Centromeric Domains
3. Discussion
4. Materials and Methods
4.1. Cell Lines
4.2. Metaphase Spread Preparation and FISH
4.3. ChIP-Seq
4.4. Bioinformatic Analysis of ChIP-Seq Data
4.5. SNV Analysis
4.6. Mitogenomic Analysis
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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EPR Chromosome | 37cen | 2PI | Genomic DNA | |||
---|---|---|---|---|---|---|
Number of Labeled Chromosomes (%) | Number of Analyzed Chromosomes | Number of Labeled Chromosomes (%) | Number of Analyzed Chromosomes | Number of Labeled Chromosomes (%) | Number of Analyzed Chromosomes | |
1cen | 60 (100) | 60 | 35 (85.4) | 41 | 10 (100) | 10 |
2cen | 3 (5.1) | 59 | 37 (100) | 37 | 10 (100) | 10 |
3cen | 53 (100) | 53 | 34 (100) | 34 | 10 (100) | 10 |
4cen | 57 (100) | 57 | 27 (71.1) | 38 | 10 (100) | 10 |
5cen | 51 (100) | 51 | 36 (100) | 36 | 10 (100) | 10 |
6cen | 12 (20.3) | 59 | 36 (100) | 36 | 1 (10) | 10 |
7cen | 52 (100) | 52 | 38 (100) | 38 | 10 (100) | 10 |
8cen | 56 (100) | 56 | 38 (100) | 38 | 10 (100) | 10 |
9cen | 49 (100) | 49 | 39 (100) | 39 | 9 (100) | 9 |
10cen | 0 (0) | 58 | 0 (0) | 34 | 0 (0) | 10 |
11cen | 48 (100) | 48 | 11 (40.7) | 27 | 13 (100) | 13 |
12cen | 48 (100) | 48 | 29 (100) | 29 | 9 (100) | 9 |
13cen | 47 (100) | 47 | 34 (100) | 34 | 9 (100) | 9 |
14cen | 41 (100) | 41 | 33 (100) | 33 | 8 (100) | 8 |
15cen | 45 (100) | 45 | 32 (100) | 32 | 9 (100) | 9 |
16cen | 33 (100) | 33 | 28 (100) | 28 | 8 (100) | 8 |
17cen | 30 (100) | 30 | 27 (100) | 27 | 8 (100) | 8 |
18cen | 17 (44.7) | 38 | 28 (100) | 28 | 8 (100) | 8 |
19cen | 45 (100) | 45 | 25 (100) | 25 | 10 (100) | 10 |
20cen | 24 (100) | 24 | 23 (100) | 23 | 8 (100) | 8 |
21cen | 24 (100) | 24 | 25 (100) | 25 | 8 (100) | 8 |
22cen | 20 (100) | 20 | 24 (100) | 24 | 8 (100) | 8 |
23cen | 20 (100) | 20 | 24 (100) | 24 | 8 (100) | 8 |
24cen | 20 (100) | 20 | 24 (100) | 24 | 8 (100) | 8 |
25cen | 20 (100) | 20 | 24 (100) | 24 | 8 (100) | 8 |
26cen | 18 (100) | 18 | 24 (100) | 24 | 8 (100) | 8 |
27cen | 18 (100) | 18 | 24 (100) | 24 | 8 (100) | 8 |
28cen | 18 (100) | 18 | 23 (100) | 23 | 7 (100) | 7 |
29cen | 4 (10.5) | 38 | 8 (36.4) | 22 | 11 (100) | 11 |
30cen | 18 (100) | 18 | 24 (100) | 24 | 8 (100) | 8 |
31cen | 17 (100) | 17 | 24 (100) | 24 | 8 (100) | 8 |
32cen | 17 (100) | 17 | 24 (100) | 24 | 8 (100) | 8 |
Xcen | 29 (100) | 29 | 15 (71.4) | 21 | 5 (100) | 5 |
Xqinter | 0 (0) | 29 | 0 (0) | 21 | 5 (100) | 5 |
Ycen | 17 (100) | 17 | 3 (25) | 12 | 6 (100) | 6 |
Position (chr11, EquCab2.0 Reference) | Reference Allele | Alternative Allele | Number of Reads Reference Allele | Number of Reads Alternative Allele | Total Number of Reads | Reference Allele Frequency | Alternative Allele Frequency |
---|---|---|---|---|---|---|---|
27648739 | T | C | 8 | 15 | 23 | 0.3 | 0.7 |
27667251 | T | C | 20 | 15 | 35 | 0.6 | 0.4 |
27671967 | C | G | 14 | 18 | 32 | 0.4 | 0.6 |
27680741 | G | C | 7 | 9 | 16 | 0.4 | 0.6 |
27680744 | C | T | 8 | 8 | 16 | 0.5 | 0.5 |
27680746 | C | T | 9 | 9 | 18 | 0.5 | 0.5 |
27712271 | C | T | 11 | 19 | 30 | 0.4 | 0.6 |
27728102 | T | A | 8 | 16 | 24 | 0.3 | 0.7 |
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Piras, F.M.; Cappelletti, E.; Abdelgadir, W.A.; Salamon, G.; Vignati, S.; Santagostino, M.; Sola, L.; Nergadze, S.G.; Giulotto, E. A Satellite-Free Centromere in Equus przewalskii Chromosome 10. Int. J. Mol. Sci. 2023, 24, 4134. https://doi.org/10.3390/ijms24044134
Piras FM, Cappelletti E, Abdelgadir WA, Salamon G, Vignati S, Santagostino M, Sola L, Nergadze SG, Giulotto E. A Satellite-Free Centromere in Equus przewalskii Chromosome 10. International Journal of Molecular Sciences. 2023; 24(4):4134. https://doi.org/10.3390/ijms24044134
Chicago/Turabian StylePiras, Francesca M., Eleonora Cappelletti, Wasma A. Abdelgadir, Giulio Salamon, Simone Vignati, Marco Santagostino, Lorenzo Sola, Solomon G. Nergadze, and Elena Giulotto. 2023. "A Satellite-Free Centromere in Equus przewalskii Chromosome 10" International Journal of Molecular Sciences 24, no. 4: 4134. https://doi.org/10.3390/ijms24044134