Table 2. Contribution of the TCAST satellite subfamilies to four most abundant WGS clusters.
| Cluster1 | Genome proportion1 | cCENH3-ChIP enrichment2 |
TCAST subfamilies3 proportions in the cluster | ||||
|---|---|---|---|---|---|---|---|
| Subfamily 1 |
Subfamily 2 |
Subfamily 3 |
Subfamily 4 |
Subfamily 5 |
|||
| CL1 | 4.5% | 0.84 | 7.18% | 0.18% | 15.27% | 35.50% | 41.25% |
| CL2 | 4% | 0.90 | 71.32% | 22.33% | 0.14% | 5.47% | 0.67% |
| CL3 | 3.1% | 1.10 | 47.12% | 7.58% | 2.20% | 39.17% | 3.88% |
| CL4 | 2.2% | 1.12 | 0.03% | 0.58% | 82.12% | 9.06% | 8.14% |
1 Clustering of WGS Illumina reads and their estimated genome proportions were obtained by RepeatExplorer2 analysis [31].
2 ChIP enrichment for cCENH3 protein was calculated by performing ChIP-seq Mapper analysis [7]. The values represent the ratio of cCENH3-ChIP hits and Input hits.
3 Satellite DNA TCAST classification into five subfamilies is based on Pavlek et al. [28]. The subfamily consensus sequences were used in RepeatExplorer2 clustering to determine the proportions of satellite subfamilies within each cluster.