Table 1.
Duplication Content of Pericentromeric and Subtelomeric Compartments
| Method | Sequence | All pairwise | Interchromosomal pairwise | Intrachromosomal pairwise | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Kb | % genome | Kb | % pair | fold* | Kb | % pair | fold* | Kb | % pair | fold* | |
| Assembly-Based** | |||||||||||
| Peri2Mb | 86,000 | 3.2% | 11,548 | 11.8% | 3.7 | 7,348 | 14.5% | 4.5 | 6,341 | 10.0% | 3.1 |
| Sub500kb | 21,000 | 0.8% | 1,290 | 1.3% | 1.7 | 1,062 | 2.1% | 2.7 | 376 | 0.6% | 0.8 |
| Repeat-Based** | |||||||||||
| Perialpha | 58,561 | 2.2% | 9,999 | 10.3% | 4.7 | 7,565 | 14.9% | 6.9 | 5,106 | 8.1% | 3.7 |
| PeriαβCERγ | 76,143 | 2.8% | 16,245 | 16.7% | 5.9 | 11,689 | 23.0% | 8.1 | 8,618 | 13.6% | 4.8 |
| Periduplicons | 23,425 | 0.9% | 9,995 | 10.2% | 11.8 | 8,824 | 17.4% | 20.0 | 3,556 | 5.6% | 6.5 |
| PeriALL | 92,090 | 3.4% | 22,769 | 23.3% | 6.8 | 17,350 | 34.2% | 10.0 | 10,863 | 17.2% | 5.0 |
| Sub1kb | 23,535 | 0.9% | 7,038 | 7.2% | 8.3 | 5,179 | 10.2% | 11.7 | 3,261 | 5.2% | 5.9 |
| PeriSubALL | 106,678 | 4.0% | 25,157 | 25.8% | 6.5 | 18,763 | 37.0% | 9.3 | 12,211 | 19.3% | 4.9 |
| TOTAL ASSEMBLY | 2,692,604 | — | 97,514 | — | — | 50,752 | — | — | 63,160 | — | — |
Fold enrichment calculated by percent of total pairwise in compartment/percent genome size of compartment.
Assembly-based compartments relied solely on positions assigned within assembly. Peri2Mb included all sequence within 2Mb of the defined centromeric ends of the assembly. Sub500kb included all sequence within 500 Kb of the defined telomeric end.
Repeat-based compartments relied solely on a minimum amount of pericentromeric and/or subtelomeric repeats within a given 400 Kb region. Perialpha required a minimum of 10 Kb. PeriαβCERγ required a minimum sum of 10KB for alpha satellite, beta satellite, CER, and/or gamma satellite. Periduplicons required at least 1Kb of CAGGG repeat (Eichler 1999) or the Duplicon4 repeat (Horvath 2000). PeriALL combined all of these compartments together. Sub(1Kb) utilized TAR and TTAGGG repeats to detect subtelomeric regions. PeriSubALL combines the sequence found in PeriALL and Sub1Kb.