Table 1. Interior CTs predicted using hierarchical clustering of effective gene density matrix.
| Species (Abbreviation) | Reference corroborating CT position | Predicted interior CT(s) | Dominant synteny with HSA chromosome |
|---|---|---|---|
| Pan troglodytes (PTR) | ref. 50 | PTR17, PTR19 | HSA17§, HSA19§ ref. 50 |
| Mus musculus (MMU) | ref. 51 | MMU7, MMU11 | HSA19§, HSA17§ Mouse Genome Sequencing Consortium68 |
| Sus scrofa (SSC) | ref. 52$ | SSC12$ | HSA17§ ref. 70 |
| Gallus gallus (GGA) | ref. 53¶ ref. 56 | GGA30¶, GGA32¶, GGA27¶, GGA28¶ | NA¶¶ International Chicken Genome Consortium59 HSA17§, HSA19§ |
CT(s) with primary hierarchy in effective gene density are located in the nuclear interior and influence CT neighbourhoods forming a non-random CT constellation. HSA, PTR, MMU, SSC and GGA are standard identifiers used to represent the human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus), pig (Sus scrofa), and chicken (Gallus gallus) chromosomes respectively. The interior CTs: HSA19 and HSA17 have the highest and second highest hierarchy in effective gene density matrix (Fig. 1) and synteny relations with diverse species are with respect to these CTs§. The spatial position of SSC12 has not been reported though it has been reported that porcine chromosomes: SSC2, SSC3, SSC4, SSC5, SSC6 and SSC7 are interior CTs52, which we have reported to hierarchically cluster with SSC12$ (Fig. 5c). Habermann et al.53 have shown that microchromosomes (such as GGA30, GGA32, GGA27, GGA28) are at the nuclear interior and macrochromosomes are at the periphery in Gallus gallus fibroblast cells¶. The predicted CT with primary hierarchy (GGA30) currently has ten annotated coding and noncoding genes and synteny information is not available. However, as microchromosomes GGA27 and GGA28 are in same hierarchical cluster as GGA30 and GGA32 and because their synteny information was previously known59, therefore we have reported using the same¶¶.