Figure 3

CarSat satellite family contains functional sequence subtypes. (A) Phylogenetic analysis of reads containing a full-length CarSat1 monomer illustrate largely distinct clades of reads associated with CENP-A (CENP-A[+]; red) or not associated with CENP-A (CENP-A[−]; gray). (B) The subset of reads containing full-length monomers was further characterized by sliding window 200 bp clustering approach (see Methods) and assigned to distinct sequence subgroups, as indicated by different colors. CENP-A[−] reads are highly similar in the 3’ end of the monomer but divide into definable major subgroups in the 5’ end; CENP-A[+] reads appear to have the inverted similarity pattern. Phylogenetic analysis of the 5’ end of CarSat1 reads shows distinct clades that distinguish CENP-A[+] from CENP-A[−] sequences. A similar analysis of the 3’ end of CarSat1 reads. Overall, [+] and [−] reads could be classified into four predominant monomer types, shown as turquoise-black and blue-black for CENP-A[−], and maroon-red and maroon-yellow for CENP-A[+]. There are smaller subfamilies, one in CENP-A[−] (pink-purple) and one in CENP-A[+] (maroon-yellow) that are far less abundant and appear to clade together. (C) Paired read frequency patterns between monomer cluster types predict that the CENP-A-containing satellites (CENP-A[+]] are spatially distinct from the non-CENP-A-containing satellites (CENP-A[−]) at dog centromeres. Relative node sizes represent read depth for each of the 200 bp windows, while lines represent a minimum threshold for paired-read connectivity. Three sequence groups are identified: CENP-A[+] array, highlighted in red, and two CENP-A[−] arrays in grey. CENP-A[−] arrays can be further divided into two groups, both minimally connected to CENP-A[+] domain through transitional monomer clusters. Model of predicted genomic organization at dog centromeres, indicating the two major types (CENP-A [+] and [−]) and predicted transition monomers at bottom.