Additional file 2 of Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

Additional file 2: Tables S1-S10. Table S1—Within-group pairwise similarity of satDNAs. Table S2—Summary of the results obtained from the read clustering analysis with multiple species analyzed simultaneously. Table S3—We have compared hundreds of repetitive units from each satellite and compared the mean divergence that exists between them (inter-repeat divergence) with the mean divergence that exists between the subunits that compose each repetitive unit (intra-repeat divergence). For the case of the sequences of the Group 1 constituted by repetitive units of 41 bp, we have considered each of its subunits (alpha and beta) of 21 and 20 bp, respectively, obtaining that the intra-repeat divergence was always greater than the inter-repeat divergence. Table S4—As for the Group 1 satellites, we have analyzed the 60 bp long satellites of Group 2. Here we verified that their repetitive units were made up of subunits of 20 bp each, which we have named alpha, beta, and gamma. The table shows the analysis of intra-repeats versus inter-repeats divergences, and it can also be seen here that the former is greater than the latter. Table S5—While Groups 1 and 2 were more homogeneous, Group 3 sequences are characterized as heterogeneous ones, as their sequences were derived from a repetition of two subunits of 29 bp and 11 bp. This table demonstrates that the divergence between alpha (29 bp) and beta (11 bp) subrepeats is greater than the divergence between complete repeats of these satellites. Thus, looking at their structure, we can affirm that the Group 3 satellites are not formed by repetitive units of 20 bp. In any case, it is possible that the ancestral satellite that gave rise to the group 3 satellites had a length of 29 bp and that later rearrangements, possibly mediated by unequal crossing over (see, for example, Navajas-Pérez et al. 2005 for RAYSI satDNA), generated a 40 bp repetitive unit formed by one unit plus one third of another, being now the unit of homogenization of these satellites. Table S6—Summary of the BLAST searches against Alligator sinensis genome. Table S7—Main features of the analyzed genomic libraries. Table S8—Results of RepeatMasking against the Repbase database. Table S9—Read mapping against single-copy genes for normalization of satDNA abundance. Table S10—log10 of normalized abundances of each satDNA, considering RepeatMasker counts from 0 to 20% of divergence.