Figure 3

Evolution by indel acquisition and coexistence of repeat variants support the 'library' hypothesis. (a) Candidate centromere repeat sequences of eight cichlids were analyzed for interspecies sequence similarity. The Princess cichlid Neolamprologus brichardi lacked centromere repeat similarity with its sister clade of Lake Malawi cichlids (shown in orange, and also including Nile tilapia). (b) Sequence alignment of candidate centromere repeats shows that Nile tilapia (Oreochromis niloticus) has a deletion relative to other cichlid species. (c) Candidate centromere repeat sequences of 15 grass species were analyzed for interspecies sequence similarity. We found two groups of species with centromere repeat sequences that were similar. The closely related Sorghum and Miscanthus species have similar 137 bp repeats (blue bars). The clade shown by red bars contains Oryza sativa (rice), which is relatively distant from the other species that have similar centromere tandem repeats (red bars). Although the centromere repeats of Oryza brachyantha and Brachypodium distachyon have repeat monomer length similar to the orange-highlighted group, no sequence similarity was found between them. Interestingly, no sequence similarity was found between the closely related Zea species and Sorghum species or between Oryza species and Brachypodium, Aegilops, or Hordeum. (d) Sequence alignment of candidate centromere repeats from eight grass species. Switchgrass (Panicum virgatum) is distinguished by the presence of a short insertion relative to the other species.