Data from: Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes

The karyotype, which is the number and shape of chromosomes, is a
fundamental characteristic of all eukaryotes. Karyotypic changes play an
important role in many aspects of evolutionary processes, including
speciation. In organisms with monocentric chromosomes, it was previously
thought that chromosome number changes were mainly caused by centric
fusions and fissions, whereas chromosome shape changes, that is changes in
arm numbers, were mainly due to pericentric inversions. However, recent
genomic and cytogenetic studies have revealed examples of alternative
cases, such as tandem fusions and centromere repositioning, found in the
karyotypic changes within and between species. Here, we employed
comparative genomic approaches to investigate whether centromere
repositioning occurred during karyotype evolution in medaka fishes. In the
medaka family (Adrianichthyidae), the three phylogenetic groups differed
substantially in their karyotypes. The Oryzias latipes species group has
larger numbers of chromosome arms than the other groups, with most
chromosomes being metacentric. The O. javanicus species group has similar
numbers of chromosomes to the O. latipes species group, but smaller arm
numbers, with most chromosomes being acrocentric. The O. celebensis
species group has fewer chromosomes than the other two groups and several
large metacentric chromosomes that were likely formed by chromosomal
fusions. By comparing the genome assemblies of O. latipes, O. javanicus,
and O. celebensis, we found that repositioning of centromere-associated
repeats might be more common than simple pericentric inversion. Our
results demonstrated that centromere repositioning may play a more
important role in karyotype evolution than previously appreciated.