Fast centromeric repeat turnover provides a glimpse into satellite DNA evolution in Nothobranchius annual killifishes

Abstract

Satellite DNA (satDNA) is rapidly evolving class of tandem repeats with some motifs being involved in centromere organization and function. Rapid co-evolution of centromeric satDNA and associated proteins has been mostly attributed to the so-called centromere drive. To identify repeats associated with centromeric regions and test for the role of meiotic drive in their evolution, we investigated satDNA across Southern and Coastal clades of African annual killifishes of the genus Nothobranchius. C-banding showed expansion of (peri)centromeric heterochromatin regions in the Southern-clade killifishes. Molecular cytogenetic and bioinformatic analyses further revealed that two previously identified satellites, Nfu-SatA and Nfu-SatB, are associated with centromeres only in one lineage of the Southern clade. Nfu-SatB was, however, detected outside centromeres also in other members of the Coastal clade, which is consistent with the "library" hypothesis of satDNA evolution. We also identified a novel satDNA, Cl-36, associated with (peri)centromeres in N. foerschi, N. guentheri and N. rubripinnis from the Coastal clade. Our findings could be explained by centromere drive shaping karyotype change and centromeric repeat turnover in Nothobranchius species with possible reversal of spindle polarity within the Southern clade.

Conserved satellite DNA motif and lack of interstitial telomeric sites in highly rearranged AfricanNothobranchiuskillifish karyotypes

“…We, however, did not reveal any demonstrably sex-linked Nfu-SatC accumulation in our sampling except for its massive accumulation on the neo-Y chromosome of N. brieni . This means that i) known multiple sex chromosomes in Nothobranchius follow different trajectories of differentiation and that ii) other species either possess homomorphic sex chromosomes at a very early stage of differentiation, or accumulate yet unstudied repeats [Voleníková et al, 2023; this study], or govern sex determination by other mechanisms (cf. [Shen and Wang, 2019; Lichilín et al, 2023; Schartl et al, 2023]).…”

“…The only protocol modification was done in N. brieni : due to observed higher sensitivity of chromatin to barium hydroxide treatment, the incubation time of this step was shortened from 3 to 2.5 min. The C-banding profiles of F. thierryi , N. guentheri and majority of other herein studied species were subject of a complementary study [Voleníková et al, 2023].…”

“…It is therefore presumed that these systems had recurrent and independent origins [Krysanov and Demidova, 2018] but a solid evidence is still missing. Nothing is further known about the genetic content and degree of differentiation of these sex chromosomes except for N. guentheri (and outgroup F. thierryi ) where banding techniques and physical mapping of certain repeats did not show considerable repeat accumulation on neo-Y [Voleníková et al, 2023].…”

“…In our complementary study [Voleníková et al, 2023], we probed Nfu-SatA, Nfu-SatB and other satDNA motifs on chromosomes of species of Southern and Coastal clade. We revealed fast turnover of (peri)centromeric satDNA repeats and possible indications of the action of meiotic drive.…”

“…We therefore investigated the patterns of distribution of Nfu-SatC satDNA and telomeric repeats in representative sampling encompassing 15 Nothobranchius species from four evolutionary lineages (Southern, Ocellatus, Coastal and Kalahari clade) and F. thierryi as an outgroup. While none of the other so far mapped repeats [Voleníková et al, 2023] indicated the existence of yet uncharacterized sex chromosomes in surveyed species, the mapping of Nfu-SatC may be particularly promising in this sense thanks to its assumed ability to accumulate preferably in regions of suppressed recombination [Štundlová et al, 2022]. In the three out of five studied species with X 1 X 2 Y sex chromosomes, we further assessed the distribution of constitutive heterochromatin, to complement already known patterns studied by Voleníková et al [2023].…”