Fast satellite DNA evolution in Nothobranchius annual killifishes

Abstract

Satellite DNA (satDNA) is a rapidly evolving class of tandem repeats, with some monomers being involved in centromere organization and function. To identify repeats associated with (peri)centromeric regions, we investigated satDNA across Southern and Coastal clades of African annual killifishes of the genus Nothobranchius. Molecular cytogenetic and bioinformatic analyses revealed that two previously identified satellites, designated here as NkadSat01-77 and NfurSat01-348, are associated with (peri)centromeres only in one lineage of the Southern clade. NfurSat01-348 was, however, additionally detected outside centromeres in three members of the Coastal clade. We also identified a novel satDNA, NrubSat01-48, associated with (peri)centromeres in N. foerschi, N. guentheri, and N. rubripinnis. Our findings revealed fast turnover of satDNA associated with (peri)centromeres and different trends in their evolution in two clades of the genus Nothobranchius.

Keywords: Centromere drive; Constitutive heterochromatin; RepeatExplorer; Repetitive sequences; satDNA.

Fig. 1

Selected representative mitotic metaphases of studied Nothobranchius species after C-banding and FISH with satDNA probes. A full set of results from all studied species is provided in Supplementary Figs. 1, 5, 6, 7, and 8. (A–C) C-banding. Arrows indicate examples of huge pericentromeric heterochromatin blocks in expected fusion sites on large metacentric chromosomes of N. krysanovi (A). Note: differences between constitutive heterochromatin amount and distribution between Southern-clade (A) and Coastal-clade species N. foerschi (B) and N. rubripinnis (C). (D–T) FISH with satDNA repeats (red signals) in species with positive results. Sex of the studied individuals is indicated and eventually underlined where both sexes (if studied) presented the same distribution pattern (i.e., except for N. orthonotus; D, E). In the case of NkadSat01-77 repeat in N. orthonotus (D, E) and N. kuhntae (F), arrows point to chromosomes lacking the (peri)centromeric signals. Polymorphic patterns regarding this feature are framed. Neo-Y chromosome in N. guentheri male (N) can be identified based on distinctive morphology. For better clarity, arrowheads point on signals after FISH with NgueSat01-63 (P) and NfurSat02-39 (Q, R) probes. Species acronyms are summarized in Table 1. Chromosomes were counterstained with DAPI (blue). Scale bar = 10 µm

Fig. 2

Phylogenetic relationships and patterns of selected satDNA monomers in inspected Nothobranchius species. Simplified phylogenetic tree is based on van der Merwe et al. (2021). The phylogenetic positions of N. kadleci and N. kuhntae were inferred from Dorn et al. (2014). Colored circles represent positive FISH signals in different chromosomal locations. The size of the circles reflects the abundance in the genome for respective satDNA. Abundance in the genome (%) is set as ranges. Lack of positive signals after FISH is demarcated by empty circles. Black crosses indicate that a given satDNA was not physically mapped in the particular species. Note that abundance in the genome might not perfectly correlate with chromosomal distribution revealed by physical mapping because some portion of respective tandem repeats may be present in low-copy clusters undetectable by FISH. Species which were subject to RepeatExplorer2 analysis are shown in bold. Numbers in grey circles in the phylogenetic tree denote distinct Nothobranchius clades: (1) Southern; (2) Ocellatus; (3) Coastal