The non-regular orbit: three satellite DNAs in Drosophila martensis (buzzatii complex, repleta group) followed three different evolutionary pathways

Abstract

The genome of species from the buzzatii cluster (buzzatii complex, repleta group) is hosted by a number of satellite DNAs (satDNAs) showing contrasting structural characteristics, genomic organization and evolution, such as pBuM-alpha (~190 bp repeats), pBuM-alpha/beta (~370 bp repeats) and the DBC-150 (~150 bp repeats). In the present study, we aimed to investigate the evolution of these three satDNAs by looking for homologous sequences in the genome of the closest outgroup species: Drosophila martensis (buzzatii complex). After PCR, we isolated and sequenced 9 alpha, 8 alpha/beta and 11 DBC-150 sequences from this species. The results were compared to all pBuM and DBC-150 sequences available in literature. After D. martensis split from the buzzatii cluster some 6 Mya, the three satDNAs evolved differently in the genome of D. martensis by: (1) maintenance of a collection of major types of ancestral repeats in the genome (alpha); (2) fixation for a single major type of ancestral repeats (alpha/beta) or (3) fixation for new divergent species-specific repeat types (DBC-150). Curiously, D. seriema and D. martensis, although belonging to different and allopatric clusters, became independently fixed for the same major type of alpha/beta ancestral repeats, illustrating a rare case of parallelism in satDNA evolution. The contrasting pictures illustrate the diversity of evolutionary pathways a satDNA can follow, defining a "non-regular orbit" with outcomes difficult to predict.

Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae)

“…Newly arising variants of a satellite DNA can rapidly replace previous copies due to concerted evolution, which results in intraspecific sequence homogenization (Plohl, 2010). The efficiency of homogenization is satellite DNA specific and depends on initial copy number, genomic location, repeat length and mode of reproduction (Dover, 1982; Stephan and Cho, 1994; Plohl et al ., 2008; Navajas-Pérez et al ., 2009; Kuhn et al ., 2010). All these changes may parallel, or even precede, species diversification (Elder and Turner, 1995; Koukalova et al ., 2010; Raskina et al ., 2011; Belyayev and Raskina, 2013).…”

The nature and organization of satellite DNAs in Petunia hybrida, related, and ancestral genomes

“…The detailed analysis here adds to information about modes of satellite amplification, and we suggest that the mechanisms-and hence consequences for monomer homogeneity and nature of tandem repeat arrays-may differ between satellite origins, their sequence, their evolutionary ages, chromosomal location, and species. Replication slippage and uneven crossing-over can change copy number, as can amplification within retroelements, while sequence homogenization can lead to divergence of sequence motifs in different species The deviation of sequence copies can provide evidence for the nature of amplification of particular variants from a common ancestor, the library hypothesis (Mestrovićet al, 1998;Kuhn et al, 2010), although there is little evidence in the Petunia species for amplification of such variants, nor of different ages of satellite DNA monomers as found in Bovidae (Escudeiro et al, 2019). Similar to oedipodine grasshoppers (Camacho et al, 2022), the Petunia satellites, however, show some point mutations combined with amplification or loss in the recently evolved hybrid species.…”

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

“…Satellite DNAs (satDNAs) are a common component, accounting for an important part of the genome in most animal and plant genomes (reviewed by [3][4][5]. In general, a genome has a varied number of satDNA families (the satellitome) [6] with varying nucleotide sequences and genomic abundance [7][8][9][10][11][12][13].…”