Concerted evolution of satellite DNA in Sarcocapnos: a matter of time

Abstract

SarkOne is a genus-specific satellite-DNA family, isolated from the genomes of the species of the genus Sarcocapnos. This satellite DNA is composed of repeats with a consensus length of 855 bp and a mean G+C content of 52.5%. We have sequenced a total of 189 SarkOne monomeric repeats belonging to a total of seven species of the genus Sarcocapnos. The comparative analysis of these sequences both at the intraspecific and the interspecific levels have revealed divergence patterns between species are proportional to between-species divergence according to the phylogeny of the genus. Our study demonstrates that the molecular drive leading to the concerted-evolution pattern of this satellite DNA is a time-dependent process by which new mutations are spreading through genomes and populations at a gradual pace. However, time is a limiting factor in the observation of concerted evolution in some pairwise comparisons. Thus, pairwise comparisons of species sharing a recent common ancestor did not reveal nucleotide sites in transitional stages higher than stage III according to the Strachan's model. By contrast, there was a gradation in the percentage of upper transition stages (IV, V, VI) the more phylogenetically distant the species were. In addition, closely related species shared a high number of polymorphic sites, but these types of sites were not common when comparing more distant species. All these data are discussed in the light of current life-cycle models of satellite-DNA evolution.

Satellite DNA in Plants: More than Just Rubbish

“…Heterochromatin is located mainly in pericentromeric and subtelomeric areas of the chromosomes but also at times may be found at interstitial locations in some of them [López-Flores and Garrido-Ramos, 2012;Plohl et al, 2012]. Satellite DNAs form families that differ in location, nucleotide sequence, sequence complexity, repeat unit length, and abundance.…”

“…Adjacent to telomeres, there are commonly subtelomeric or telomere-associated sequences, which are tandem repeats with a variety of lengths and degrees of repetitiveness [Henderson, 1995;Louis and Vershinin, 2005;López-Flores and Garrido-Ramos, 2012]. Monomer length is not conserved in subtelomeric satellite DNAs, ranging from 38 bp of the VicTR-B repeats of V. sativa to the 2,226 bp of the CL18 repetitive family of banana [Čížková et al, 2013].…”

“…Homogenizing mechanisms would spread new sequence variants appearing in individual repeat units of a family of sequences, and changes would fix in a population of randomly mating individuals by sexual reproduction according to a time-dependent 2-step process called molecular drive, which leads to concerted evolution. This process results in rapid divergence of satellite sequences in reproductively isolated groups of organisms [Dover, 1986;Pérez-Gutiérrez et al, 2012;Plohl et al, 2012]. Pérez-Gutiérrez et al [2012] demonstrated that in the absence of selective and biological constraints, the rate of concerted evolution of a family of satellite DNA sequences should depend basically on the divergence time between species.…”

“…This process results in rapid divergence of satellite sequences in reproductively isolated groups of organisms [Dover, 1986;Pérez-Gutiérrez et al, 2012;Plohl et al, 2012]. Pérez-Gutiérrez et al [2012] demonstrated that in the absence of selective and biological constraints, the rate of concerted evolution of a family of satellite DNA sequences should depend basically on the divergence time between species. In this case, the expected stages of transition during the spread of a sequence variant towards its fixation can be defined [Strachan et al, 1985;NavajasPérez et al, 2007].…”

“…The class I elements or retrotransposons are the most abundant with a predominant presence of LTR-retrotransposons [López-Flores and Garrido-Ramos, 2012;Lee and Kim, 2014]. Nevertheless, not only transposable elements increase the size of plant genomes, but satellite DNAs also contribute greatly to plant genomes.…”