Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks

Abstract

The ubiquity of satellite DNA (satDNA) sequences has raised much controversy over the abundance of divergent monomer variants and the long-time nucleotide sequence stability observed for many satDNA families. In this work, we describe the satDNA BIV160, characterized in nine species of the three main bivalve clades (Protobranchia, Pteriomorphia and Heteroconchia). BIV160 monomers are similar in repeat size and nucleotide sequence to satDNAs described earlier in oysters and in the clam Donax trunculus. The broad distribution of BIV160 satDNA indicates that similar variants existed in the ancestral bivalve species that lived about 540 million years ago; this makes BIV160 the most ancient satDNA described so far. In the species examined, monomer variants are distributed in quite a complex pattern. This pattern includes (i) species characterized by a specific group of variants, (ii) species that share distinct group(s) of variants and (iii) species with both specific and shared types. The evolutionary scenario suggested by these data reconciles sequence uniformity in homogenization-maintained satDNA arrays with the genomic richness of divergent monomer variants formed by diversification of the same ancestral satDNA sequence. Diversified repeats can continue to evolve in a non-concerted manner and behave as independent amplification-contraction units in the framework of a 'library of satDNA variants' representing a permanent source of monomers that can be amplified into novel homogeneous satDNA arrays. On the whole, diversification of satDNA monomers and copy number fluctuations provide a highly dynamic genomic environment able to form and displace satDNA sequence variants rapidly in evolution.

Satellite DNA in Plants: More than Just Rubbish

“…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]. However, the overall variability profile of satellite DNA monomers in a genome is a complex feature that depends on genomic conservation and divergence of satellite DNAs, distribution and homogenization patterns among variants, putative selective constraints imposed on them, reproduction mode, and population factors [Plohl et al, 2010[Plohl et al, , 2012. Therefore, concerted evolution may be slowed down due to satellite DNA location, organization and repeat copy number [Navajas-Pérez et al, 2005b, 2009c, functional constraints [Mravinac et al, 2005], or biological factors [Luchetti et al, 2003;Robles et al, 2004;Suárez-Santiago et al, 2007].…”

Novel Repeated DNAs in the Antarctic Polyplacophoran <b><i>Nuttallochiton</i></b> <b><i>mirandus </i></b>(Thiele, 1906)

“…Firstly identified by Gaffney et al [2003] in Crassostrea virginica , Pearl is widely diffused in bivalve mollusks, such as Pectinidae and Veneridae 217 [Plohl et al, 2010;Šatović and Plohl, 2013]. However, HOR structures were not detected in Pearl.…”

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

“…Unfortunately, we could not examine the genomic and/or chromosomal organization of DBC-150 variants in D. martensis because living strains are no longer available in Drosophila stock centers. Studies of satDNA from diverse animal and plant groups suggest that its evolution might proceed by rounds of shuffling of a same pool of major ancestral repeats, with very little divergence after speciation events (e.g., Bruvo et al 2003;Cesari et al 2003;Mravinac et al 2005;Contento et al 2005;Ellingsen et al 2007;Plohl et al 2009). This mode of satDNA evolution is in contrast with the classical view of new mutations (and consequently new satDNA variants) being accumulated and homogenized gradually after speciation events (Strachan et al 1985).…”

“…SatDNA families can show a rapid rate of inter-specific evolutionary changes concerning DNA sequence, copy number and chromosome location (Ugarkovic and Plohl 2002;Adega et al 2006;Macas et al 2006;Kuhn et al 2008;Koukalova et al 2009); but a few show high levels of conservation between species separated for long evolutionary times, e.g., *100 million years among sturgeons (Robles et al 2004) or more than 500 million years among bivalves (Plohl et al 2009). In the Triticeae grasses for example, it is evident that particular satellite sequences also show characteristic and contrasting evolutionary patterns from both short-term and longer evolutionary history (Alkhimova et al 2004;Contento et al 2005).…”