Evolution of ancient satellite DNAs in sturgeon genomes

Robles, Francisca; Herrán, Roberto de la; Ludwig, Arne; Rejón, Carmelo Ruiz; Rejón, M. Ruíz; Garrido-Ramos, Manuel A.

doi:10.1016/j.gene.2004.06.001

Cited by 105 publications

(115 citation statements)

References 27 publications

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“…In this case, the BIV160 satDNA family may be about 540 million years old, thus representing the oldest described satDNA. Among ancient satDNAs, the PstI family in sturgeons is thought to be 4100 million years old (Robles et al, 2004), whereas the identification of sequences related to the primate-specific a-satDNAs in the transcriptome of zebrafish moved the age of this sequence back to the origin of bonefishes, about 400 million years ago (Li and Kirby, 2003). The observed distribution of the three Mytilus satellites shared with species from the subclass Pteriomorphia indicates that an expansion should have occurred about 150 million years ago, at the onset of the genus (Martinez-Lage et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

“…Consequently, variability profiles of these monomers do not allow linking variants to the species of origin. Although it is difficult to understand the real causes and consequences of this phenomenon, at present there are two plausible explanations: (a) once established, a mutational profile is favoured because of constraints imposed on the sequence in the heterochromatic environment (Ohta and Dover, 1984;Dover, 1987;Mravinac et al, 2002Mravinac et al, , 2005Meštrović et al, 2006a;Plohl et al, 2008) and (b) accumulation and spread of new mutations in a repetitive family is slow owing to biological aspects of DNA sequence evolution in these organisms (Luchetti et al, , 2006Robles et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2009

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

et al. 2009

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“…The rapid changes in copy number and nucleotide sequence of satDNAs may result in the evolution of genus and species-specific repeats (Pons and Gillepsie, 2004;Mravinac and Plohl, 2010), as these repetitive units are usually highly homogenized within a species due to concerted evolution. Although satDNA has been occasionally considered as phylogenetically informative of different under-species hierarchical ranks, such as ecotype-specific variants (Hall et al, 2003), populations (Feliciello et al, 2011) or phylogeographic clades (Robles et al, 2004), detailed studies on sequence variation at the intraspecific level are still very scarce.…”

Section: Introductionmentioning

confidence: 99%

Sequence variability of the MspI satellite DNA family of the pinewood nematode Bursaphelenchus xylophilus at different geographic scales

Vieira

Castagnone

Mallez

et al. 2014

Molecular Phylogenetics and Evolution

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a b s t r a c tTandemly repeated sequences known as satellite DNA (satDNA) generally exhibit complex evolutionary patterns of concerted evolution in which mutations are homogenized and fixed in a stochastic process of molecular drive. Here, the nucleotidic variability of the MspI satDNA family of the pinewood nematode Bursaphelenchus xylophilus is analyzed in order to understand the evolutionary dynamics of satDNA at the intraspecific level. A total of 425 MspI monomer units, either PCR-amplified from isolates of local (Peninsula of Setúbal, Portugal) or worldwide origin, or retrieved from the B. xylophilus genome sequence, were characterized and compared. Whatever their origin, sliding window analysis of sequence variability patterns among monomers revealed low, moderate and highly variant domains, indicating that variable levels of evolutionary constraint may act upon the entire monomers. The phylogenetic inference based on the different sets of MspI satDNA family for this species shows a broad polymorphism of the individual monomers, which were distributed into four main clusters. However, such clustering appeared independent from the geographic origin of the nematodes, and could not discriminate isolates or groups of geographically close isolates. Rather, the formation of different phylogenetic groups within this satDNA family suggests an a priori embodying of a set of diverging repeats from a common ancestor satDNA library, which have been differently amplified along the evolutionary pathway of this species. The present work improves knowledge on the evolutionary dynamics of satDNA at the intraspecific level, and provides new information on satDNA sequence variability among natural populations sampled at a local geographic scale.

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“…The phylogenetic relationships among extant acipenseriform groups has been the subject of numerous, detailed works (e.g., Grande and Bemis, 1991;Birstein and DeSalle, 1998;Ludwig et al, 2001;Robles et al, 2004). With a robust hypothesis on the relationships among these groups being available, it is of much interest to date the origin of these groups since this is crucial, in fact, for clarifying acipenseriform evolution and historical biogeography.…”

Section: Introductionmentioning

confidence: 99%

Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes)

Peng

Ludwig

Wang

et al. 2007

Molecular Phylogenetics and Evolution

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Evolution of ancient satellite DNAs in sturgeon genomes

Cited by 105 publications

References 27 publications

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

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

Sequence variability of the MspI satellite DNA family of the pinewood nematode Bursaphelenchus xylophilus at different geographic scales

Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes)

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