Molecular organization and phylogenetic analysis of 5S rDNA in crustaceans of the genus Pollicipesreveal birth-and-death evolution and strong purifying selection

Abstract

BackgroundThe 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units that consist of a transcribing region (5S) and a variable nontranscribed spacer (NTS), in higher eukaryotes. Until recently the 5S rDNA was thought to be subject to concerted evolution, however, in several taxa, sequence divergence levels between the 5S and the NTS were found higher than expected under this model. So, many studies have shown that birth-and-death processes and selection can drive the evolution of 5S rDNA. In analyses of 5S rDNA evolution is found several 5S rDNA types in the genome, with low levels of nucleotide variation in the 5S and a spacer region highly divergent. Molecular organization and nucleotide sequence of the 5S ribosomal DNA multigene family (5S rDNA) were investigated in three Pollicipes species in an evolutionary context.ResultsThe nucleotide sequence variation revealed that several 5S rDNA variants occur in Pollicipes genomes. They are clustered in up to seven different types based on differences in their nontranscribed spacers (NTS). Five different units of 5S rDNA were characterized in P. pollicipes and two different units in P. elegans and P. polymerus. Analysis of these sequences showed that identical types were shared among species and that two pseudogenes were present. We predicted the secondary structure and characterized the upstream and downstream conserved elements. Phylogenetic analysis showed an among-species clustering pattern of 5S rDNA types.ConclusionsThese results suggest that the evolution of Pollicipes 5S rDNA is driven by birth-and-death processes with strong purifying selection.

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

“…These findings agree with the widespread idea that 5S rDNA repeats are transposed from one genome location to another (Rooney and Ward, 2005;Datson and Murray, 2006). Intermixed organization of NTS sequences was also found by Gornung et al (2007); Perina et al (2011);Vierna et al (2011) in molluscs, crustacean and fishes species.…”

“…Similarly, other species showed NTSs of different sizes in the same contig. This agrees with other species, as previously reported (for example, in molluscs , arthropods (Perina et al, 2011) and chordates (Gornung et al, 2007)). In this work, we add to this list more chordate, annelid, arthropod, cephalochordate, placozoan, cnidarian and molluscan species.…”

“…However, many reports have been recently published in which the concerted evolution model did not explain the intragenomic divergence found in some organisms, mainly (but not exclusively) within the non-transcribed spacer (NTS) region (Rooney and Ward, 2005;Fujiwara et al, 2009;Vierna et al, 2009Vierna et al, , 2011Freire et al, 2010;Ú beda-Manzanaro et al, 2010;Perina et al, 2011;Vizoso et al, 2011). Other evolutionary models (birth-and-death evolution; mixed process of concerted and birth-and-death evolution (Nei and Rooney, 2005)) have been proposed to drive the evolution of 5S rDNA (Rooney and Ward, 2005;Fujiwara et al, 2009;Vierna et al, 2009Vierna et al, , 2011Freire et al, 2010;Ú beda-Manzanaro et al, 2010;Perina et al, 2011;Vizoso et al, 2011).…”

“…Reports on the evolution of 5S rDNA in various animal and fungi groups have been published during the last few years, and all (Martins and Wasko, 2004;Vierna et al, 2009Vierna et al, , 2011Freire et al, 2010;Ú bedaManzanaro et al, 2010;Perina et al, 2011;Vizoso et al, 2011) except one (Rooney and Ward, 2005) have relied on data obtained from PCR-cloning-sequencing techniques. Even though these procedures are appropriate when working with non-model organisms, they may not give a complete picture of the features and diversity of this multigene family.…”

“…The evolution of 5S ribosomal DNA (5S rDNA) has been studied in some groups of organisms, mainly within genera or within families (for example, Martins and Wasko (2004); Rooney and Ward (2005); Vierna et al (2009Vierna et al ( , 2011; Freire et al (2010); Perina et al (2011); Vizoso et al (2011)). Nevertheless, several intriguing features, such as high conservation along evolution in contrast to high intragenomic divergence, a plastic genomic organization and linkage to other genes, make this multigene family an interesting issue in evolutionary genetics that deserves a large-scale analysis.…”