Systematic analysis and evolution of 5S ribosomal DNA in metazoans

Abstract

Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12 766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades.

U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization

“…We predicted the secondary structure of the five U1 snDNA consensus sequences, as this can be an indicator of its functionality or pseudogenicity (Figure 6b). Lineages 1 and 2 contained the four conserved sites described in Vierna et al (2013) (Figure 6b), and they showed the same pattern, with four helices, as the consensus secondary structure of U1 snRNA reported in Vierna et al (2013). The secondary structure of lineage 1 showed higher stability (ΔG = − 56.0 kcal mol − 1 ) than lineage 2 (ΔG = − 54.6 kcal mol − 1 ).…”

“…The analysis for sequence diversity was conducted using DNASP v5.10 (Librado and Rozas, 2009) excluding positions with gaps in the alignments. The G+C content was calculated with the MEGA v5.0 (Tamura et al, 2011) software, and the prediction of secondary structure and Gibbs free energy (ΔG) for the different sequence lineages was performed with RNAFold (Hofacker, 2003), applying a constrained folding to avoid the pairing of the four conserved motifs, according to Vierna et al (2013).…”

“…In addition, concerted evolution would hardly explain the long persistence of the truncated pseudogenic copies in both species. A mixed process of concerted evolution and birth-anddeath evolution (Nei and Rooney, 2005) has been proposed for other multigene families, such as 5S rDNAs in distinct groups (Freire et al, 2010;Pinhal et al, 2011;Merlo et al, 2012;Vierna et al, 2013), but the U1 family in grasshoppers fits better to the birth-and-death model.…”

Molecular Cytogenetics in Digenean Parasites: Linked and Unlinked Major and 5S rDNAs, B Chromosomes and Karyotype Diversification

“…Furthermore, the presence of linked and unlinked signals in species belonging to the family Bucephalidae is in accordance with results obtained from other organisms. The presence of 5S rDNA linked to other multigene families, including major rDNA, is a common situation in fungi, nematodes, and crustaceans [Drouin and de Sá, 1995;Vierna et al, 2013]. The study of the molecular organization of the linked tandem arrays in those groups demonstrated that, at least in some cases, closely related species showed differences in both tandem arrangement and gene orientation and led to suggestions that those 5S rRNA gene linkages were repeatedly established and lost during the evolution of their genomes [Drouin and de Sá, 1995;García and Kovařík, 2013].…”

Initial virome characterization of the common cnidarian lab modelNematostella vectensis

“…As expected, we have observed a significantly higher number of virus-mapping reads in the adult female library where rRNA was depleted with RiboMinus TM treatment (dataset "Schwaiger et al rRNA-depleted") when compared to the rest of the datasets. However, it needs to be taken into account that commercially available probes used for rRNA depletion are not designed for non-bilaterian animals and are less efficient in depleting the 5S small ribosomal subunit due to its high sequence variability between different animal phyla [50], which might compromise the library depth available to low-frequency viruses. Therefore, a truly unbiased search for RNA viruses would certainly gain from an rRNA depletion method custom-fitted for N. vectensis sequences.…”