Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in species of the family Batrachoididae

Úbeda-Manzanaro, María; Merlo, Manuel Alejandro; Palazón, José Luis; Sarasquete, Carmen; Rebordinos, Laureana

doi:10.1139/g10-048

Cited by 22 publications

(34 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The occurrence of microsatellites in the NTSs has been reported in several marine organisms (Ota et al, 2003;Alves-Costa et al, 2006), and it seems to be a common feature in the Chondrichthyes group (Rocco et al, 2005;Pasolini et al, 2006;Pinhal et al, 2009). Some authors have suggested that the presence of microsatellite sequences favours the maintenance of tandem arrays of multigene families (Liao and Weiner, 1995;Úbeda-Manzanaro et al, 2010b). Microsatellites can stabilize DNA structures, acting as "hot spots" for recombination, and therefore might function as an initiation site for the main mechanisms of concerted evolution, such as gene conversion or unequal cross-over (Liao and Weiner, 1995;Chistiakov et al, 2006).…”

Section: Resultsmentioning

confidence: 96%

“…These families fundamentally evolve in a concerted fashion, in which the sequences of the units are homogenised by various mechanisms as gene conversion or unequal crossing-over. However, some authors have reported an alternative evolution model (birth-anddeath model) of these multigene families in other species (Úbeda-Manzanaro et al, 2010b;Vierna et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Analysis of three multigene families as useful tools in species characterization of two closely-related species, Dicentrarchus labrax, Dicentrarchus punctatus and their hybrids

et al. 2010

Self Cite

View full text Add to dashboard Cite

By analyzing three multigene families, two closely related and commercially important species, Dicentrarchus labrax and Dicentrarchus punctatus, were characterized by cytogenetic and molecular methods. The interspecies hybrid Dicentrarchus labrax (♀) × Dicentrarchus punctatus (♂) was also analyzed. The multigene families studied were the 5S rDNA, 45S rDNA and the U2 snRNA. A microsatellite GTT motif was found within the non transcribed spacers (NTS) of the 5S rDNA from the two species. However, hexanucleotide duplication next to this microsatellite was observed in the D. labrax and hybrid clones, but not in D. punctatus. The U2 snRNA appeared to be linked to the U5 gene and showed two variant sequences, in both D. labrax and D. punctatus. They differed in one insertion/deletion of 7 nucleotides. The first internal transcribed spacer (ITS-1) region showed higher nucleotide variability in D. punctatus than in D. labrax. Nucleotide polymorphism within species and also nucleotide divergence between species were determined in the different gene regions. In a FISH analysis we obtained three chromosomal markers, because the 5S rDNA, 18S rDNA and U2 snRNA probes hybridized each in three different chromosome pairs. Hence none of them was co-localized. The 5S rDNA cluster and U2 snRNA were localized in acrocentric chromosome pairs, while the 18S rRNA gene probe hybridized in a subtelocentric pair. Finally, the usefulness of the results in developing tools for phylogenetic analysis and species identification are discussed in relation to other fish species.

show abstract

Section: Resultsmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Analysis of three multigene families as useful tools in species characterization of two closely-related species, Dicentrarchus labrax, Dicentrarchus punctatus and their hybrids

et al. 2010

Self Cite

View full text Add to dashboard Cite

show abstract

“…Moreover, given the high degree of homogeneity in the 5S rRNA genes usually observed within species, several authors have used them as species-specific markers [Manchado et al, 2006a]. In other studies, however, intensive dynamism has been observed in this gene, leading to phenomena such as pseudogenes [Frederiksen et al, 1997;Martins et al, 2002;Freire et al, 2010], different types of 5S rDNA [Vierna et al, 2009;Freire et al, 2010;Úbeda-Manzanaro et al, 2010a] and linkage to other multigene families [Drouin and Moniz de Sá, 1995;Manchado et al, 2006b;Freire et al, 2010]. Recent studies have shown the presence of elements such as tRNA-derived short interspersed nuclear elements (SINEs), long terminal repeats (LTRs) and microsatellites, among others, in the NTSs of fishes ( fig.…”

Section: Evolution Of the 5s Rdna: Concerted Evolution Versus Birth-amentioning

confidence: 99%

“…Therefore, an increasing number of authors have rejected the exclusivity of concerted evolution as the model which explains the 5S rDNA evolution [Rooney and Ward, 2005;Fujiwara et al, 2009;Vierna et al, 2009;Freire et al, 2010;Úbeda-Manzanaro et al, 2010a;Perina et al, 2011;Pinhal et al, 2011]. However, they also observed a homogenization process within each different type of 5S rDNA obtained, and hence they concluded that a mixed model between concerted and birth-and-death evolution is the most probable for the 5S rDNA multigene family.…”

Section: Evolution Of the 5s Rdna: Concerted Evolution Versus Birth-amentioning

confidence: 99%

High Evolutionary Dynamism in 5S rDNA of Fish: State of the Art

Rebordinos

Cross

Merlo³

2013

Cytogenet Genome Res

View full text Add to dashboard Cite

The 5S ribosomal DNA (rDNA) consists of one transcriptional unit of about 120 base pairs, which is separated from the next unit by a non-transcribed spacer (NTS). The coding sequence and the NTS together form a repeat unit which can be found in hundreds to thousands of copies tandemly repeated in the genomes. The NTS regions seem to be subject to rapid evolution. The first general model of evolution of these multigene families was referred to as divergent evolution, based on studies using hemoglobin and myoglobin as model systems. Later studies showed that nucleotide sequences of different multigene family members are more closely related within species than between species. This observation led to a new model of multigene family evolution, termed concerted evolution. Another model of evolution, named the birth-and-death model, has been found to be more suitable to explain the long-term evolution of these multigene families. According to this model, new genes originate by successive duplications, and these new genes are either maintained for a long time or are lost, or else degenerate into pseudogenes. In this review we describe different sources of variability in the 5S rDNA genes observed in several distinct fish species. This variability is mainly referred to NTSs and includes the presence of other multigene families (mainly LINEs, SINEs, non-LTR retrotransposons, and U snRNA families). Different types of microsatellites have also been found to contribute to the increase of variability in this region. Our recent results suggest that horizontal transfer contributes to the increase of diversity in the NTSs of some species. Variability in the 5S rDNA coding region affecting the stability of the structure, but without effects on the function of the 5S rRNA, is also described. Retrotransposons seem to be responsible for the high dynamism of 5S rDNA, while microsatellites acting as recombination hot spots could stabilize a wide variety of unusual DNA structures, affecting DNA replication and enhancing or decreasing promoter activity in gene expression. The relationship between the high variability found at molecular level and the low variability found at chromosomal level is also discussed.

show abstract

“…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).…”

Section: Introductionmentioning

confidence: 99%

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

et al. 2013

View full text Add to dashboard Cite

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.

show abstract

Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in species of the family Batrachoididae

Cited by 22 publications

References 37 publications

Analysis of three multigene families as useful tools in species characterization of two closely-related species, Dicentrarchus labrax, Dicentrarchus punctatus and their hybrids

Analysis of three multigene families as useful tools in species characterization of two closely-related species, Dicentrarchus labrax, Dicentrarchus punctatus and their hybrids

High Evolutionary Dynamism in 5S rDNA of Fish: State of the Art

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

Contact Info

Product

Resources

About