Long-Term Evolution of 5S Ribosomal DNA Seems to Be Driven by Birth-and-Death Processes and Selection in Ensis Razor Shells (Mollusca: Bivalvia)

Vierna, Joaquín; González‐Tizón, Ana M.; Martı́nez-Lage, Andrés

doi:10.1007/s10528-009-9255-1

Cited by 29 publications

(38 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In conclusion, the long-term evolution of 5S rDNA in Pharidae has been mainly driven by birthand-death processes and purifying selection. Nevertheless, homogenising mechanisms, such as unequal crossing-overs (favoured by the tandem organisation of 5S rDNA repeats) and gene conversions have been probably taking part, in agreement with what was previously reported on Ensis species (Vierna et al, 2009(Vierna et al, , 2010. Interestingly, recent studies in various animal groups have come to the same conclusion (Fujiwara et Linked units of 5S rDNA and U1 snDNA J Vierna et al Figure 4 Phylogenetic relationships of the 100 nucleotides upstream the 5S ribosomal DNA transcription start site of Ensis species.…”

Section: Discussionsupporting

confidence: 90%

“…We could suppose that divergent NTSs are located at different arrays where they have evolved independently, but we have shown that some species (S. patula and E. cultellus) have divergent NTS organised in tandem. In the same way, a few clones containing a-and d-, and a-and g-NTSs were characterised in E. directus (Vierna et al, 2009), and other studies found an intermixed organisation of 5S rDNA variants in grey mullets and E. macha (Gornung et al, 2007;Fernández-Tajes and Méndez, 2009). These findings support the idea that 5S rDNA frequently moves on within genomes (see below).…”

Section: Discussionsupporting

confidence: 75%

“…Using the primers 5S-Univ-F and 5S-Univ-R (Vierna et al, 2009), we serendipitously amplified complete U1 snDNA sequences flanked by two partial 5S rDNA repeats in the species Ensis magnus (Schumacher, 1817) and P. legumen. From these sequences, different primer pairs annealing at the 5S and U1 regions of razor shells were designed using GeneFisher (Giegerich et al, 1996) (Table 2).…”

Section: Animalsmentioning

confidence: 99%

“…After performing several combinations, we divided the NTSs into seven supergroups and 17 groups. Each supergroup was named using a Roman numeral and each group was denoted by a Greek letter following Vierna et al (2009). Supergroups and groups contained sequences belonging to one or more species.…”

Section: Alignmentsmentioning

confidence: 99%

“…Therefore, recent studies have pointed out to a more complex evolutionary scenario in which birth-and-death processes generate new 5S rDNA variants that may be homogenised by unequal crossing-overs and gene conversions. For instance, in Ensis razor shells (Schumacher, 1817), the long-term evolution of 5S rDNA was found to be driven by birth-and-death processes and selection, and it was suggested that homogenising mechanisms were also taking part within each variant in each species (Vierna et al, 2009). Later on, it was proposed that the levels of intragenomic divergence-much higher within the 5S rDNA than within the major ribosomal geneswere due to the more flexible organisation of 5S rDNA, meaning that homogenisation processes were more efficient within the array(s) of major ribosomal genes, as they may occur in a smaller number.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

et al. 2011

View full text Add to dashboard Cite

The linkage between 5S ribosomal DNA and other multigene families has been detected in many eukaryote lineages, but whether it provides any selective advantage remains unclear. In this work, we report the occurrence of linked units of 5S ribosomal DNA (5S rDNA) and U1 small nuclear DNA (U1 snDNA) in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera. We obtained several clones containing partial or complete repeats of both multigene families in which both types of genes displayed the same orientation. We provide a comprehensive collection of razor shell 5S rDNA clones, both with linked and nonlinked organisation, and the first bivalve U1 snDNA sequences. We predicted the secondary structures and characterised the upstream and downstream conserved elements, including a region at À25 nucleotides from both 5S rDNA and U1 snDNA transcription start sites. The analysis of 5S rDNA showed that some nontranscribed spacers (NTSs) are more closely related to NTSs from other species (and genera) than to NTSs from the species they were retrieved from, suggesting birth-and-death evolution and ancestral polymorphism. Nucleotide conservation within the functional regions suggests the involvement of purifying selection, unequal crossing-overs and gene conversions. Taking into account this and other studies, we discuss the possible mechanisms by which both multigene families could have become linked in the Pharidae lineage. The reason why 5S rDNA is often found linked to other multigene families seems to be the result of stochastic processes within genomes in which its high copy number is determinant.

show abstract

Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 75%

Section: Animalsmentioning

confidence: 99%

Section: Alignmentsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

et al. 2011

View full text Add to dashboard Cite

show abstract

Evolutionary Dynamics of the 5S rDNA Gene Family in the Mussel Mytilus: Mixed Effects of Birth-and-Death and Concerted Evolution

et al. 2010

View full text Add to dashboard Cite

In higher eukaryotes, the gene family encoding the 5S ribosomal RNA (5S rRNA) has been used (together with histones) to showcase the archetypal example of a gene family subject to concerted evolution. However, recent studies have revealed conspicuous features challenging the predictions of this model, including heterogeneity of repeat units, the presence of functional 5S gene variants as well as the existence of 5S rDNA divergent pseudogenes lacking traces of homogenization. In the present work, we have broadened the scope in the evolutionary study of ribosomal gene families by studying the 5S rRNA family in mussels, a model organism which stands out among other animals due to the heterogeneity it displays regarding sequence and organization. To this end, 48 previously unknown 5S rDNA units (coding and spacer regions) were sequenced in five mussel species, leading to the characterization of two new types of units (referred to here as small-beta 5S rDNA and gamma-5S rDNA) coexisting in the genome with alpha and beta rDNA units. The intense genetic dynamics of this family is further supported by the first description of an association between gamma-5S rDNA units and tRNA genes. Molecular evolutionary and phylogenetic analyses revealed an extensive lack of homology among spacer sequences belonging to different rDNA types, suggesting the presence of independent evolutionary pathways leading to their differentiation. Overall, our results suggest that the long-term evolution of the 5S rRNA gene family in mussels is most likely mediated by a mixed mechanism involving the generation of genetic diversity through birth-and-death, followed by a process of local homogenization resulting from concerted evolution in order to maintain the genetic identities of the different 5S units, probably after their transposition to independent chromosomal locations.

show abstract

The 5S rDNA High Dynamism in Diplodus sargus is a Transposon-Mediated Mechanism. Comparison with Other Multigene Families and Sparidae Species

et al. 2013

View full text Add to dashboard Cite

There has been considerable discussion in recent years on the evolution of the tandemly repeated multigene families, since some organisms show a concerted model whereas others show a birth-and-death model. This controversial subject extends to several species of fish. In this study, three species of the Sparidae family (Pagrus pagrus, P. auriga and Diplodus sargus) and an interspecific hybrid (P. pagrus (♀) × P. auriga (♂)) have been studied at both molecular and cytogenetic level, taking three different multigene families (5S rDNA, 45S rDNA and U2 snDNA). Results obtained with the 5S rDNA in P. pagrus and P. auriga are characterized by a considerable degree of conservation at the two levels; however, an extraordinary variation was observed in D. sargus at the two levels, which has never been found in other fishes studied to date. As a consequence of this, the evolutionary model of the multigene families is discussed considering the results obtained and others from the bibliography. The result obtained in the hybrid allowed the recombination frequency in each multigene family to be estimated.

show abstract

Long-Term Evolution of 5S Ribosomal DNA Seems to Be Driven by Birth-and-Death Processes and Selection in Ensis Razor Shells (Mollusca: Bivalvia)

Cited by 29 publications

References 29 publications

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

Evolutionary Dynamics of the 5S rDNA Gene Family in the Mussel Mytilus: Mixed Effects of Birth-and-Death and Concerted Evolution

The 5S rDNA High Dynamism in Diplodus sargus is a Transposon-Mediated Mechanism. Comparison with Other Multigene Families and Sparidae Species

Contact Info

Product

Resources

About