Two Different Size Classes of 5S rDNA Units Coexisting in the Same Tandem Array in the Razor Clam Ensis macha: Is This Region Suitable for Phylogeographic Studies?

Fernández‐Tajes, Juan; Méndez, Josefina

doi:10.1007/s10528-009-9276-9

Cited by 7 publications

(4 citation statements)

References 45 publications

(47 reference statements)

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“…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%

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

et al. 2011

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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.

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Section: Discussionsupporting

confidence: 75%

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

et al. 2011

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“…The length of the 5S units was about 275–300 bp for D. trunculus , about 450 bp for D. variegatus and around 500 bp for fragments obtained from the other two Donax species with minimal variation (1–12 bp) among clones (Table 2 ). Taking as reference the 5S rRNA sequences available in other bivalve species [ 9 , 17 , 25 , 26 , 44 , 55 ], the coding region was assigned to 120 bp in the four cases and the non-transcribed spacer (NTS) region to the remaining sequence (Table 2 ). BLASTn analysis corroborated the identity of the limited region and indicated that no other coding sequence was included in the 5S rDNA repeat unit.…”

Section: Resultsmentioning

confidence: 99%

“…But bivalve molluscs stand out for being one of the most extensively studied group of organisms regarding 5S rDNA and ITS region, showing high levels of gene organization as well as a vast diversity of gene arrangements. Molecular organization of ITS region and 5S rDNA has been studied in cockles [ 26 – 28 , 43 ], mussels [ 44 ], oysters [ 9 , 10 ], scallops [ 41 , 42 , 45 , 46 , 55 ], razor clams [ 25 , 99 , 100 ] and Veneroida clams [ 3 ], but it have never been studied in the wedge clams of the genus Donax .…”

Section: Introductionmentioning

confidence: 99%

Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae)

2018

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BackgroundThe whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated.ResultsThe length of the 5S repeat presented little variation among species, except D. trunculus that differed from the rest of the Donax species in 170–210 bp. The deduced coding region covered 120 bp, and showed recognizable internal control regions (ICRs) involved in the transcription. The length of non-transcribed spacer region (NTS) ranged from 157 bp to 165 bp in Donax trunculus and from 335 bp to 367 bp in the other three species. The conservation degree of transcriptional regulatory regions was analysed revealing a conserved TATA-like box in the upstream region. Regarding ITS sequences, the four Donax species showed slight size differences among clones due to the variation occurring in the ITS1 and ITS2, except Donax variegatus did not display size differences in the ITS2. The total length of the ITS sequence ranged between 814 and 1014 bp. Resulting phylogenetic trees display that the two ribosomal DNA regions provide well-resolved phylogenies where the four European Donax species form a single clade receiving high support in nodes. The topology obtained with 5S sequences was in agreement with Donax evolutionary relationships inferred from several sequences of different nature in previous studies.ConclusionsThis is not only a basic research work, where new data and new knowledge is provided about Donax species, but also have allowed the authentication of these wedge clams and offers future applications to provide other genetic resources.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0684-x) contains supplementary material, which is available to authorized users.

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“…In the case of a multigene family subjected to effective concerted evolution, all the copies within a genome are expected to be identical and represented by the Sanger sequenced reference sequence. However, intragenomic sequence variation in multigene families is common in several eukaryotic lineages 19,69,[78][79][80] , and sometimes involves size variation 81,82 . In these cases, a Sanger sequence can be considered as a consensus of all the divergent copies of the amplified gene.…”

Section: Discussionmentioning

confidence: 99%

Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros

Luca

Kooistra

Sarno

et al. 2021

Sci Rep

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Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as “noise” in electropherograms and these variants have been characterised through cloning and sequencing of subsamples of amplified products. However, this approach limits the number of detectable variants and provides no information about the abundance of each variant. In this study, we investigated concerted evolution by using environmental time-series metabarcoding data, single strain high-throughput sequencing (HTS) and a collection of Sanger reference barcode sequences. We used six species of the marine planktonic diatom genus Chaetoceros as study system. Abundance plots obtained from environmental metabarcoding and single strain HTS showed the presence of a haplotype far more abundant than all the others (the “dominant” haplotype) and identical to the reference sequences of that species obtained with Sanger sequencing. This distribution fitted best with Zipf’s law among the rank abundance/ dominance models tested. Furthermore, in each strain 99% of reads showed a similarity of 99% with the dominant haplotype, confirming the efficiency of the homogenisation mechanism of concerted evolution. We also demonstrated that minor haplotypes found in the environmental samples are not only technical artefacts, but mostly intragenomic variation generated by incomplete homogenisation. Finally, we showed that concerted evolution can be visualised inferring phylogenetic networks from environmental data. In conclusion, our study provides an important contribution to the understanding of concerted evolution and to the interpretation of DNA barcoding and metabarcoding data based on multigene family markers.

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Two Different Size Classes of 5S rDNA Units Coexisting in the Same Tandem Array in the Razor Clam Ensis macha: Is This Region Suitable for Phylogeographic Studies?

Cited by 7 publications

References 45 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)

Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae)

Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros

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