Vertebrate evolution reflected in the evolution of nuclear ribosomal internal transcribed spacer 2

Kupriyanova, N. S.; Shibalev, D. V.; Voronov, A. S.; Netchvolodov, Kirill K.; Kurako, T. A.; Ryskov, A. P.

doi:10.1016/j.gene.2012.07.024

Cited by 4 publications

(8 citation statements)

References 20 publications

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“…The corresponding sequence for Muridae is different (CGTCCG^TGCGCCGA) [21]. These sequences are present practically in all analyzed vertebrates' ITS2s, and contain very rare substitutions [3].…”

Section: Resultsmentioning

confidence: 99%

“…Recently, we published the paper in which two different types of phylogenetic trees were constructed on the basis of the ITS2s primary structures alignment for almost 60 reptiles belonging to different orders, and some other animals [3]. All these ITS2s differ significantly by sizes, and primary structures of functionally neutral regions.…”

Section: Introductionmentioning

confidence: 99%

“…So, we used (i) GeneBee Services program [4,5] which had made it possible to carry out synchronous total automated alignment of the group of sequences of any sizes with subsequent construction of the unrooted trees based on this alignment. (ii) The other phylogenetic tree was constructed on the basis of manual alignment with the help of the Bayesian inference method (the MrBayes program) [3].…”

Section: Introductionmentioning

confidence: 99%

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The New Mode of Thought of Vertebrates’ Evolution

Ns¹,

Ap²

2014

J Phylogenetics Evol Biol

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Molecular phylogeny of the reptiles does not accept the basal split of squamates into Iguania and Scleroglossa that is in conflict with morphological evidence. The classical phylogeny of living reptiles places turtles at the base of the tree. Analyses of mitochondrial DNA and nuclear genes join crocodilians with turtles and places squamates at the base of the tree. Alignment of the reptiles' ITS2s with the ITS2 of chordates has shown a high extent of their similarity in ancient conservative regions with Cephalochordate Branchiostoma floridae, and a less extent of similarity with two Tunicata, Saussurea tunicate, and Rinodina tunicate. We have performed also an alignment of ITS2 segments between the two break points coming into play in 5.8S rRNA maturation of Branchiostoma floridae in pairs with orthologs from different vertebrates where it was possible. A similarity for most taxons fluctuates between about 50 and 70%. This molecular analysis coupled with analysis of phylogenetic trees constructed on a basis of manual alignment, allows us to hypothesize that primitive chordates being the nearest relatives of simplest vertebrates represent the real base of the vertebrate phylogenetic tree.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The New Mode of Thought of Vertebrates’ Evolution

Ns¹,

Ap²

2014

J Phylogenetics Evol Biol

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“…The “insert” helix is totally absent only in Sorex , although it is truncated in several other placentals; this helix is not present in the marsupials, and we do not yet know about Ornithorhynchus . It is absent in birds and reptiles [ 25 ].…”

Section: Resultsmentioning

confidence: 99%

“…ITS sequence and the alignments should help in the continuing effort to unravel just how RNA processing proceeds in the nucleolus, a longstanding focus of research [ 22 , 24 ]. For ITS2, the regions important to transcript processing are fairly well known and are present in all eukaryotes, including reptiles, birds and mammals (see discussion in Kupriyanova [ 25 ]). For ITS1, which has been much less studied, the discovery of a highly conserved site ( Figure 1A , red bracket) common to birds and mammals should be a useful aid to recognizing the nucleotide positions important for cofactor binding for this spacer.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Mammalian rDNA Internal Transcribed Spacers

Coleman

2013

PLoS ONE

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Nuclear rDNA Internal Transcribed Spacers, ITS1 and ITS2, are widely used for eukaryote phylogenetic studies from the ordinal level to the species level, and there is even a database for ITS2 sequences. However, ITS regions have been ignored in mammalian phylogenetic studies, and only a few rodent and ape sequences are represented in GenBank. The reasons for this dearth, and the remedies, are described here. We have recovered these sequences, mostly >1 kb in length, for 36 mammalian species. Sequence alignment and transcript folding comparisons reveal the rRNA transcript secondary structure. Mammalian ITS regions, though quite long, still fold into the recognizable secondary structure of other eukaryotes. The ITS2 in particular bears the four standard helix loops, and loops II and III have the hallmark characters universal to eukaryotes. Both sequence and insertions/deletions of transcript secondary structure helices observed here support the four superorder taxonomy of Placentalia. On the family level, major unique indels, neatly excising entire helices, will be useful when additional species are represented, resulting in significant further understanding of the details of mammalian evolutionary history. Furthermore, the identification of a highly conserved element of ITS1 common to warm-blooded vertebrates may aid in deciphering the complex mechanism of RNA transcript processing. This is the last major group of terrestrial vertebrates for which rRNA ITS secondary structure has been resolved.

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Evolution of ribosomal internal transcribed spacers in Deuterostomia

Dyomin

Volodkina

Koshel

et al. 2017

Molecular Phylogenetics and Evolution

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Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown. A possible role of GC-based gene conversion in Deuterostomia ITS evolutionary changes is hypothesized. The first example of non-LTR retrotransposon insertion into ITS sequence in Deuterostomia is described in turtle Geochelone nigra. The roles of mobile genetic element insertions in the evolution of ITS sequences in some Sauropsida taxa are discussed as well.

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Vertebrate evolution reflected in the evolution of nuclear ribosomal internal transcribed spacer 2

Cited by 4 publications

References 20 publications

The New Mode of Thought of Vertebrates’ Evolution

The New Mode of Thought of Vertebrates’ Evolution

Analysis of Mammalian rDNA Internal Transcribed Spacers

Evolution of ribosomal internal transcribed spacers in Deuterostomia

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