iBet uBet web content aggregator. Adding the entire web to your favor.
iBet uBet web content aggregator. Adding the entire web to your favor.



Link to original content: http://pubmed.ncbi.nlm.nih.gov/36983793/
Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome of Zootoca vivipara (Squamata, Lacertidae) - PubMed Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Feb 24;13(3):637.
doi: 10.3390/life13030637.

Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome of Zootoca vivipara (Squamata, Lacertidae)

Marcello Mezzasalma  1 , Teresa Capriglione  2 , Larissa Kupriyanova  3 , Gaetano Odierna  2 , Maria Michela Pallotta  4 , Agnese Petraccioli  2 , Orfeo Picariello  2 , Fabio M Guarino  2
Affiliations

Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome of Zootoca vivipara (Squamata, Lacertidae)

Marcello Mezzasalma et al. Life (Basel). .

Abstract

Transposable elements (TEs) constitute a considerable fraction of eukaryote genomes representing a major source of genetic variability. We describe two DNA sequences isolated in the lizard Zootoca vivipara, here named Zv516 and Zv817. Both sequences are single-copy nuclear sequences, including a truncation of two transposable elements (TEs), SINE Squam1 in Zv516 and a Tc1/Mariner-like DNA transposon in Zv817. FISH analyses with Zv516 showed the occurrence of interspersed signals of the SINE Squam1 sequence on all chromosomes of Z. vivipara and quantitative dot blot indicated that this TE is present with about 4700 copies in the Z. vivipara genome. FISH and dot blot with Zv817 did not produce clear hybridization signals. Bioinformatic analysis showed the presence of active SINE Squam 1 copies in the genome of different lacertids, in different mRNAs, and intronic and coding regions of various genes. The Tc1/Mariner-like DNA transposon occurs in all reptiles, excluding Sphenodon and Archosauria. Zv817 includes a trait of 284 bp, representing an amniote ultra-conserved element (UCE). Using amniote UCE homologous sequences from available whole genome sequences of major amniote taxonomic groups, we performed a phylogenetic analysis which retrieved Prototheria as the sister group of Metatheria and Eutheria. Within diapsids, Testudines are the sister group to Aves + Crocodylia (Archosauria), and Sphenodon is the sister group to Squamata. Furthermore, large trait regions flanking the UCE are conserved at family level.

Keywords: DNA transposons; SINEs; Tc1/Mariner; amniotes; evolutionarily conserved elements; reptiles; squamates.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Electrophoresis on 1.5% agarose gel with RAPD PCR products using primer pair 3 (see Table 1) of male (A) and female (B) specimens of Z. vivipara from Pourtalet with relative blank reactions (A’ and B’) and sequences of main bands of lanes A (Zv516 on the left) and B (Zv817 on the right). L = DNA ladder (100 bp). Segments showing identity with SINE Squam1 and TC1-Mariner transposable elements are highlighted in yellow and light blue in the two sequences, respectively.
Figure 2
Figure 2
Schematic representation of the alignment of the 5′ trait (685 bp) of Zv817 from Z. vivipara with homologous sequences from amniote WGS, and below is with the amniote consensus UCE sequence. The hatched trait represents the conserved amniote UCE.
Figure 3
Figure 3
FISH with Zv561 probe on metaphase plates of female from Pourtalet (2n = 35; Z1Z2W; W telocentric).
Figure 4
Figure 4
Phylogenetic tree with ML (1000 bootstrap replicates) and BI (6,000,000 generations) using the UCE isolated in Zv817 and homologous sequences from available deposited WGS. * = bootstrap values > 75; ** = Bayesian posterior support values > 0.97.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Biémont C., Vieira C. Junk DNA as an evolutionary force. Nature. 2006;443:521–524. doi: 10.1038/443521a. - DOI - PubMed
    1. Chalopin D., Naville M., Plard F., Galiana D., Volff J.N. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol. Evol. 2015;7:567–580. doi: 10.1093/gbe/evv005. - DOI - PMC - PubMed
    1. Kidwell M.G., Lisch D.R. Perspective: Transposable elements, parasitic DNA, and genome evolution. Evolution. 2001;55:1–24. - PubMed
    1. Feschotte C. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 2008;9:397–405. doi: 10.1038/nrg2337. - DOI - PMC - PubMed
    1. Kordis D. Transposable elements in reptilian and avian (Sauropsida) genomes. Cytogenet. Genome Res. 2010;127:94–111. doi: 10.1159/000294999. - DOI - PubMed

LinkOut - more resources