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RUDI, a short interspersed element of the V-SINE superfamily widespread in molluscan genomes

Abstract

Short interspersed elements (SINEs) are non-autonomous retrotransposons that are widespread in eukaryotic genomes. They exhibit a chimeric sequence structure consisting of a small RNA-related head, an anonymous body and an AT-rich tail. Although their turnover and de novo emergence is rapid, some SINE elements found in distantly related species retain similarity in certain core segments (or highly conserved domains, HCD). We have characterized a new SINE element named RUDI in the bivalve molluscs Ruditapes decussatus and R. philippinarum and found this element to be widely distributed in the genomes of a number of mollusc species. An unexpected structural feature of RUDI is the HCD domain type V, which was first found in non-amniote vertebrate SINEs and in the SINE from one cnidarian species. In addition to the V domain, the overall sequence conservation pattern of RUDI elements resembles that found in ancient AmnSINE (~310 Myr old) and Au SINE (~320 Myr old) families, suggesting that RUDI might be among the most ancient SINE families. Sequence conservation suggests a monophyletic origin of RUDI. Nucleotide variability and phylogenetic analyses suggest long-term vertical inheritance combined with at least one horizontal transfer event as the most parsimonious explanation for the observed taxonomic distribution.

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Acknowledgments

We thank Mary Sopta for critical reading and language editing of the manuscript. We also wish to thank the Editor and two anonymous Reviewers whose comments and suggestions substantially improved the manuscript.

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Correspondence to Andrea Luchetti.

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Funding

This work has been supported by RFO-UNIBO funding to AL and BM, and by Research Fund of Ministry of Science, Education and Sports of Republic of Croatia, project no. 098-0982913-2756 to MP.

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Authors declare that they have no conflict of interest.

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All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Additional information

Communicated by M. A. Van Sluys.

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438_2016_1194_MOESM1_ESM.jpg

Supplementary Fig. S1 Alignment of the RUDI consensus sequences, including the V domain consensus taken from Vassetzky and Kramerov (2013). Nucleotide shading represents similarity ≥60 %. The general structure of the element is shown below with colored boxes. The green box shows alignment with the V domain consensus sequence (JPEG 2128 kb)

Supplementary material 2 (PDF 64 kb)

Supplementary material 3 (PDF 77 kb)

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Luchetti, A., Šatović, E., Mantovani, B. et al. RUDI, a short interspersed element of the V-SINE superfamily widespread in molluscan genomes. Mol Genet Genomics 291, 1419–1429 (2016). https://doi.org/10.1007/s00438-016-1194-z

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Keywords

  • Short interspersed nuclear elements
  • Mollusca
  • Highly conserved domain
  • Horizontal transfer
  • Vertical inheritance