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Viruses 2017, 9(4), 78; doi:10.3390/v9040078

LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types

1
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
2
Present address: UC Davis Genome Center-GBSF, University of California, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
Academic Editors: David J. Garfinkel and Katarzyna J. Purzycka
Received: 31 January 2017 / Revised: 4 April 2017 / Accepted: 4 April 2017 / Published: 11 April 2017
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Abstract

Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highlydiversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families in A. vaga belong to four major lineages, three of which are rotiferspecific and encode a dUTPase domain. However only one lineage contains a canonical envlike fusion glycoprotein acquired from paramyxoviruses (non-segmented negative-strand RNA viruses), although smaller ORFs with transmembrane domains may perform similar roles. A different ORF3 type encodes a GDSL esterase/lipase, which was previously identified as ORF1 in several clades of non-LTR retrotransposons, and implicated in membrane targeting. Yet another ORF3 type appears in unrelated LTR-retrotransposon lineages, and displays strong homology to DEDDy-type exonucleases involved in 3′-end processing of RNA and single-stranded DNA. Unexpectedly, each of the enzymatic ORF3s is also associated with different subsets of Penelope-like Athena retroelement families. The unusual association of the same ORF types with retroelements from different classes reflects their modular structure with a high degree of flexibility, and points to gene sharing between different groups of retroelements. View Full-Text
Keywords: retrovirus-like transposable elements; envelope gene (ENV); DEDDy exonuclease; GDSL esterase; dUTPase retrovirus-like transposable elements; envelope gene (ENV); DEDDy exonuclease; GDSL esterase; dUTPase
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Rodriguez, F.; Kenefick, A.W.; Arkhipova, I.R. LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types. Viruses 2017, 9, 78.

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