title: LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types.
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 representativeAdineta vaga. We performed a comprehensive analysis ofA. vagaretroelements, and found that bdelloid long terminal repeat (LTR)retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding togagandpolgenes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families inA. vagabelong to four major lineages, three of which are rotiferspecific and encode a dUTPase domain. However only one lineage contains a canonicalenvlike 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 ofPenelope-likeAthenaretroelement 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.
authors.affiliation: Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA. frodriguez@mbl.edu.
authors.forename: Fernando
authors.initials: F
authors.lastname: Rodriguez
authors.affiliation: Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA. awkenefick@ucdavis.edu.|Present address: UC Davis Genome Center-GBSF, University of California, Davis, CA 95616, USA. awkenefick@ucdavis.edu.
authors.forename: Aubrey W
authors.initials: AW
authors.lastname: Kenefick
authors.affiliation: Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA. iarkhipova@mbl.edu.
authors.forename: Irina R
authors.initials: IR
authors.lastname: Arkhipova
mesh_terms: D000818:Animals; D014644:Genetic Variation; D016366:Open Reading Frames; D018626:Retroelements; D012403:Rotifera / Q000235:genetics*; D017385:Sequence Homology
chemical_list: D018626:Retroelements
keywords: DEDDy exonuclease; GDSL esterase; dUTPase; envelope gene (ENV); retrovirus-like transposable elements