Abstract

BackgroundUnicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans.ResultsScreening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage.ConclusionsS. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.

Highlights

  • Unicellular species make up the majority of eukaryotic diversity, most studies on transposable elements (TEs) have centred on multicellular host species

  • S. rosetta harbours a greater diversity of TE families than M. brevicollis The S. rosetta (ATCC 50818) genome was found to have a minimum of 20 full-length TE families when screened through both RepeatMasker and BLAST searches

  • The choanoflagellate S. rosetta harbours a diverse complement of TEs, which are mainly orthologous to families present within metazoan genomes

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Summary

Introduction

Unicellular species make up the majority of eukaryotic diversity, most studies on transposable elements (TEs) have centred on multicellular host species. Class II TEs are DNA transposons which transpose as a DNA copy, often by a “cut and paste” mechanism that results in the entire element being removed from the host chromosome and reinserted into a new position in the genome. This process is facilitated by a Transposase (Tnpase) protein for most DNA transposons, which binds to flanking inverted terminal repeats (ITRs) creating double-stranded breaks and allowing the integration of the transposon at a new genomic location

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