Abstract
BackgroundDIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. They have been previously reported in only a few diverse eukaryote species, describing a patchy distribution, and little is known about their origin and dynamics. Recently, we have shown that these retrotransposons are common among decapods, which calls into question the distribution of DIRS1-like retrotransposons among eukaryotes.ResultsTo determine the distribution of DIRS1-like retrotransposons, we developed a new computational tool, ReDoSt, which allows us to identify well-conserved DIRS1-like elements. By screening 274 completely sequenced genomes, we identified more than 4000 DIRS1-like copies distributed among 30 diverse species which can be clustered into roughly 300 families. While the diversity in most species appears restricted to a low copy number, a few bursts of transposition are strongly suggested in certain species, such as Danio rerio and Saccoglossus kowalevskii.ConclusionIn this study, we report 14 new species and 8 new higher taxa that were not previously known to harbor DIRS1-like retrotransposons. Now reported in 61 species, these elements appear widely distributed among eukaryotes, even if they remain undetected in streptophytes and mammals. Especially in unikonts, a broad range of taxa from Cnidaria to Sauropsida harbors such elements. Both the distribution and the similarities between the DIRS1-like element phylogeny and conventional phylogenies of the host species suggest that DIRS1-like retrotransposons emerged early during the radiation of eukaryotes.
Highlights
DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons
Identification of putative DIRS1-like retrotransposons in eukaryote genomes To study the distribution of DIRS1-like retrotransposons among genomes, we developed a new computational tool that we call ReDoSt (Retrotransposon Domain and Structure)
Using ReDoSt, we identified 4310 copies of putative DIRS1-like elements distributed among 32 diverse species out of the 274 well-sequenced genomes tested (Table 2)
Summary
DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. The first ORF encodes a putative GAG protein, the second the YR, and the third a pol region composed of three distinct domains: a reverse transcriptase (RT), a RNase H (RH), and a methyltransferase (MT). The element integration occurs by recombination between the 3-bp ITR junction sequence (complementary to the circular junction) and an identical sequence in the genome, which does not produce any target site duplications. Their unique structure distinguishes DIRS1-like retrotransposons from other YR-encoding elements, known as the DIRS order [2] that includes the Ngaro, Viper and PAT elements. The PAT retrotransposons (PAT-like elements, TOC elements and kangaroo) are bounded by some “Split” Direct Repeats (SDRs) and can contain tyrosine recombinaseencoding regions in an inverted orientation [5]
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