Abstract
Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes—insertions or deletions, or indels—are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., <30 bp) deletions than do other vertebrate genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion—ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a “wrong” (i.e., ectopic, or non-allelic) template sequence—typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome—a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.
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Acknowledgments
This work was supported by the National Science Foundation (REU supplement to NSF-DEB 1021489 to R.L.M.). We thank members of the Mueller lab and two anonymous reviewers for helpful comments and discussion.
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Matthew Blake Frahry and Cheng Sun have contributed equally.
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Supplemental File 1
Terminal to internal (T:I) ratios of individual LTR retrotransposon families for fully sequenced vertebrate genomes and all salamanders based on datasets of equivalent sizes (118,164 reads). Each data point represents one LTR retrotransposon family; families contain different numbers of elements. Outliers are excluded. Supplementary material 1 (PDF 17 kb)
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Frahry, M.B., Sun, C., Chong, R.A. et al. Low Levels of LTR Retrotransposon Deletion by Ectopic Recombination in the Gigantic Genomes of Salamanders. J Mol Evol 80, 120–129 (2015). https://doi.org/10.1007/s00239-014-9663-7
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DOI: https://doi.org/10.1007/s00239-014-9663-7