Abstract
Transposable elements (TEs) are repetitive sequences of DNA that replicate and proliferate throughout genomes. Taken together, all the TEs in a genome form a diverse community of sequences, which can be studied to draw conclusions about genome evolution. TE diversity can be measured using models for ecological community diversity that consider species richness and evenness. Several models predict TE diversity decreasing as genomes expand because of selection against ectopic recombination and/or competition among TEs to garner host replicative machinery and evade host silencing mechanisms. Salamanders have some of the largest vertebrate genomes and highest TE loads. Salamanders of the genus Plethodon, in particular, have genomes that range in size from 20 to 70 Gb. Here, we use Oxford Nanopore sequencing to generate low-coverage genomic sequences for four species of Plethodon that encompass two independent genome expansion events, one in the eastern clade (Plethodon cinereus, 29.3 Gb vs. Plethodon glutinosus, 38.9 Gb) and one in the western clade (Plethodon vehiculum, 46.4 Gb vs Plethodon idahoensis, 67.0 Gb). We classified the TEs in these genomes and found > 40 TE superfamilies, accounting for 22–27% of the genomes. We calculated Simpson’s and Shannon’s diversity indices to quantify overall TE diversity. In both pairwise comparisons, the diversity index values for the smaller and larger genome were almost identical. This result indicates that, when genomes reach extremely large sizes, they maintain high levels of TE diversity at the superfamily level, in contrast to predictions made by previous studies on smaller genomes.
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Data Availability
Sequence data are deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA749318.
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Not applicable.
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Acknowledgements
We acknowledge members of A. Haley’s Master’s Degree committee, D. Sloan and M. Stenglein, for valuable assistance. We thank members of the Mueller and Sloan labs for discussion. We thank M. Itgen for Plethodon tissues. We thank E. Anderson for assistance running Prowler. Funding was provided by the National Science Foundation (1911585 to RLM) and Colorado State University.
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Funding was provided by the National Science Foundation (1911585 to RLM) and Colorado State University.
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Animal use was done in accordance with Colorado State University’s IACUC protocol number 17-7189A.
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Haley, A.L., Mueller, R.L. Transposable Element Diversity Remains High in Gigantic Genomes. J Mol Evol 90, 332–341 (2022). https://doi.org/10.1007/s00239-022-10063-3
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DOI: https://doi.org/10.1007/s00239-022-10063-3