Mol Biol Evol
December 1, 2018;
Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.
We sequenced the genome of the strawberry poison frog, Oophaga pumilio, at a depth of 127.5× using variable insert size libraries. The total genome size is estimated to be 6.76 Gb, of which 4.76 Gb are from high copy number repetitive elements with low differentiation across copies. These repeats encompass DNA transposons, RNA transposons, and LTR retrotransposons, including at least 0.4 and 1.0 Gb of Mariner/Tc1 and Gypsy elements, respectively. Expression data indicate high levels of gypsy and Mariner/Tc1 expression in ova of O. pumilio compared with Xenopus laevis. We further observe phylogenetic evidence for horizontal transfer (HT) of Mariner elements, possibly between fish and frogs. The elements affected by HT are present in high copy number and are highly expressed, suggesting ongoing proliferation after HT. Our results suggest that the large amphibian genome sizes, at least partially, can be explained by a process of repeated invasion of new transposable elements that are not yet suppressed in the germline. We also find changes in the spliceosome that we hypothesize are related to permissiveness of O. pumilio to increases in intron length due to transposon proliferation. Finally, we identify the complement of ion channels in the first genomic sequenced poison frog and discuss its relation to the evolution of autoresistance to toxins sequestered in the skin.
Mol Biol Evol
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Fig. 1. Bayesian gene trees reconstructed for annotation of O. pumilio genes in the nACHR (A) and SCNA (B) gene families, and nucleotide sequences of the CHRNE gene. Nodal support and branch labeling/coloring follow in fig. 2.
Fig. 2. Bayesian gene tree of the voltage-gated sodium channel alpha subunit (SCNA) gene family and amino acid replacements identified as possibly associated with toxin autoresistance in O. pumilio (A), with their positions on a schematic voltage-gated sodium channel (B). Branches are colored and labeled based on the closest X. tropicalis ortholog, and nomenclature follows ENSEMBL annotations. Asterisks on internodes denote Bayesian posterior probabilities and aBayes support values above 0.95. Clades resulting from amniote-specific gene family expansions were collapsed to improve visualization.
Fig. 3. Total sequence content of TEs as classified using a tblastx against the RepBase database. Among low differentiated TE families, we identified 1 Gb of Gypsy elements, 298 Mb of Copia elements, 255 Mb of hAT sequence, 197 Mb of Mariner elements, and 181 Mb of Tc1 elements in O. pumilio.
Fig. 4. Bimodal distribution of nucleotide similarity for repeat contigs identified using RepDeNovo compared with Mariner-4_DR consensus sequence from D. rerio. The presence of two peaks is consistent with two waves of proliferation after HT of an element between fish and frogs. Danio and Oophaga diverged 480MYA. The distribution of nucleotide similarity is not consistent with vertical transmission from a common ancestor.
Fig. 5. Phylogenetic relationships between horizontally transmitted repetitive elements in O. pumilio (black) and annotated TE Tc1-3_SSa (red), a salmon TE in RepBase. Similar patterns are observed in other TE families. For each of the most diverse TEs that are candidates for HT, the RepBase element lies within the diversity of TEs in O. pumilio. All of these diverse and rapidly proliferating horizontally transferred elements are a close match with a TE from freshwater fish.
Fig. 6. Total amount of expressed sequence for TE classes in O. pumilio and X. laevis. Gypsy and Mariner elements are expressed at significantly higher levels in O. pumilio, but Tc1 elements are not. We observe an excess of germline expression of Gypsy (t = 7.007; P = 0.006393) and Mariner sequences (t = 7.1938; P = 0.005313) in O. pumilio compared with Xenopus.
Fig.7. Expression level for transcripts is positively correlated with nucleotide similarity with Mariner-4_DR (Danio rerio) consensus sequence in RepBase. Such a result is expected if recently transferred transposons invade genomes that lack repressors for the new TEs (F = 3.956; df = 5; P = 0.002128).