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Mol Biol Evol January 1, 2018; 35 (12): 2913-2927.
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Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.

Rogers RL , Zhou L , Chu C , Márquez R , Corl A , Linderoth T , Freeborn L , MacManes MD , Xiong Z , Zheng J , Guo C , Xun X , Kronforst MR , Summers K , Wu Y , Yang H , Richards-Zawacki CL , Zhang G , Nielsen R .

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.

PubMed ID: 30517748
PMC ID: PMC6278860
Article link: Mol Biol Evol
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Species referenced: Xenopus laevis
Genes referenced: chrna1 chrna1.2 chrna2 chrna3 chrna4 chrna5 chrna6 chrna7 chrna9 chrnb1 chrnb2 chrnb4 chrnd chrne chrng nodal pum1 scn1a scn2a scn3a scn4a scn5a tcim tes

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References [+] :
Albuquerque, The pharmacology of batrachotoxin. V. A comparative study of membrane properties and the effect of batrachotoxin on sartorius muscles of the frogs Phyllobates aurotaenia and Rana pipiens. 1973, Pubmed