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Genome Biol 2017 Oct 24;181:198. doi: 10.1186/s13059-017-1335-7.
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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.

Elurbe DM , Paranjpe SS , Georgiou G , van Kruijsbergen I , Bogdanovic O , Gibeaux R , Heald R , Lister R , Huynen MA , van Heeringen SJ , Veenstra GJC .

BACKGROUND: Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. However, little is known about the consequences of this duplication at the level of the genome, the epigenome, and gene expression. RESULTS: The X. laevis genome consists of two subgenomes, referred to as L (long chromosomes) and S (short chromosomes), that originated from distinct diploid progenitors. Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes from the point of genome duplication until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination has played a significant role in the loss of DNA. To assess innovations in the X. laevis subgenomes we examined p300-bound enhancer peaks that are unique to one subgenome and absent from X. tropicalis. A large majority of new enhancers comprise transposable elements. Finally, to dissect early and late events following interspecific hybridization, we examined the epigenome and the enhancer landscape in X. tropicalis × X. laevis hybrid embryos. Strikingly, young X. tropicalis DNA transposons are derepressed and recruit p300 in hybrid embryos. CONCLUSIONS: The results show that erosion of X. laevis genes and functional regulatory elements is associated with repeats and non-allelic homologous recombination and furthermore that young repeats have also contributed to the p300-bound regulatory landscape following hybridization and whole-genome duplication.

PubMed ID: 29065907
PMC ID: PMC5655803
Article link: Genome Biol
Grant support: [+]

Species referenced: Xenopus laevis
Genes referenced: anp32e crebbp ctcf eomes gata1 mecom otud7b pax4 plag1 plekho1 prdm16 six3 six6 slc2a2 sox18 tbx21 tes tp53 vps45

GEO Series: GSE90898: NCBI
GSE92382: Xenbase,  NCBI

Article Images: [+] show captions
References [+] :
Ashkenazy, FastML: a web server for probabilistic reconstruction of ancestral sequences. 2012, Pubmed