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Genome Biol. 2017 Oct 24;18(1):198. doi: 10.1186/s13059-017-1335-7.

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.

Author information

1
Radboud University Medical Center, Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands.
2
Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands.
3
Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia.
4
St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.
5
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.
6
Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
7
Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia.
8
Radboud University Medical Center, Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands. huynen@cmbi.ru.nl.
9
Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands. s.vanheeringen@science.ru.nl.
10
Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands. g.veenstra@science.ru.nl.

Abstract

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.

KEYWORDS:

Enhancers; Epigenomics; Genome evolution; Interspecific hybridization; Pseudogenes; Whole genome duplication

PMID:
29065907
PMCID:
PMC5655803
DOI:
10.1186/s13059-017-1335-7
[Indexed for MEDLINE]
Free PMC Article

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