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Preliminary functional annotation of the sheep genome
In the absence of detailed functional annotation for any livestock genome, we used comparative genomics to predict ovine regulatory elements using human data. Reciprocal liftOver was used to predict the ovine genome location of ENCODE promoters and enhancers, along with 12 chromatin states built using 127 diverse epigenome.
Here we make available t... morehe following files:
a) Sheep_epigenome_predicted_features.tar.gz: contains the final reciprocal best alignment from ENCODE proximal as well as chromHMM ROADMAP features. The result of reciprocal liftOver.
b) liftOver_sheep_temporary_files.tar.gz: We have
added a new tar file with liftOver temporary files
i) LiftOver temporary files mapping human to sheep,
ii) LiftOver temporary files mapping sheep back to human and
iii) Dictionary files containing the link between human to sheep coordinates for exact best-reciprocal files.
Building a comparative sheep functional annotation.
Our approach exploited the wealth of functional annotation data generated by the Epigenome Roadmap and ENCODE studies. We performed reciprocal liftOver (minMatch=0.1), meaning elements that mapped to sheep also needed to map in the reverse direction back to human with high quality. This bi-directional comparative mapping approach was applied to 12 chromatin states defined using 5 core histone modification marks, H3K4me3, H3K4me1, H3K36me3, H3K9me3, H3K27me3. Mapping success is given in Supplementary Table 9. The same approach was applied to ENCODE marks derived from 94 cell types (https://www.encodeproject.org/data/annotations/v2/) with DNase-seq and TF ChIP-seq.
Sheep Genome Functional Annotation Reveals Proximal Regulatory Elements Contributed to the Evolution of Modern Breeds
Marina Naval-Sanchez, Quan Nguyen, Sean McWilliam, Laercio R. Porto-Neto, Ross Tellam, Tony Vuocolo, Antonio Reverter, Miguel Perez-Enciso , Rudiger Brauning, Shannon Clarke, Alan McCulloch, Wahid Zamani, Saeid Naderi, Hamid Reza Rezaei, Francois Pompanon, Pierre Taberlet, Kim C. Worley, Richard A. Gibbs, Donna M. Muzny, Shalini N. Jhangiani, Noelle Cockett, Hans Daetwyler and James Kijas
Creative Commons Attribution 4.0 International Licence
Naval Sanchez, Marina; Nguyen, Quan; McWilliam, Sean; Porto Neto, Laercio; Reverter-Gomez, Toni; Kijas, James (2017): Preliminary functional annotation of the sheep genome. v1. CSIRO. Data Collection.
All Rights (including copyright) CSIRO 2017.
The metadata and files (if any) are available to the public.
OCE Post Doc - Conseq Animal Domesticati
Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here, we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) t... moreo identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrates that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species. less
Marina Naval Sanchez
Laercio Porto Neto
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