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Preliminary functional annotation of the sheep genome

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About this Collection

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... more


Genomics


https://doi.org/10.4225/08/5a03a9c39a0ba


2016


2017


CSIRO Enquiries
CSIROEnquiries@csiro.au
1300 363 400

Sheep Functional Annotation Comparative


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


CSIRO (Australia)


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. https://doi.org/10.4225/08/5a03a9c39a0ba


All Rights (including copyright) CSIRO 2017.


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About this Project

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... more


James Kijas





Marina Naval Sanchez


Quan Nguyen


Sean McWilliam


Laercio Porto Neto


Toni Reverter-Gomez


James Kijas


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