Abstract
Sheep is an important livestock in the world for meat, dairy and wool production. The third version of sheep reference genome has been recently assembled, but sheep DNA methylome has not been profiled yet. In this study, we report the comprehensive sheep methylome with 94.38% cytosine coverage at single base resolution by sequencing DNA samples from Longissimus dorsi of dizygotic Sunit sheep, which were bred in different habitats. We also compared methylomes between the twin sheep. DNA methylation status at genome-scale differentially methylated regions (DMRs), functional genomic regions and 248 DMR-containing genes were identified between the twin sheep. Gene ontology (GO) and KEGG annotations of these genes were performed to discover computationally predicted function. Lipid metabolism, sexual maturity and tumor-associated categories were observed to significantly enrich DMR-containing genes. These findings could be used to illustrate the relationship between phenotypic variations and gene methylation patterns.
Highlights
DNA methylation at the 5 position of cytosine is common in genomes of fungi, plants and animals [1, 2]
To study the general methylation pattern of sheep as well as the DNA methylation divergence induced by different habitat, we chose a pair of 6-month-old female twin sheep as DNA sample donors
DNA sample was extracted from Longissimus dorsi of each sheep to generate whole-genome size DNA methylome maps using bisulfite sequencing (BS-seq) method [29]. 786 million BS-seq raw reads were generated from Sheep A, and 805 million from Sheep B
Summary
DNA methylation at the 5 position of cytosine is common in genomes of fungi, plants and animals [1, 2]. Whole genome bisulfite sequencing (BS-seq) was first used in Arabidopsis thaliana DNA methylome studies [20, 21], and was proved to be effective to profile accurate, unbiased and high-coverage DNA methylation landscapes in model animals like human, mice and rat [3, 22, 23]. We described the comprehensive sheep Longissimus dorsi (LD) muscle DNA methylome with 94.38% cytosine coverage at single base resolution using BS-seq This high coverage sheep LD methylome provides resource to profile widespread genomic CG and non-CG methylation (CHG and CHH contexts (H = A, T or C)) patterns. This resource provides insight into the development of animal husbandry, and helps understand the process of species evolution and differentiation during domestication
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