Whole genome bisulfite sequencing reveals unique adaptations to high-altitude environments in Tibetan chickens

Abstract

BackgroundTibetan chickens living at high altitudes show specific adaptations to high-altitude conditions, but the epigenetic modifications associated with these adaptations have not been characterized.ResultsWe investigated the genome-wide DNA methylation patterns in Tibetan chicken blood by using whole genome bisulfite sequencing. Generally, Tibetan chickens exhibited analogous methylation patterns to that of lowland chickens. A total of 3.92% of genomic cytosines were methylcytosines and 51.22% of cytosines in CG contexts were methylated, which was less than those in lowland chicken (55.69%). Moreover, the base adjacent to the methylcytosines of mCHGs in Tibetan chickens had a preference for T, which was different from that in lowland chickens. In Tibetan chickens, the methylation levels in the promoter were relatively low, while the gene body was also maintained in a hypomethylated state. DNA methylation levels in regions upstream of the transcription start site of genes were negatively correlated with the level of gene expression, and DNA methylation of gene body regions was also negatively related to gene expression.ConclusionsWe generated the genome-wide DNA methylation patterns in Tibetan chickens and our results will be helpful for future epigenetic studies related to adaptations to high-altitude conditions.

Analysis of DNA Methylation Profiles in Mandibular Condyle of Chicks With Crossed Beaks Using Whole-Genome Bisulfite Sequencing

“…Approximately 4.3% of cytosine sites were methylated, which is lower than the cortical bones in mice from 6.06 to 6.48% ( Wei et al, 2020 ). The highest proportion of CG methylation in this study was similar to that found in other species ( Wei et al, 2020 ) and tissues ( Li C. W. et al, 2015 ; Li J. X. et al, 2015 ; Zhang et al, 2018 ; Tan et al, 2020 ). Among the gene functional regions, TSSs presented the lowest methylation levels, which was consistent with the results in chickens’ liver ( Tan et al, 2020 ) and blood ( Zhang et al, 2018 ), but inconsistent in cortical bones of mice ( Wei et al, 2020 ).…”

Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO2 Levels

“…Thus the low methylation observed in our data may be specific to the species, tissue, or stage of development. To date, whole-genome bisulfite sequencing studies in G. gallus and other avian species have reported global CpG methylation rates between 50 and 65% (Li et al, 2015;Derks et al, 2016;Lee et al, 2017;Zhang et al, 2017Zhang et al, , 2018, which is lower than the 60-80% that has been reported in mammalian studies. It is possible that the low levels of CpG methylation detected in our data can be attributed to lower CpG methylation rates in avian genomes.…”

“…Additionally, numerous epigenome-wide association studies (EWAS) have been performed in humans and mice to identify loci at which methylation level is significantly associated with complex and disease traits (Orozco et al, 2015;reviewed in Flanagan, 2015). Bisulfite-sequencing approaches allow for genome-wide assessment of DNA methylation patterns, yet this approach has been underutilized in the chicken thus far (Li et al, 2015;Lee et al, 2017;Zhang et al, 2017Zhang et al, , 2018).…”

Gaps in genetic knowledge affect conservation management of kiwi (Apteryx) species

“…For example, identifying local adaptations as indicated by outlier allele frequencies suggestive of genes under diversifying selection, or by correlations between allele frequency and environmental factors, will require larger sample sizes (at least 8-12 samples per site; Landguth & Schwartz 2014, Pastenes et al 2017, Zhen et al 2017, Homola et al 2019. On the other hand, local adaptation indicated by differences in patterns of gene expression or genomic methylation profiles might require fewer samples (three or fewer depending on the method of comparative analysis; Zhang et al 2018, Xin et al 2019.…”