Comparative DNA Methylome of the Chicken and Pig: An Evolutionary Bridge Between Avian and Mammalian

DNA methylation is a well-studied epigenetic mechanism that plays a crucial role in cellular processes including gene regulation and genome organization/stability. As part of the FAANG initiative, this pilot study aims at cataloging DNA-methylation at a single-base resolution of 8 reference tissues (liver, spleen, lung, muscle, adipose, hypothalamus, cerebral cortex and cerebellum) of the pig and chicken (two adults) from the FAANG-ASA collections. Reduced Representation Bisulfite Sequencing (RRBS) with double-enzyme (MspI&TaqI) digestion and increased selected-fragment size were used to enhance the genome-wide CpG coverage. About 50M high-quality reads per library was obtained from the first effort across 30 RRBS-libraries from a single-end sequencing of 114cycles on a HiSeq2500. Average mapping efficiency was 64.34±0.87 and 62.44±0.62% using BS-Seeker2 for chickens and pigs, respectively. Overall methylated cytosines in the CG/CHG/CHH context were 24.01±1.47/1.21±0.28/1.04±0.35 for the chicken and 43.42±1.51/1.14±0.16/1.01±0.23 for the pig (bisulfite-conversion rate>99.0%). The data will be deposited in public data repositories and the study will further be extended to enhance genome coverage. Further analysis includes a comparison of the DNA methylome between tissues to obtain deeper insights into how the DNA methylation regulates the functioning genomes. Moreover, chickens and pigs are important livestock and model organisms that bridge the evolutionary gaps between avian and mammals; hence a comparative study of DNA-methylomes should reveal an evolutionary footprint of the functional DNA-methylation. Furthermore, the FAANG-reference samples are valuable resources with wealthy epigenetic information that will enable the multi-level data integration and advance our understanding of the functional genomes and regulating epigenomes in livestock.