Large-scale chromosomal changes lead to genome-level expression alterations, environmental adaptation and speciation in bovines

Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen) and was sheared by a g-TUBE device (Covaris) with 20kb settings. Sheared DNA was purified and concentrated with AmpureXP beads (Agencourt) and used for SMRT bell preparation according to manufacturer's protocol (Pacific Biosciences; 20-kb template preparation using BluePippin size selection (Sagescience). Size selected and isolated SMRT bell fractions were purified using AmpureXP beads (Beckman Coulter, Inc.). Finally, purified SMRT bells were used for primer (V3)-and polymerase (2.0) binding according to manufacturer’s binding calculator (Pacific Biosciences). Single-molecule sequencing was done on a PacBio Sequel system. And Five 270 bp paired-end libraries were constructed using Illumina's paired-end kits according to the manufacturer's instructions. The libraries were sequenced on Illumina HiSeq 2500 platforms. For Hi-C sequencing, nuclear DNA from blood of the same individual was cross-linked, then cut with a restriction enzyme, leaving pairs of distantly located but physically interacted DNA molecules attached to one another(Lieberman-Aiden, et al. 2009). The sticky ends of these digested fragments were biotinylated and then ligated to each other to form chimeric circles. Biotinylated circles, which were chimeras of the physically associated DNA molecules from the original cross-linking, were enriched, sheared and sequenced