Supporting data for "De novo assembly of the cattle reference genome with single-molecule sequencing"

Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the <i>Bos taurus</i> reference genome (UMD3.1.1), which was created using now-outdated technologies and suffers from a variety of deficiencies and inaccuracies. We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a <i>de novo</i> assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb, and is &gt;250x more continuous than the original assembly, with contig N50 &gt;25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.