Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

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Published in Communications Biology, v. 1, article no. 197, p. 1-8.

© The Author(s) 2018

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This work was supported by Morris Animal Foundation Grant D15EQ-019 and the NRPS8 Horse Genome Coordinator Fund. E.S.R. is an ARCS scholar. Support for C.J.F. was provided by the National Institutes of Health (NIH) (1K01OD015134 and L40 TR001136). The FAANG data (C.J.F, J.L.P., R.R.B.) was generated with the support of the Grayson Jockey Club Foundation.

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The sequence read datasets generated during the current study are available in the NCBI SRA repository under accession SRP126689. The final assembly generated during the current study is available in the NCBI Genbank repository under accession GCA_002863925.1. The mitochondrial sequence has been deposited into GenBank (accession number MH586816). We also provide intermediate assemblies produced during the process, a de novo assembly based solely on the PacBio data, and phased variant calls from the 10× longranger pipeline in a CyVerse Data Commons repository at https://doi.org/10.7946/P20348.

Data from Sarkar et al. used in variant calling and genotyping are found in the Sequence Read Archive at BioSample SAMN03838869 and SAMN03838867, experiment accession numbers SRX1097022 and SRX1097495, respectively.

Supplementary Information accompanies this paper at https://doi.org/10.1038/s42003-018-0199-z.

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