Improved reference genome for the domestic horse increases assembly contiguity and composition

Authors

• Theodore S. Kalbfleisch, University of LouisvilleFollow
• Edward S. Rice, University of California Santa Cruz
• Michael S. DePriest Jr., University of Louisville
• Brian P. Walenz, National Human Genome Research Institute
• Matthew S. Hestand, Katholieke Universiteit Leuven
• Joris R. Vermeesch, Katholieke Universiteit Leuven
• Brendan L. O'Connell, University of California Santa Cruz
• Ian T. Fiddes, University of California Santa Cruz
• Alisa O. Vershinina, University of California Santa Cruz
• Nedda F. Saremi, University of California Santa Cruz
• Jessica L. Petersen, University of Nebraska-LincolnFollow
• Carrie J. Finno, University of California, Davis
• Rebecca R. Bellone, University of California, Davis
• Molly E. McCue, University of Minnesota, St. Paul
• Samantha A. Brooks, University of Florida
• Ernest Bailey, University of Kentucky
• Ludovic Orlando, Museum of Denmark
• Richard E. Green, University of California Santa Cruz
• Donald C. Miller, Cornell University
• Douglas F. Antczak, Cornell University
• James N. MacLeod, University of Kentucky

Document Type

Article

Date of this Version

2018

Citation

COMMUNICATIONS BIOLOGY | (2018) 1:197

Comments

© The Author(s) 2018

Open access

DOI: 10.1038/s42003-018-0199-z

Abstract

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.