Improved reference genome for the domestic horse increases assembly contiguity and composition. (December 2018)

• Record Type: Journal Article
• Authors: Kalbfleisch, Theodore; Rice, Edward; DePriest, Michael; Walenz, Brian; Hestand, Matthew; Vermeesch, Joris; O′Connell, Brendan; Fiddes, Ian; Vershinina, Alisa; Saremi, Nedda; Petersen, Jessica; Finno, Carrie; Bellone, Rebecca; McCue, Molly; Brooks, Samantha; Bailey, Ernest; Orlando, Ludovic; Green, Richard; Miller, Donald; Antczak, Douglas; MacLeod, James
• Is Part Of: Communications biology. Volume 1:Number 1(2018)
• Page Start: 1
• Page End: 8
• Publication Date: 2018-12
• Subjects: Systems biology -- Periodicals; 570.113
• DOI: 10.1038/s42003-018-0199-z
• Languages: English
• ISSNs: 2399-3642

Abstract

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. Theodore Kalbfleisch et al. present an improved genome assembly for the domestic horse by combining short- and long-read data, as well as proximity ligation data. They improve contiguity of the assembly by 40-fold, with a 10-fold reduction in gaps.