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

  • Author(s): Kalbfleisch, Theodore S
  • Rice, Edward S
  • DePriest, Michael S
  • Walenz, Brian P
  • Hestand, Matthew S
  • Vermeesch, Joris R
  • O Connell, Brendan L
  • Fiddes, Ian T
  • Vershinina, Alisa O
  • Saremi, Nedda F
  • Petersen, Jessica L
  • Finno, Carrie J
  • Bellone, Rebecca R
  • McCue, Molly E
  • Brooks, Samantha A
  • Bailey, Ernest
  • Orlando, Ludovic
  • Green, Richard E
  • Miller, Donald C
  • Antczak, Douglas F
  • MacLeod, James N
  • et al.
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.

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