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

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

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish (US)
Article number197
JournalCommunications Biology
Volume1
Issue number1
DOIs
StatePublished - Dec 1 2018

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Horses
Genes
Genome
Chromosomes
horses
Scaffolds
genome
Chemical analysis
chromosomes
genome assembly
genomics
Genomics
Ligation
Technology
Research
methodology

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Medicine (miscellaneous)

Cite this

Kalbfleisch, T. S., Rice, E. S., DePriest, M. S., Walenz, B. P., Hestand, M. S., Vermeesch, J. R., ... MacLeod, J. N. (2018). Improved reference genome for the domestic horse increases assembly contiguity and composition. Communications Biology, 1(1), [197]. https://doi.org/10.1038/s42003-018-0199-z

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

In: Communications Biology, Vol. 1, No. 1, 197, 01.12.2018.

Research output: Contribution to journalArticle

Kalbfleisch, TS, Rice, ES, DePriest, MS, Walenz, BP, Hestand, MS, Vermeesch, JR, O′Connell, BL, Fiddes, IT, Vershinina, AO, Saremi, NF, Petersen, JL, Finno, CJ, Bellone, RR, McCue, ME, Brooks, SA, Bailey, E, Orlando, L, Green, RE, Miller, DC, Antczak, DF & MacLeod, JN 2018, 'Improved reference genome for the domestic horse increases assembly contiguity and composition', Communications Biology, vol. 1, no. 1, 197. https://doi.org/10.1038/s42003-018-0199-z
Kalbfleisch TS, Rice ES, DePriest MS, Walenz BP, Hestand MS, Vermeesch JR et al. Improved reference genome for the domestic horse increases assembly contiguity and composition. Communications Biology. 2018 Dec 1;1(1). 197. https://doi.org/10.1038/s42003-018-0199-z
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. / Improved reference genome for the domestic horse increases assembly contiguity and composition. In: Communications Biology. 2018 ; Vol. 1, No. 1.
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