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Communications biology2018; 1; 197; doi: 10.1038/s42003-018-0199-z

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

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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Publication Date: 2018-11-16 PubMed ID: 30456315PubMed Central: PMC6240028DOI: 10.1038/s42003-018-0199-zGoogle Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article presents an improved reference genome for domestic horses called EquCab3, which provides a more contiguous and comprehensive genetic map than the previous version, EquCab2.

Background

  • The genomic reference for domestic horses, EquCab2, was introduced in 2007. Despite being of good quality, it had several limitations typically seen in first-generation Sanger assemblies.
  • In 2014, the equine genomics research community initiated a project to enhance the horse’s reference sequence. Their aim was to build on the robust foundation of EquCab2 by integrating new short-read data, long-read data, and proximity ligation data.

Introduction of EquCab3

  • The researchers created EquCab3, an advanced reference genome for domestic horses that provides higher assembly contiguity and composition.
  • The count of non-N bases in the incorporated chromosomes in EquCab3 is 2.41 Gb, up from 2.33 Gb in EquCab2, indicating an increased genetic map coverage.

Improved Contiguity

  • The researchers enhanced the contiguity nearly 40-fold, with a contig N50 of 4.5 Mb. The term “contig N50” is a statistical measure of the average length of a set of sequences (contigs).
  • Scaffold contiguity was also increased to the extent that all but one of the 32 chromosomes is made up of a single scaffold. Scaffolds are sets of overlapping DNA pieces that together represent a consensus region of DNA

Significance of the Study

  • This research will significantly benefit the field of equine genomics by providing a more accurate, complete, and usable genomic reference for the domestic horse.
  • The enhanced genome map can be instrumental for biological research and practical applications ranging from evolutionary studies to equine health management.

Cite This Article

APA
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. Commun Biol, 1, 197. https://doi.org/10.1038/s42003-018-0199-z

Publication

Communications biology
ISSN: 2399-3642
NlmUniqueID: 101719179
Country: England
Language: English
Volume: 1
Pages: 197
PII: 197

Researcher Affiliations

Kalbfleisch, Theodore S
  • Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40292, USA. ted.kalbfleisch@louisville.edu.
Rice, Edward S
  • Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, 95064, USA.
DePriest, Michael S
  • Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40292, USA.
Walenz, Brian P
  • Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Hestand, Matthew S
  • Center for Human Genetics, Katholieke University Leuven (KU Leuven), 3000, Leuven, Belgium.
Vermeesch, Joris R
  • Center for Human Genetics, Katholieke University Leuven (KU Leuven), 3000, Leuven, Belgium.
O Connell, Brendan L
  • Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, 95064, USA.
  • Medical and Molecular Genetics, Oregon Health and Science University, Portland, OR, 97239, USA.
Fiddes, Ian T
  • Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, 95064, USA.
  • 10x Genomics, Inc., Pleasanton, CA, 94566, USA.
Vershinina, Alisa O
  • Department of Ecology and Evolutionary Biology, UC Santa Cruz, Santa Cruz, CA, 95064, USA.
Saremi, Nedda F
  • Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, 95064, USA.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska - Lincoln, Lincoln, NE, 68583-0908, USA.
Finno, Carrie J
  • Department of Population Health and Reproduction, University of California, Davis, CA, 95616, USA.
Bellone, Rebecca R
  • Department of Population Health and Reproduction, University of California, Davis, CA, 95616, USA.
  • Veterinary Genetics Laboratory, University of California, Davis, CA, 95616, USA.
McCue, Molly E
  • Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
Brooks, Samantha A
  • UF Genetics Institute, Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.
Bailey, Ernest
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40546, USA.
Orlando, Ludovic
  • Centre for GeoGenetics, Natural History Museum of Denmark, 1350K, Copenhagen, Denmark.
  • Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France.
Green, Richard E
  • Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, 95064, USA.
Miller, Donald C
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
Antczak, Douglas F
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
MacLeod, James N
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40546, USA.

Grant Funding

  • K01 OD015134 / NIH HHS
  • L40 TR001136 / NCATS NIH HHS

Conflict of Interest Statement

I.T.F. is an employee of 10× Genomics, Inc. R.E.G. is a co-founder and scientific adviser of Dovetail Genomics, LLC. The other authors declare no competing interests.

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