Improved reference genome for the domestic horse increases assembly contiguity and composition
Theodore S Kalbfleisch1, Edward S Rice2, Michael S DePriest3
1Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40292, USA. ted.kalbfleisch@louisville.edu.
Communications Biology
|November 21, 2018
Summary
The new EquCab3 reference genome significantly enhances horse genome contiguity and composition using advanced sequencing data. This improved equine genome assembly provides a more complete genetic blueprint for horses.
Area of Science:
- Genomics
- Comparative Genomics
- Bioinformatics
Background:
- The EquCab2 reference genome, released in 2007, represented a significant achievement but shared limitations common to early-generation genome assemblies.
- Advances in sequencing technologies and computational methods necessitate updated and improved reference genomes.
Purpose of the Study:
- To present EquCab3, a substantially improved reference genome assembly for the domestic horse (Equus caballus).
- To enhance the contiguity and accuracy of the equine reference genome.
Main Methods:
- Integration of new short-read, long-read, and proximity ligation data.
- Building upon the existing EquCab2 assembly.
- Utilizing advanced computational assembly techniques.
Main Results:
- The EquCab3 assembly increased the count of non-N bases from 2.33 Gb (EquCab2) to 2.41 Gb.
- Achieved a nearly 40-fold improvement in contiguity, with a contig N50 of 4.5 Mb.
- Enhanced scaffold contiguity, with 31 out of 32 chromosomes represented as single scaffolds.
Conclusions:
- EquCab3 represents a major advancement in the quality and completeness of the horse reference genome.
- The improved assembly will facilitate future equine genomics research, including genetic studies and breeding advancements.
- This enhanced reference genome provides a more robust foundation for understanding horse genetics and diversity.
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