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- Title
Improved reference genome for the domestic horse increases assembly contiguity and composition.
- Authors
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.
- 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.
- Subjects
NUCLEOTIDE sequencing; GENOMES; HORSES; CHROMOSOMES; COMPUTATIONAL biology
- Publication
Communications Biology, 2018, Vol 1, Issue 1, pN.PAG
- ISSN
2399-3642
- Publication type
Article
- DOI
10.1038/s42003-018-0199-z