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

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

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.

Journal: Communications biology
DOI: 10.1038/s42003-018-0199-z
Year: 2018

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