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

作者：Ted Kalbfleisch, Edward S. Rice, Michael S. DePriest, Brian P. Walenz, Matthew S. Hestand, Joris Robert 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 Edward Green, Donald C. Miller, Douglas F. Antczak, James N. MacLeod · 发表于：Communications Biology · 年份：2018 · DOI：10.1038/s42003-018-0199-z · 被引用次数：297 · 研究领域：Genetic and phenotypic traits in livestock、Genetic diversity and population structure、Genetic Mapping and Diversity in Plants and Animals

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.