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

Theodore S. Kalbfleisch; Edward S. Rice; Michael S. DePriest; Brian P. Walenz; Matthew S. Hestand; Joris R. 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 E. Green; Donald C. Miller; Douglas F. Antczak; James N. MacLeod

doi:10.1038/s42003-018-0199-z

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

Theodore S. Kalbfleisch, Edward S. Rice, Michael S. DePriest, Brian P. Walenz, Matthew S. Hestand, Joris R. 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 E. Green, Donald C. Miller, Douglas F. AntczakJames N. MacLeod

Animal Science

Research output: Contribution to journal › Article › peer-review

163 Scopus citations

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.

Original language	English (US)
Article number	197
Journal	Communications biology
Volume	1
Issue number	1
DOIs	https://doi.org/10.1038/s42003-018-0199-z
State	Published - Dec 1 2018

ASJC Scopus subject areas

Medicine (miscellaneous)
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

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Kalbfleisch, T. S., Rice, E. S., DePriest, M. S., Walenz, B. P., Hestand, M. S., Vermeesch, J. R., O′Connell, B. L., Fiddes, I. T., Vershinina, A. O., Saremi, N. F., Petersen, J. L., Finno, C. J., Bellone, R. R., McCue, M. E., Brooks, S. A., Bailey, E., Orlando, L., Green, R. E., Miller, D. C., ... MacLeod, J. N. (2018). Improved reference genome for the domestic horse increases assembly contiguity and composition. Communications biology, 1(1), Article 197. https://doi.org/10.1038/s42003-018-0199-z

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', Communications biology, vol. 1, no. 1, 197. https://doi.org/10.1038/s42003-018-0199-z

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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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AU - Orlando, Ludovic

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

Abstract

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