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

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

146 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
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

Bibliographical note

Publisher Copyright:
© 2018, The Author(s).

Funding

This work was supported by Morris Animal Foundation Grant D15EQ-019 and the NRPS8 Horse Genome Coordinator Fund. E.S.R. is an ARCS scholar. Support for C.J.F. was provided by the National Institutes of Health (NIH) (1K01OD015134 and L40 TR001136). The FAANG data (C.J.F, J.L.P., R.R.B.) was generated with the support of the Grayson Jockey Club Foundation. Alignment and assembly work for this project were performed on the University of Louisville Cardinal Research Cluster. The authors are grateful to Mr. Harrison Simrall for his assistance in installing and running many of the applications used in this work. We also wish to thank Wim Meert for PacBio runs and library preparations, and Peter A. Schweitzer who prepared the libraries for the 10× Genomics data generated for the project. Finally, we would like to thank Drs. Tomas Bergström, Sofia Mikko, Agnes Viluma, Göran Andersson, and Petr Horin for their insightful review of the MHC locus for this assembly.

Funders	Funder number
NRPS8 Horse Genome Coordinator Fund
National Institutes of Health (NIH)	L40 TR001136
National Institutes of Health (NIH)
NIH Office of the Director	K01OD015134
NIH Office of the Director
Morris Animal Foundation	D15EQ-019
Morris Animal Foundation

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

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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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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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AU - Brooks, Samantha A.

AU - Bailey, Ernest

AU - Orlando, Ludovic

AU - Green, Richard E.

AU - Miller, Donald C.

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

Abstract

Bibliographical note

Funding

ASJC Scopus subject areas

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