De novo assembly of the cattle reference genome with single-molecule sequencing

Authors: Rosen, Benjamin - Ben; Bickhart, Derek; SCHNABEL, ROBERT - University Of Missouri; KOREN, SERGEY - National Institutes Of Health (NIH); ELSIK, CHRISTINE - University Of Missouri; TSENG, ELIZABETH - Pacific Biosciences Inc; ROWAN, TROY - University Of Missouri; LOW, WAI - University Of Adelaide; ZIMIN, ALEKSEY - Johns Hopkins University; COULDREY, CHRISTINE - Collaborator; HALL, RICHARD - Pacific Biosciences Inc; Li, Wenli; RHIE, ARANG - National Institutes Of Health (NIH); GHURYE, JAY - University Of Maryland; MCKAY, STEPHANIE - University Of Vermont; THIBAUD-NISSEN, FRANCOISE - National Institutes Of Health (NIH); HOFFMAN, JINNA - National Institutes Of Health (NIH); MURDOCH, BRENDA - University Of Idaho; Snelling, Warren; McDaneld, Tara; HAMMOND, JOHN - The Pirbright Institute; SCHWARTZ, JOHN - The Pirbright Institute; NANDOLO, WILSON - Lilongwe University Of Agriculture And Natural Resources; HAGEN, DARREN - Oklahoma State University; DREISCHER, CHRISTIAN - Computomics Gmbh; SCHULTHEISS, SEBATIAN - Computomics Gmbh; Schroeder, Steven - Steve; PHILLIPPY, ADAM - National Institutes Of Health (NIH); Cole, John; Van Tassell, Curtis - Curt; Liu, Ge - George; Smith, Timothy - Tim; MEDRANO, JUAN - University Of California, Davis

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2020
Publication Date: 3/1/2020
Citation: Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M.,Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. 2020. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience. 9(3):1-9. https://doi.org/10.1093/gigascience/giaa021.
DOI: https://doi.org/10.1093/gigascience/giaa021

Interpretive Summary: Genomic tools have enabled major advances in the genetic improvement of cattle since the release of the cattle reference genome in 2004. These tools require an accurate and complete genome assembly. We have applied the latest DNA sequencing and scaffolding technologies to generate an improved reference genome for cattle, ARS-UCD1.2. We used the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version but have improved the genome quality many fold. We also generated data to more accurately define what genes are present in cattle. This data has been made publicly available through NCBI.

Technical Abstract: Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and suffers from a variety of deficiencies and inaccuracies. We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb, and is >250x more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.