Supporting data for "De novo assembly of the cattle reference genome with single-molecule sequencing"

Dataset type: Genome-Mapping, Genomic, Transcriptomic
Data released on December 16, 2019

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 These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and suffers from a variety of deficiencies and inaccuracies.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.

Additional details

Read the peer-reviewed publication(s):


Additional information:

https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Bos_taurus/106/

Github links:

https://github.com/njdbickhart/CattleAssemblyScripts

Accessions (data generated as part of this study):

BioProject: PRJNA386670
BioProject: PRJNA434299
BioProject: PRJNA379574
BioProject: PRJNA263600
BioProject: PRJNA294306
BioProject: PRJNA305942
BioProject: PRJNA371462





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
206014020-W-Milk-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
206014056-W-Milk-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
207016597-W2-Blood-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
207016597-W2-Milk-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
208000916-W2-Blood-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
208000916-W2-Milk-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
208000940-W2-Blood-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
208000940-W2-Milk-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
208000943-W2-Blood-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
208000943-W2-Milk-RNA9913bovinecattleBos taurus Description:RNA extracted from female Bos taurus (...
Sex:female
Analyte type:RNA
...
+
Displaying 1-10 of 493 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive16.32 KB2019-11-26
GitHub archivearchive37.63 MB2019-11-26
readme.txtTEXT2.79 KB2019-12-16
Displaying 1-3 of 3 File(s).
Funding body Awardee Award ID Comments
National Institute of Food and Agriculture D M Bickhart 5090-31000-026-06-I
National Institute of Food and Agriculture R D Schnabel 2016-68004-24827
National Institute of Food and Agriculture R D Schnabel 2013-67015-21202
National Institute of Food and Agriculture R D Schnabel 2015-67015-23183
National Institutes of Health R D Schnabel 1R01HD084353-01A1
USDA Hatch R D Schnabel MO-HAAS0001
Biotechnology and Biological Sciences Research Council J A Hammond BB/M027155/1
Biotechnology and Biological Sciences Research Council J A Hammond BBS/E/I/00007035
Biotechnology and Biological Sciences Research Council J A Hammond BBS/E/I/000070358
Biotechnology and Biological Sciences Research Council J A Hammond BBS/E/I/00007039
USDA/NRSP8 Animal Genome T P L Smith
USDA ARS Meat Animal Research Center T P L Smith
Neogen T P L Smith, J F Medrano
Zoetis T P L Smith, J F Medrano
Date Action
December 16, 2019 Dataset publish
March 16, 2020 Manuscript Link added : 10.1093/gigascience/giaa021
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample HFD.33604.55206
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 Sample Attribute added : of Sample LJA 203
March 18, 2020 sample "LJA 203" appeared twice in the sample list once for each of two projects, CIH merged the two samples together including both BioProject IDs.