Cited by 857Genomics and Phylogenetic StudiesGenetic and phenotypic traits in livestockGenomic variations and chromosomal abnormalities

The DOI matches its Crossref record; 32 of the 35 references it cites were found in a registry or an index, and 1 are not checked yet.

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

Open access

Rosen, Benjamin D, Bickhart, Derek M, Schnabel, Robert D, Koren, Sergey, Elsik, Christine G, Tseng, Elizabeth, Rowan, Troy N, Low, Wai Y, Zimin, Aleksey, Couldrey, Christine, Hall, Richard, Li, Wenli, Rhie, Arang, Ghurye, Jay, McKay, Stephanie D, Thibaud-Nissen, Françoise, Hoffman, Jinna, Murdoch, Brenda M, Snelling, Warren M, McDaneld, Tara G, Hammond, John A, Schwartz, John C, Nandolo, Wilson, Hagen, Darren E, Dreischer, Christian, Schultheiss, Sebastian J, Schroeder, Steven G, Phillippy, Adam M, Cole, John B, Van Tassell, Curtis P, Liu, George, Smith, Timothy P L, Medrano, Juan F·2020·GigaScience

DOI 10.1093/gigascience/giaa021PMC PMC7081964

Open this paper in CoChat — free account Open PDF

Abstract

BACKGROUND: 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 These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. RESULTS: 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 >250× 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. CONCLUSIONS: We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/gigascience/giaa021

Cites

32 of 33 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 11,200
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEMPreprint
Li, H. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1303.3997 · Cited by 10,846
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J. R., Young, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112963 · Cited by 9,130
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,260
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEMPreprint
Li, H. (2014) · arXiv (Cornell University) · doi:10.6084/m9.figshare.963153.v1 · Cited by 5,155
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chin, C.-S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,029
Haplotype-based variant detection from short-read sequencing
Garrison, E., & Marth, G. (2012) · arXiv · doi:10.48550/arxiv.1207.3907 · Cited by 3,700

Flagged first, then by citations

Show all 35 references

2 of the 35 references couldn’t be matched to a known paper.

Research works printed but not linked: 1

Null, 2019, Using the ARS-UCD1.2 reference genome in U.S. evaluations, Interbull Bull, 55, 30

Sorted by citations

Items 601–700 of 857

Additional file 10 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040699
Additional file 2 of Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population
do Bem, R. D., Benfica, L. F., Silva, D. A., Carrara, E. R., Brito, L. F., Mulim, H. A., Borges, M. S., Cyrillo, J. N. D. S. G., Canesin, R. C., Bonilha, S. F. M., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26410026
Additional file 4 of Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds
Friedrich, J., Bailey, R. I., Talenti, A., Chaudhry, U., Ali, Q., Obishakin, E. F., Ezeasor, C., Powell, J., Hanotte, O., Tijjani, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26654056
Additional file 2 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
Schmidtmann, C., Schönherz, A. A., Guldbrandtsen, B., Marjanovic, J., Calus, M., Hinrichs, D., & Thaller, G. (2021) · Figshare · doi:10.6084/m9.figshare.14176192
Additional file 6 of Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome
Hermisdorff, Í. D. C., Costa, R. B., de Albuquerque, L. G., Pausch, H., & Kadri, N. K. (2020) · Figshare · doi:10.6084/m9.figshare.13212659
Additional file 2 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2024) · Figshare · doi:10.6084/m9.figshare.26590973
Additional file 2 of Using expression data to fine map QTL associated with fertility in dairy cattle
van den Berg, I., Chamberlain, A. J., MacLeod, I. M., Nguyen, T. V., Goddard, M. E., Xiang, R., Mason, B., Meier, S., Phyn, C. V. C., Burke, C. R., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26730391
Additional file 2 of Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
Rafter, P., Gormley, I. C., Purfield, D. C., Parnell, A. C., Naderi, S., & Berry, D. P. (2021) · Figshare · doi:10.6084/m9.figshare.16863880
Additional file 3 of Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance
Cai, Z., Iso‐Touru, T., Sanchez, M.-P., Kadri, N. K., Bouwman, A. C., Chitneedi, P., MacLeod, I. M., Vander-Jagt, C. J., Chamberlain, A. J., Gredler, B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26749229
Additional file 2 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
Marrella, M. A., & Biase, F. H. (2024) · Figshare · doi:10.6084/m9.figshare.26582306
Additional file 3 of Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds
Friedrich, J., Bailey, R. I., Talenti, A., Chaudhry, U., Ali, Q., Obishakin, E. F., Ezeasor, C., Powell, J., Hanotte, O., Tijjani, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26654053
Additional file 26 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040765
Additional file 2 of Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle
Low, W. Y., Rosen, B. D., Ren, Y., Bickhart, D. M., To, T., Martin, F. J., Billis, K., Sonstegard, T. S., Sullivan, S. T., Hiendleder, S., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19711493
Additional file 2 of Profiling the immune epigenome across global cattle breeds
Powell, J., Talenti, A., Fisch, A., Hemmink, J. D., Paxton, E. A., Toye, P. G., Santos, I., Ferreira, B. R., Connelley, T., Morrison, L. J., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26591009
Additional file 5 of Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
Neumann, G. B., Korkuć, P., Reißmann, M., Wolf, M. J., May, K., König, S., & Brockmann, G. A. (2024) · Figshare · doi:10.6084/m9.figshare.26628532
Additional file 1 of Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
Neumann, G. B., Korkuć, P., Reißmann, M., Wolf, M. J., May, K., König, S., & Brockmann, G. A. (2024) · Figshare · doi:10.6084/m9.figshare.26628520
Additional file 1 of Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds
Harish, A., Lopes-Pinto, F., Eriksson, S., & Johansson, A. M. (2024) · Figshare · doi:10.6084/m9.figshare.25045381
Additional file 4 of Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals
Mulim, H. A., Brito, L. F., Pinto, L. F. B., Ferraz, J. B. S., Grigoletto, L., Silva, M. R., & Pedrosa, V. B. (2022) · Figshare · doi:10.6084/m9.figshare.19367525
Additional file 11 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040702
Additional file 1 of An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle
Keogh, K. A., Kenny, D. A., Alexandre, P. A., McGee, M., & Reverter, A. (2024) · Figshare · doi:10.6084/m9.figshare.25341233
Additional file 12 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040705
Additional file 2 of Allele-specific binding variants causing ChIP-seq peak height of histone modification are not enriched in expression QTL annotations
Ghoreishifar, M., Chamberlain, A. J., Xiang, R., Prowse-Wilkins, C., Lopdell, T., Littlejohn, M. D., Pryce, J. E., & Goddard, M. E. (2024) · Figshare · doi:10.6084/m9.figshare.26122862
Additional file 4 of Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle
Benfica, L. F., Brito, L. F., do Bem, R. D., Mulim, H. A., Glessner, J., Braga, L. G., Gloria, L. S., Cyrillo, J. N. D. S. G., Bonilha, S. F. M., & Mercadante, M. E. Z. (2024) · Figshare · doi:10.6084/m9.figshare.26666671
Additional file 19 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040732
Additional file 16 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040723
Additional file 6 of Using expression data to fine map QTL associated with fertility in dairy cattle
van den Berg, I., Chamberlain, A. J., MacLeod, I. M., Nguyen, T. V., Goddard, M. E., Xiang, R., Mason, B., Meier, S., Phyn, C. V. C., Burke, C. R., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26730403
Additional file 4 of Using expression data to fine map QTL associated with fertility in dairy cattle
van den Berg, I., Chamberlain, A. J., MacLeod, I. M., Nguyen, T. V., Goddard, M. E., Xiang, R., Mason, B., Meier, S., Phyn, C. V. C., Burke, C. R., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26730397
Additional file 5 of Variants at the ASIP locus contribute to coat color darkening in Nellore cattle
Trigo, B. B., Utsunomiya, A. T. H., Fortunato, A. A. A. D., Milanesi, M., Torrecilha, R. B. P., Lamb, H. J., Nguyen, L. T., Ross, E. M., Hayes, B. J., Padula, R. C. M., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14509518
Additional file 7 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040687
Additional file 14 of Long-range linkage disequilibrium in French beef cattle breeds
Hou, A. E., Rocha, D., Venot, É., Blanquet, V., & Philippe, R. (2021) · Figshare · doi:10.6084/m9.figshare.15047770
Additional file 5 of Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome
Hermisdorff, Í. D. C., Costa, R. B., de Albuquerque, L. G., Pausch, H., & Kadri, N. K. (2020) · Figshare · doi:10.6084/m9.figshare.13212656
Additional file 2 of The genomes of precision edited cloned calves show no evidence for off-target events or increased de novo mutagenesis
Jivanji, S., Harland, C., Cole, S., Brophy, B., Garrick, D. J., Snell, R., Littlejohn, M. D., & Laible, G. (2021) · Figshare · doi:10.6084/m9.figshare.14803985
Additional file 1 of Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome
Hermisdorff, Í. D. C., Costa, R. B., de Albuquerque, L. G., Pausch, H., & Kadri, N. K. (2020) · Figshare · doi:10.6084/m9.figshare.13212644
Additional file 1 of Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle
Tiplady, K., Lopdell, T., Reynolds, E., Sherlock, R. G., Keehan, M., Johnson, T., Pryce, J., Davis, S. R., Spelman, R. J., Harris, B. L., et al. (2021) · Figshare · doi:10.6084/m9.figshare.15026536
Additional file 3 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2024) · Figshare · doi:10.6084/m9.figshare.26590976
Additional file 4 of Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success
Häfliger, I. M., Seefried, F. R., Spengeler, M., & Drögemüller, C. (2021) · Figshare · doi:10.6084/m9.figshare.17254349
Additional file 1 of Investigation of rumen long noncoding RNA before and after weaning in cattle
Marceau, A., Gao, Y., Baldwin, R. L., Li, C.-J., Jiang, J., Liu, G. E., & Ma, L. (2022) · Figshare · doi:10.6084/m9.figshare.20363582
Additional file 3 of A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application
Grant, J. R., Herman, E. K., Barlow, L. D., Miglior, F., Schenkel, F. S., Baes, C. F., & Stothard, P. (2024) · Figshare · doi:10.6084/m9.figshare.27140575
Additional file 1 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2024) · Figshare · doi:10.6084/m9.figshare.26590970
Additional file 2 of Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery
Crysnanto, D., & Pausch, H. (2020) · Figshare · doi:10.6084/m9.figshare.12726521
Additional file 3 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
Somenzi, E., Partel, E., Barbato, M., Osorio, A. M. C., Colli, L., Franceschi, N., Mantovani, R., Pilla, F., Komjanc, M., Achilli, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26714986
Additional file 7 of Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
Poisson, W., Prunier, J., Carrier, A., Gilbert, I., Mastromonaco, G., Albert, V., Taillon, J., Bourret, V., Droit, A., Côté, S. D., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22621960
Additional file 2 of Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle
Benfica, L. F., Brito, L. F., do Bem, R. D., Mulim, H. A., Glessner, J., Braga, L. G., Gloria, L. S., Cyrillo, J. N. D. S. G., Bonilha, S. F. M., & Mercadante, M. E. Z. (2024) · Figshare · doi:10.6084/m9.figshare.24987966
Additional file 6 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
Somenzi, E., Partel, E., Barbato, M., Osorio, A. M. C., Colli, L., Franceschi, N., Mantovani, R., Pilla, F., Komjanc, M., Achilli, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26714995
Additional file 2 of Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
Neumann, G. B., Korkuć, P., Reißmann, M., Wolf, M. J., May, K., König, S., & Brockmann, G. A. (2024) · Figshare · doi:10.6084/m9.figshare.26628523
Additional file 13 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040711
Additional file 3 of Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
Neumann, G. B., Korkuć, P., Reißmann, M., Wolf, M. J., May, K., König, S., & Brockmann, G. A. (2024) · Figshare · doi:10.6084/m9.figshare.26628526
Additional file 27 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040768
Additional file 3 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
Marrella, M. A., & Biase, F. H. (2024) · Figshare · doi:10.6084/m9.figshare.26582309
Additional file 1 of Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population
do Bem, R. D., Benfica, L. F., Silva, D. A., Carrara, E. R., Brito, L. F., Mulim, H. A., Borges, M. S., Cyrillo, J. N. D. S. G., Canesin, R. C., Bonilha, S. F. M., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26409864
Additional file 3 of Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle
Tiplady, K., Lopdell, T., Reynolds, E., Sherlock, R. G., Keehan, M., Johnson, T., Pryce, J. E., Davis, S. R., Spelman, R. J., Harris, B. L., et al. (2021) · Figshare · doi:10.6084/m9.figshare.15026542
Additional file 7 of Using expression data to fine map QTL associated with fertility in dairy cattle
van den Berg, I., Chamberlain, A. J., MacLeod, I. M., Nguyen, T. V., Goddard, M. E., Xiang, R., Mason, B., Meier, S., Phyn, C. V. C., Burke, C. R., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26730406
Additional file 1 of Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance
Cai, Z., Iso‐Touru, T., Sanchez, M.-P., Kadri, N. K., Bouwman, A. C., Chitneedi, P., MacLeod, I. M., Vander-Jagt, C. J., Chamberlain, A. J., Gredler, B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26308951
Additional file 5 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
Mulim, H. A., Pedrosa, V. B., Pinto, L. F. B., Tiezzi, F., Maltecca, C., Schenkel, F. S., & Brito, L. F. (2024) · Figshare · doi:10.6084/m9.figshare.26754166
Additional file 5 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
Somenzi, E., Partel, E., Barbato, M., Osorio, A. M. C., Colli, L., Franceschi, N., Mantovani, R., Pilla, F., Komjanc, M., Achilli, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26714992
Additional file 8 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
Somenzi, E., Partel, E., Barbato, M., Osorio, A. M. C., Colli, L., Franceschi, N., Mantovani, R., Pilla, F., Komjanc, M., Achilli, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26715001
Additional file 4 of Congenital syndromic Chiari-like malformation (CSCM) in Holstein cattle: towards unravelling of possible genetic causes
Jacinto, J. G. P., Letko, A., Häfliger, I. M., Drögemüller, C., & Agerholm, J. S. (2024) · Figshare · doi:10.6084/m9.figshare.26743274
Additional file 1 of Congenital syndromic Chiari-like malformation (CSCM) in Holstein cattle: towards unravelling of possible genetic causes
Jacinto, J. G. P., Letko, A., Häfliger, I. M., Drögemüller, C., & Agerholm, J. S. (2024) · Figshare · doi:10.6084/m9.figshare.26743265
Additional file 3 of Profiling the immune epigenome across global cattle breeds
Powell, J., Talenti, A., Fisch, A., Hemmink, J. D., Paxton, E. A., Toye, P. G., Santos, I. K. F. D. M., Ferreira, B. R., Connelley, T., Morrison, L. J., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26591012
Additional file 17 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040726
Additional file 6 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
Mulim, H. A., Pedrosa, V. B., Pinto, L. F. B., Tiezzi, F., Maltecca, C., Schenkel, F. S., & Brito, L. F. (2024) · Figshare · doi:10.6084/m9.figshare.26754169
Additional file 4 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
Mulim, H. A., Pedrosa, V. B., Pinto, L. F. B., Tiezzi, F., Maltecca, C., Schenkel, F. S., & Brito, L. F. (2024) · Figshare · doi:10.6084/m9.figshare.26754163
Additional file 3 of An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle
Keogh, K. A., Kenny, D. A., Alexandre, P. A., McGee, M., & Reverter, A. (2024) · Figshare · doi:10.6084/m9.figshare.26688248
Additional file 1 of Profiling the immune epigenome across global cattle breeds
Powell, J., Talenti, A., Fisch, A., Hemmink, J. D., Paxton, E. A., Toye, P. G., Santos, I., Ferreira, B. R., Connelley, T., Morrison, L. J., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26591006
Additional file 1 of Breed identification using breed-informative SNPs and machine learning based on whole genome sequence data and SNP chip data
Zhao, C., Wang, D., Teng, J., Yang, C., Zhang, X., Wei, X., & Zhang, Q. (2024) · Figshare · doi:10.6084/m9.figshare.26591489
Additional file 2 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
Mulim, H. A., Pedrosa, V. B., Pinto, L. F. B., Tiezzi, F., Maltecca, C., Schenkel, F. S., & Brito, L. F. (2024) · Figshare · doi:10.6084/m9.figshare.26384707
Additional file 9 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
Marrella, M. A., & Biase, F. H. (2024) · Figshare · doi:10.6084/m9.figshare.26582327
Additional file 9 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2024) · Figshare · doi:10.6084/m9.figshare.26590994
Additional file 1 of Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle
Low, W. Y., Rosen, B. D., Ren, Y., Bickhart, D. M., To, T., Martin, F. J., Billis, K., Sonstegard, T. S., Sullivan, S. T., Hiendleder, S., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19711490
Additional file 5 of Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle
Lam, S., Zeidan, J., Miglior, F., Suárez‐Vega, A., Gómez-Redondo, I., Fonseca, P. A. S., Guan, L. L., Waters, S., & Cánovas, Á. (2020) · Figshare · doi:10.6084/m9.figshare.13070941
Additional file 2 of Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle
Smith, J. L., Wilson, M. L., Nilson, S. M., Rowan, T. N., Schnabel, R. D., Decker, J. E., & Seabury, C. M. (2022) · Figshare · doi:10.6084/m9.figshare.20329753
Additional file 10 of Long-range linkage disequilibrium in French beef cattle breeds
Hou, A. E., Rocha, D., Venot, É., Blanquet, V., & Philippe, R. (2021) · Figshare · doi:10.6084/m9.figshare.15047755
Additional file 1 of Effect of enhanced plane of nutrition in early life on the transcriptome and proteome of the anterior pituitary gland in Angus heifer calves
Keogh, K. A., Kelly, A. K., & Kenny, D. A. (2024) · Figshare · doi:10.6084/m9.figshare.26488358
Additional file 1 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
Marrella, M. A., & Biase, F. H. (2024) · Figshare · doi:10.6084/m9.figshare.26582303
Additional file 4 of The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle
Lloret‐Villas, A., Pausch, H., & Leonard, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22807379
Additional file 3 of Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals
Mulim, H. A., Brito, L. F., Pinto, L. F. B., Ferraz, J. B. S., Grigoletto, L., Silva, M. R., & Pedrosa, V. B. (2022) · Figshare · doi:10.6084/m9.figshare.19367522
Additional file 3 of Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment
Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24159309
Additional file 15 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040720
Additional file 1 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
Mulim, H. A., Pedrosa, V. B., Pinto, L. F. B., Tiezzi, F., Maltecca, C., Schenkel, F. S., & Brito, L. F. (2024) · Figshare · doi:10.6084/m9.figshare.26384558
Additional file 1 of Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
Rafter, P., Gormley, I. C., Purfield, D. C., Parnell, A. C., Naderi, S., & Berry, D. P. (2021) · Figshare · doi:10.6084/m9.figshare.16863877
Additional file 8 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2024) · Figshare · doi:10.6084/m9.figshare.26590991
Additional file 2 of A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle
Corbeau, J., Grohs, C., Jourdain, J., Boussaha, M., Besnard, F., Barbat, A., Plassard, V., Rivière, J., Hamelin, C., Mortier, J. R., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25876307
Additional file 28 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040771
Additional file 2 of Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals
Mulim, H. A., Brito, L. F., Pinto, L. F. B., Ferraz, J. B. S., Grigoletto, L., Silva, M. R., & Pedrosa, V. B. (2022) · Figshare · doi:10.6084/m9.figshare.19367519
Additional file 2 of Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds
Harish, A., Lopes-Pinto, F., Eriksson, S., & Johansson, A. M. (2024) · Figshare · doi:10.6084/m9.figshare.25045654
Additional file 12 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
Schmidtmann, C., Schönherz, A. A., Guldbrandtsen, B., Marjanovic, J., Calus, M., Hinrichs, D., & Thaller, G. (2021) · Figshare · doi:10.6084/m9.figshare.14176183
Additional file 1 of Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery
Crysnanto, D., & Pausch, H. (2020) · Figshare · doi:10.6084/m9.figshare.12726518
Additional file 5 of Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle
Tiplady, K., Lopdell, T., Reynolds, E., Sherlock, R. G., Keehan, M., Johnson, T., Pryce, J. E., Davis, S. R., Spelman, R. J., Harris, B. L., et al. (2021) · Figshare · doi:10.6084/m9.figshare.15026548
Additional file 1 of Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide
Gao, Y., Li, J., Cai, G., Wang, Y., Yang, W., Li, Y., Zhao, X., Li, R., Gao, Y., Tuo, W., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19695933
Additional file 10 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2024) · Figshare · doi:10.6084/m9.figshare.26590997
Additional file 1 of A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application
Grant, J. R., Herman, E. K., Barlow, L. D., Miglior, F., Schenkel, F. S., Baes, C. F., & Stothard, P. (2024) · Figshare · doi:10.6084/m9.figshare.27140569
Additional file 1 of Single-step genome-wide association analyses of claw horn lesions in Holstein cattle using linear and threshold models
Li, B., Barden, M., Kapsona, V. V., Sánchez-Molano, E., Anagnostopoulos, A., Griffiths, B. E., Bedford, C., Dai, X., Coffey, M., Psifidi, A., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22626139
Additional file 5 of Congenital syndromic Chiari-like malformation (CSCM) in Holstein cattle: towards unravelling of possible genetic causes
Jacinto, J. G. P., Letko, A., Häfliger, I. M., Drögemüller, C., & Agerholm, J. S. (2024) · Figshare · doi:10.6084/m9.figshare.26743277
Additional file 8 of Using expression data to fine map QTL associated with fertility in dairy cattle
van den Berg, I., Chamberlain, A. J., MacLeod, I. M., Nguyen, T. V., Goddard, M. E., Xiang, R., Mason, B., Meier, S., Phyn, C. V. C., Burke, C. R., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26730409
Additional file 24 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
Wong, K., Abascal, F., Ludwig, L., Aupperle‐Lellbach, H., Grassinger, J. M., Wright, C. W., Allison, S. J., Pinder, E., Phillips, R. M., Romero, L. P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24040759
Additional file 6 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2024) · Figshare · doi:10.6084/m9.figshare.26590985
Additional file 1 of A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle
Corbeau, J., Grohs, C., Jourdain, J., Boussaha, M., Besnard, F., Barbat, A., Plassard, V., Rivière, J., Hamelin, C., Mortier, J. R., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25876240
Additional file 2 of Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle
Lam, S., Zeidan, J., Miglior, F., Suárez-Vega, A., Gómez-Redondo, I., Fonseca, P. A. S., Guan, L. L., Waters, S., & Cánovas, Á. (2020) · Figshare · doi:10.6084/m9.figshare.13070932
Additional file 1 of Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies
Ren, Y., Tseng, E., Smith, T. P. L., Hiendleder, S., Williams, J. L., & Low, W. Y. (2024) · Figshare · doi:10.6084/m9.figshare.26574904
Additional file 7 of Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds
Friedrich, J., Bailey, R. I., Talenti, A., Chaudhry, U., Ali, Q., Obishakin, E. F., Ezeasor, C., Powell, J., Hanotte, O., Tijjani, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26654065

Authors: 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.
Affiliations: Agricultural Research Service (US)
University of Missouri (US)
National Institutes of Health (US)
Pacific Biosciences (United States) (US)
The University of Adelaide (AU)
Johns Hopkins University (US)
Livestock Improvement Corporation (NZ)
University of Maryland, College Park (US)
University of Vermont (US)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894,
University of Idaho (US)
The Pirbright Institute (GB)
Lilongwe University of Agriculture and Natural Resources (MW)
Oklahoma State University (US)
Computomics GmbH , Christophstr. 32, 72072 Tübingen,
USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory , USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350,
University of California, Davis (US)
Corresponding author: Rosen, Benjamin D
Smith, Timothy P L
ORCID: Rosen, Benjamin D
Bickhart, Derek M
Schnabel, Robert D
Koren, Sergey
Elsik, Christine G
Tseng, Elizabeth
Rowan, Troy N
Low, Wai Y
Zimin, Aleksey
Couldrey, Christine
Hall, Richard
Li, Wenli
Rhie, Arang
Ghurye, Jay
McKay, Stephanie D
Murdoch, Brenda M
Snelling, Warren M
McDaneld, Tara G
Hammond, John A
Schwartz, John C
Nandolo, Wilson
Hagen, Darren E
Schultheiss, Sebastian J
Schroeder, Steven G
Phillippy, Adam M
Cole, John B
Van Tassell, Curtis P
Liu, George
Smith, Timothy P L
Medrano, Juan F
Venue: GigaScience
Publisher: Oxford University Press (OUP)
Published: 2020-03-01
Volume: 9
Issue: 3
ISSN: 2047-217X (ISSN-L)
DOI: 10.1093/gigascience/giaa021
PMC: PMC7081964
OpenAlex: W3011183076
Cited by: 802
References: 35
Citations by year: 2026: 84 · 2025: 102 · 2024: 165 · 2023: 145 · 2022: 125 · 2021: 120 · 2020: 59
FWCI: 37.47
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor, 18 d)
Locations: GigaScience (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
eScholarship (California Digital Library) (submittedVersion)
eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders: U.S. Department of Agriculture (8042-31000-001-00-D, 8042-31000-002-00-D, 5090-31000-026-00-D, 3040-31000-100-00-D)
National Institute of Food and Agriculture (5090-31000-026-06-I, 2016-68004-24827, 2013-67015-21202, MO-HAAS0001, 2015-67015-23183)
U.S. National Library of Medicine
National Institutes of Health
Biotechnology and Biological Sciences Research Council (BB/M027155/1, BBS/E/I/00007035, BBS/E/I/00007038, BBS/E/I/00007039)
National Human Genome Research Institute
Korea Health Industry Development Institute
Ministry of Health (HI17C2098)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Keywords: cattle, de novo genome assembly, single-molecule sequencing, genome annotation, cattle genomics
MeSH terms: RNA-Seq, Animals, Breeding, Cattle, Polymorphism, Genetic, Reference Standards, Genome, Sequence Analysis, DNA, Genomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks