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EquCab3, an Updated Reference Genome for the Domestic Horse

https://doi.org/10.1101/306928
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ijc.30120openalex-snapshot
Host genetic influence on papillomavirus‐induced tumors in the horse
inferredcites →https://doi.org/10.1002/ijc.30744openalex-snapshot
A missense mutation in damage‐specific DNA binding protein 2 is a genetic risk factor for limbal squamous cell carcinoma in horses
inferredcites →https://doi.org/10.1016/0378-1119(94)90713-7openalex-snapshot
The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region
inferredcites →https://doi.org/10.1016/j.joca.2011.01.011openalex-snapshot
Brother of CDO (BOC) expression in equine articular cartilage
inferredcites →https://doi.org/10.1073/pnas.1416991111openalex-snapshot
Prehistoric genomes reveal the genetic foundation and cost of horse domestication
inferredcites →https://doi.org/10.1073/pnas.1513696112openalex-snapshot
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments
inferredcites →https://doi.org/10.1089/cmb.2006.13.1028openalex-snapshot
A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bti310openalex-snapshot
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btn548openalex-snapshot
Aggressive assembly of pyrosequencing reads with mates
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot
Quality control and preprocessing of metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt476openalex-snapshot
The MaSuRCA genome assembler
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.123356.111openalex-snapshot
Cactus: Algorithms for genome multiple sequence alignment
inferredcites →https://doi.org/10.1101/gr.193474.115openalex-snapshot
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
inferredcites →https://doi.org/10.1101/gr.233460.117openalex-snapshot
Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
inferredcites →https://doi.org/10.1111/age.12717openalex-snapshot
Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project
inferredcites →https://doi.org/10.1111/j.1365-2052.2010.02116.xopenalex-snapshot
Pleiotropic effects of pigmentation genes in horses
inferredcites →https://doi.org/10.1111/j.1365-2052.2010.02118.xopenalex-snapshot
Structural annotation of equine protein‐coding genes determined by mRNA sequencing
inferredcites →https://doi.org/10.1126/science.1168594openalex-snapshot
The Earliest Horse Harnessing and Milking
inferredcites →https://doi.org/10.1126/science.1178158openalex-snapshot
Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.287.5461.2196openalex-snapshot
A Whole-Genome Assembly of Drosophila
inferredcites →https://doi.org/10.1126/science.aam5298openalex-snapshot
Ancient genomic changes associated with domestication of the horse
inferredcites →https://doi.org/10.1126/science.aao3297openalex-snapshot
Ancient genomes revisit the ancestry of domestic and Przewalski’s horses
inferredcites →https://doi.org/10.1159/000151313openalex-snapshot
A 4,103 marker integrated physical and comparative map of the horse genome
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12864-017-3943-8openalex-snapshot
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
inferredcites →https://doi.org/10.1186/s13059-015-0728-8openalex-snapshot
Bipartite structure of the inactive mouse X chromosome
inferredcites →https://doi.org/10.1186/s13104-016-1900-2openalex-snapshot
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
inferredcites →https://doi.org/10.1371/journal.pgen.1000909openalex-snapshot
Whole-Genome SNP Association in the Horse: Identification of a Deletion in Myosin Va Responsible for Lavender Foal Syndrome
inferredcites →https://doi.org/10.1371/journal.pgen.1002451openalex-snapshot
A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies
inferredcites →https://doi.org/10.1371/journal.pgen.1003211openalex-snapshot
Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds
inferredcites →https://doi.org/10.1371/journal.pgen.1006467openalex-snapshot
Allelic Variation in CXCL16 Determines CD3+ T Lymphocyte Susceptibility to Equine Arteritis Virus Infection and Establishment of Long-Term Carrier State in the Stallion
inferredcites →https://doi.org/10.1371/journal.pone.0078280openalex-snapshot
Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse
inferredcites →https://doi.org/10.1371/journal.pone.0124375openalex-snapshot
Annotation of the Protein Coding Regions of the Equine Genome
inferredcites →https://doi.org/10.1371/journal.pone.0126852openalex-snapshot
Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.therwi.2023.100055openalex-snapshot
Genomic insights into southern white rhinoceros (Ceratotherium simum simum) reproduction: Revealing granulosa cell gene expression
inferred← citeshttps://doi.org/10.1016/j.tvjl.2025.106347openalex-snapshot
Exploring the genetic influences on equine analgesic efficacy through genome-wide association analysis of ranked pain responses
inferred← citeshttps://doi.org/10.1038/s41598-019-53102-8openalex-snapshot
Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse
inferred← citeshttps://doi.org/10.1038/s41598-024-57872-8openalex-snapshot
Predicted genetic burden and frequency of phenotype-associated variants in the horse
inferred← citeshttps://doi.org/10.1080/1828051x.2026.2626608openalex-snapshot
The genome-wide legacy of Baroque horse breeds
inferred← citeshttps://doi.org/10.1101/2021.07.28.453868openalex-snapshot
Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed
inferred← citeshttps://doi.org/10.1101/482315openalex-snapshot
Mountain lion genomes provide insights into genetic rescue of inbred populations
inferred← citeshttps://doi.org/10.1111/age.12753openalex-snapshot
Comprehensive characterization of horse genome variation by whole‐genome sequencing of 88 horses
inferred← citeshttps://doi.org/10.1111/tan.15387openalex-snapshot
Diversity of major histocompatibility complex ( MHC ) and natural killer cell receptor ( NKR ) genes and their interactions in domestic horses
inferred← citeshttps://doi.org/10.1186/s12917-024-04139-zopenalex-snapshot
Preliminary investigation of potential links between pigmentation variants and opioid analgesic effectiveness in horses during cerebrospinal fluid centesis
inferred← citeshttps://doi.org/10.1371/journal.pgen.1011285openalex-snapshot
An endothelial regulatory module links blood pressure regulation with elite athletic performance
inferred← citeshttps://doi.org/10.1371/journal.ppat.1009254openalex-snapshot
Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease
inferred← citeshttps://doi.org/10.17520/biods.2020005openalex-snapshot
The origins and genetic characteristics of domestic horses
inferred← citeshttps://doi.org/10.21203/rs.3.rs-21956/v1openalex-snapshot
Whole-genome sequencing of a Brazilian naturalized horse breed resistant to arid climate for identifying single nucleotide variants and insertions/deletions
inferred← citeshttps://doi.org/10.21203/rs.3.rs-6975941/v1openalex-snapshot
Deciphering the transcription regulation of bovine papillomavirus (BPV)-associated equine sarcoids through OMIC integrated approach
inferred← citeshttps://doi.org/10.3389/fgene.2018.00278openalex-snapshot
RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
inferred← citeshttps://doi.org/10.3389/fgene.2021.758366openalex-snapshot
Genetic Variation and the Distribution of Variant Types in the Horse
inferred← citeshttps://doi.org/10.3390/ani10081310openalex-snapshot
Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information
inferred← citeshttps://doi.org/10.3390/ani12111435openalex-snapshot
Copy Number Variation (CNV): A New Genomic Insight in Horses
inferred← citeshttps://doi.org/10.3390/ani12151958openalex-snapshot
A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus)
inferred← citeshttps://doi.org/10.3390/ani15121705openalex-snapshot
Identification of Two Genetic Haplotypes Associated with the Roan Coat Color in the American Quarter Horse and Other Equine Breeds
inferred← citeshttps://doi.org/10.3390/genes10070503openalex-snapshot
Landscape of Overlapping Gene Expression in The Equine Placenta
inferred← citeshttps://doi.org/10.3390/genes10120976openalex-snapshot
Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines
inferred← citeshttps://doi.org/10.3390/genes11111378openalex-snapshot
The Genetic Basis of Obesity and Related Metabolic Diseases in Humans and Companion Animals
inferred← citeshttps://doi.org/10.3390/genes12101501openalex-snapshot
A Novel QTL and a Candidate Gene Are Associated with the Progressive Motility of Franches-Montagnes Stallion Spermatozoa after Thaw
inferred← citeshttps://doi.org/10.3390/ijms241511947openalex-snapshot
Standardization of a Sex-Sorting Protocol for Stallion Spermatozoa by Means of Absolute RT-qPCR
inferred← citeshttps://doi.org/10.3390/life12111893openalex-snapshot
The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research
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