Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

• Publication year

  2017

• Venue

  Nature Genetics

• Publication date

  2017-03-06

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/ng.3802PMID 28263316PMCID PMC5909822
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

  2016cited by this paper
• Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data

  2016cited by this paper
• Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

  2016cited by this paper
• Long-read sequence assembly of the gorilla genome

  2016cited by this paper
• Phased diploid genome assembly with single-molecule real-time sequencing

  2016cited by this paper
• BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

  2016cited by this paper
• StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

  2015cited by this paper
• Assembly and diploid architecture of an individual human genome via single-molecule technologies

  2015cited by this paper
• Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

  2015cited by this paper
• Genetic variation and the de novo assembly of human genomes

  2015cited by this paper
• BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

  2015cited by this paper
• Design and Characterization of a 52K SNP Chip for Goats

  2014cited by this paper
• Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

  2014cited by this paper
• Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

  2014cited by this paper
• Definition of the Cattle Killer Cell Ig–like Receptor Gene Family: Comparison with Aurochs and Human Counterparts

  2014cited by this paper
• Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

  2014cited by this paper
• Comparative genomic data of the Avian Phylogenomics Project

  2014cited by this paper
• SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

  2014cited by this paper
• Trimmomatic: a flexible trimmer for Illumina sequence data

  2014cited by this paper
• Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

  2014cited by this paper
• Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

  2014cited by this paper
• Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

  2014cited by this paper
• Kraken: ultrafast metagenomic sequence classification using exact alignments

  2014cited by this paper
• Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

  2013cited by this paper
• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

  2013cited by this paper
• Characterizing and measuring bias in sequence data

  2013cited by this paper
• Reducing assembly complexity of microbial genomes with single-molecule sequencing

  2013cited by this paper
• Comprehensive genotyping of the USA national maize inbred seed bank

  2013cited by this paper
• High-throughput genome scaffolding from in-vivo DNA interaction frequency

  2013cited by this paper
• Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

  2013cited by this paper
• Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

  2013cited by this paper
• Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

  2013cited by this paper
• Reassessing the Determinants of Breeding Synchrony in Ungulates

  2012cited by this paper
• Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

  2012cited by this paper
• A whole-genome radiation hybrid panel for goat

  2012cited by this paper
• Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

  2012cited by this paper
• Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

  2012cited by this paper
• Haplotype-based variant detection from short-read sequencing

  2012cited by this paper
• Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

  2012cited by this paper
• Hybrid error correction and de novo assembly of single-molecule sequencing reads

  2012cited by this paper
• LUMPY: a probabilistic framework for structural variant discovery

  2012cited by this paper
• Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

  2011cited by this paper
• Rapid whole genome optical mapping of Plasmodium falciparum

  2011cited by this paper
• Copy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogaster

  2011cited by this paper
• Assembly of large genomes using second-generation sequencing.

  2010cited by this paper
• Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites

  2010cited by this paper
• The sheep genome reference sequence: a work in progress.

  2010cited by this paper
• Real-time DNA sequencing from single polymerase molecules.

  2010cited by this paper
• The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

  2009cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009cited by this paper
• A whole-genome assembly of the domestic cow, Bos taurus

  2009cited by this paper
• Development and Characterization of a High Density SNP Genotyping Assay for Cattle

  2009cited by this paper
• Spontaneous mapping of number and space in adults and young children.

  2009cited by this paper
• Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

  2009cited by this paper
• Q-band karyotype of the goat (Capra hircus) and the relation between goat and bovine Q-bands.

  2009cited by this paper
• Real-Time DNA Sequencing from Single Polymerase Molecules

  2009cited by this paper
• Scaffolding and validation of bacterial genome assemblies using optical restriction maps

  2008cited by this paper
• Genome assembly forensics: finding the elusive mis-assembly

  2008cited by this paper
• The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

  2008cited by this paper
• Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes.

  2008cited by this paper
• Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

  2007cited by this paper
• A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences

  2006cited by this paper
• Versatile and open software for comparing large genomes

  2004cited by this paper
• Theoretical and practical advances in genome halving

  2004cited by this paper
• Finishing the euchromatic sequence of the human genome

  2004cited by this paper
• Finishing the euchromatic sequence of the human genome

  2004cited by this paper
• Finishing the euchromatic sequence of the human genome

  2004cited by this paper
• Hierarchical scaffolding with Bambus.

  2003cited by this paper
• Capturing Chromosome Conformation

  2002cited by this paper
• Initial sequencing and analysis of the human genome

  2001cited by this paper
• BIOINFORMATICS APPLICATIONS NOTE

  2001cited by this paper
• A whole-genome assembly of Drosophila.

  2000cited by this paper
• Base-calling of automated sequencer traces using phred. II. Error probabilities.

  1998cited by this paper
• Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

  1998cited by this paper
• Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

  1995cited by this paper
• Chromosomal evolution in bovids: a comparison of cattle, sheep and goat G- and R-banded chromosomes and cytogenetic divergences among cattle, goat and river buffalo sex chromosomes

  1995cited by this paper
• Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping.

  1993cited by this paper

• Phylogenomic analysis of Cervidae provides insights into antler origin and evolution.

  2026cites this paper
• Distribution and shared evolutionary history of the Fumonisin and AAL toxin biosynthetic gene clusters

  2026cites this paper
• Chromosome-scale genome assembly and annotation of the water monitor lizard, Varanus salvator.

  2026cites this paper
• Epigenetic and transcriptional profiling of secondary hair follicle stem cells during cashmere growth.

  2026cites this paper
• Effects of Age on Slaughter Performance and Meat Quality of Shanbei White Cashmere Goat and Optimization of Slaughter Strategies.

  2026cites this paper
• Genome characteristics and identification of reproduction-related genes in Southwest meat goats.

  2026cites this paper
• Genome scan for runs of homozygosity in Saanen goats selected under tropical environments reveals candidate genes for adaptive and production traits

  2025cites this paper
• Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies

  2025cites this paper
• Several variants on chromosome 10 are associated with coarse hair diameter in Dazu black goats (Capra hircus).

  2025cites this paper
• Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes

  2025cites this paper
• Whole-genome survey information revealed the genome characteristics, mitochondrial genome diversity and evolutionary patterns of Stomatopoda species

  2025cites this paper
• Capsular polysaccharide of Mycoplasma mycoides subsp. capri contributes to phenotypic diversity promoting distinctive immune responses

  2025influential citation
• Inbreeding and population structure in the Swedish Landrace goat and a signature of selection in the region of the casein genes

  2025cites this paper
• Whole-genome sequencing and variants data of 304 indigenous goats from Southwest China

  2025cites this paper
• The unique morphological basis and repeated evolutionary origins of personate flowers in Penstemon

  2025cites this paper
• A genome-wide study of ruminants uncovers two endogenous retrovirus families recently active in goats

  2025cites this paper
• Genomic and Molecular Mechanisms of Goat Environmental Adaptation

  2025cites this paper
• Multi-level regulation of hindgut homeostasis by volatile fatty acid administration in dairy goats: linking microbial metabolism to epithelial inflammation and barrier function

  2025cites this paper
• Phenotypic, transcriptomic, and genomic analyses reveal the spatiotemporal patterns and associated genes of coarse hair density in goats

  2025cites this paper
• A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium

  2025cites this paper
• Genomic Tools for Medicinal Properties of Goat Milk for Cosmetic and Health Benefits: A Narrative Review

  2025influential citation
• The expression of genes in different sites of gut tract regulates the meat quality of semitendinosus muscle in sheep and goats

  2025cites this paper
• Whole-genome sequencing reveals complex structural variations at a major locus linked to pigmented spot sizes in Tianfu goats

  2025cites this paper
• The variability of goat microRNA genes is strongly shaped by functional constraints

  2025cites this paper
• Nanopore sequencing in veterinary medicine: from concepts to clinical applications

  2025cites this paper
• SimGBS: a rapid method for simulating large-scale genotyping-by-sequencing data

  2025cites this paper
• Inferring Domestic Goat Demographic History Through Ancient Genome Imputation

  2025influential citation
• A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

  2025cites this paper
• Old Goats: 3,000 years of genetic connectivity of the domestic goat in Ireland

  2025cites this paper
• Genome-Wide Inference of Essential Genes in Dirofilaria immitis Using Machine Learning

  2025cites this paper
• Investigation of selection signatures of dairy goats using whole-genome sequencing data

  2025cites this paper
• A chromosome-level genome assembly of Termitomyces fuliginosus using Oxford Nanopore and Hi-C sequencing.

  2025cites this paper
• Genomic advancements in goat breeding: enhancing productivity, disease resistance, and sustainability in India’s rural economy

  2025cites this paper
• Potential SNPs and candidate genes influencing growth characteristics in Pakistani Beetal goat identified by GWAS analysis

  2025cites this paper
• Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination

  2025cites this paper
• Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection

  2025cites this paper
• Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences

  2025cites this paper
• Spatial variation and associated genes of total hair follicle density in goats

  2025cites this paper
• Whole-genome sequencing resources of 301 indigenous Tibetan sheep from the Himalayan region

  2025cites this paper
• The Metabolome in Different Sites of Gut Tract Regulates the Meat Quality of Longissimus Dorsi Muscle

  2025cites this paper
• Population structure and genome-wide association study of body conformation traits of two native goat breeds in China

  2025cites this paper
• Genomic Advancements in Assessing Growth Performance, Meat Quality, and Carcass Characteristics of Goats in Sub-Saharan Africa: A Systematic Review

  2025influential citation
• Chromosome-length genome assembly of the critically endangered Mountain bongo (Tragelaphus eurycerus isaaci): a resource for conservation and comparative genomics

  2025cites this paper
• Multi-level genomic convergence of secondary aquatic adaptation in marine mammals

  2025cites this paper
• Genomic Dissection of Chinese Yangtze River Delta White Goat Based on Whole Genome Sequencing

  2025cites this paper
• The unique morphological basis and parallel evolutionary history of personate flowers in Penstemon

  2024cites this paper
• Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations

  2024cites this paper
• Chromosome-level dairy goat genome reveals the regulatory landscape of lactation.

  2024cites this paper
• Examination of homozygosity runs and selection signatures in native goat breeds of Henan, China

  2024cites this paper
• Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits

  2024cites this paper
• Identification of novel cattle (Bos taurus) genes and biological insights of their function in pre-implantation embryo development

  2024cites this paper
• A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation

  2024cites this paper
• Structural Variations in Oil Crops: Types, and Roles on Domestication and Breeding

  2024cites this paper
• Chromosome-level genome assembly of the cashmere goat

  2024cites this paper
• Computational Identification of Milk Trait Regulation Through Transcription Factor Cooperation in Murciano-Granadina Goats

  2024cites this paper
• Genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)

  2024influential citation
• The transcriptional landscape underlying larval development and metamorphosis in the Malabar grouper (Epinephelus malabaricus)

  2024cites this paper
• Investigating the footprint of post-domestication dispersal on the diversity of modern European, African and Asian goats

  2024influential citation
• Application of Pan-Omics Technologies in Research on Important Economic Traits for Ruminants

  2024cites this paper
• The Evolution and Role of Molecular Tools in Measuring Diversity and Genomic Selection in Livestock Populations (Traditional and Up-to-Date Insights): A Comprehensive Exploration

  2024cites this paper
• A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats

  2024cites this paper
• The goat pan-genome reveals patterns of gene loss during domestication

  2024cites this paper
• North American pitseed goosefoot (Chenopodium berlandieri) is a genetic resource to improve Andean quinoa (C. quinoa)

  2024cites this paper
• Genomic regions underlying variation in wattles, horns, and supernumerary teats phenotypes in Egyptian goats

  2024cites this paper
• Identification of nonsense variants in the genomes of 15 Murciano-Granadina bucks and analysis of their segregation in parent-offspring trios.

  2024cites this paper
• Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

  2024cites this paper
• Ganoderma lucidum: Insights on host range, diagnosis, and management strategies

  2024cites this paper
• Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance

  2024cites this paper
• Identification of novel genes in cattle (Bos taurus) and biological insights into their function in embryo development

  2024cites this paper
• The African introgression of Murciano Granadina goats has a Moroccan origin and displays remarkable levels of inter-individual variability.

  2024cites this paper
• Chromosome-scale genome assembly of Lepus oiostolus (Lepus, Leporidae)

  2024cites this paper
• Whole-genome resource sequences of 57 indigenous Ethiopian goats

  2024influential citation
• A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families

  2024cites this paper
• QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules

  2024cites this paper
• Constructing a draft Indian cattle pangenome using short-read sequencing

  2024cites this paper
• Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U‐genome for wheat improvement

  2024cites this paper
• Chromosome-scale scaffolding of the fungus gnat genome (Diptera: Bradysia coprophila)

  2024cites this paper
• Chromosome-level genome assembly and annotation of rare and endangered tropical bivalve, Tridacna crocea

  2024cites this paper
• The landscape of long non-coding RNA expression in the goat brain.

  2024cites this paper
• Genetic Basis and Evolutionary Forces of Sexually Dimorphic Color Variation in a Toad-Headed Agamid Lizard

  2024cites this paper
• Gene expression profiles in specific skeletal muscles and meat quality characteristics of sheep and goats

  2024cites this paper
• A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation

  2024cites this paper
• The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

  2024cites this paper
• A chromosome-level genome assembly of the Peruvian Algarrobo (Neltuma pallida) provides insights on its adaptation to its unique ecological niche

  2024cites this paper
• Genome-Wide Association Study of Body Conformation Traits in Tashi Goats (Capra hircus)

  2024influential citation
• Extensive population structure highlights an apparent paradox of stasis in the impala (Aepyceros melampus)

  2024influential citation
• De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore

  2024cites this paper
• Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats

  2024cites this paper
• Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

  2024cites this paper
• Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression

  2024cites this paper
• Multiomic meta-analysis suggests a correlation between steroid hormone-related genes and litter size in goats.

  2024cites this paper
• Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus

  2024cites this paper
• The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish

  2023cites this paper
• Chromosome-level genome assembly for the angiosperm Silene conica

  2023cites this paper
• A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

  2023cites this paper
• The African Goat Improvement Network: a scientific group empowering smallholder farmers

  2023cites this paper
• Efficient Management of Database Resources in Large-Scale Data Centers

  2023cites this paper
• Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae

  2023cites this paper
• Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus

  2023cites this paper
• Characterization and profiling of the microRNA in small extracellular vesicles isolated from goat milk samples collected during the first week postpartum

  2023cites this paper