Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs and structural variants, as well as 137.02-Mb sequences harboring 1737 protein-coding genes that were absent in the reference assembly, revealing variants left by selection. Our results illustrate the power of whole-genome de novo sequencing relative to resequencing and provide valuable genetic resources that enable effective use of pigs in both agricultural production and biomedical research.
Why don't pigs get diabetes? Explanations for variations in diabetes susceptibility in human populations living in a diabetogenic environment
A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly
Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape
Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat
Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing
Considerations on pig models for appetite, metabolic syndrome and obese type 2 diabetes: From food intake to metabolic disease
Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds
Absence of a human ortholog of rodent Kupffer cell galactose-binding receptor encoded by the CLEC4f gene
Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement
Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle
The porcine translational research database: a manually curated, genomics and proteomics-based research resource
Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction
The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcγR) in the Göttingen minipig
A Western-Type Dietary Pattern Induces an Atherogenic Gene Expression Profile in the Coronary Arteries of the Ossabaw Pig
Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs
Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization
Deep Genome Resequencing Reveals Artificial and Natural Selection for Visual Deterioration, Plateau Adaptability and High Prolificacy in Chinese Domestic Sheep
Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data
PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene.
Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of Meishan Pigs by Whole Genome Sequencing.
New Gene Markers Expressed in Porcine Oviductal Epithelial Cells Cultured Primary In Vitro Are Involved in Ontological Groups Representing Physiological Processes of Porcine Oocytes.
The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication.
Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs (Sus-scrofa).
The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size.
Human-mediated admixture and selection shape the diversity on the modern swine (Sus scrofa) Y chromosomes.
Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads.
Auditory perception is the ability to receive and interpret information attained by the ears. Here is the latest research on factors and underlying mechanisms that influence auditory perception.