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Spontaneous mutations and transmission distortions of genic copy number variants shape the standing genetic variation in Picea glauca

https://doi.org/10.1101/103796
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1 of the 94 references listed on this page is in the Retraction Watch database as retracted (export 2026-10-28): 10.7554/elife.12248 (notice 2018-04-12).

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

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PlatinumCNV: A Bayesian Gaussian mixture model for genotyping copy number polymorphisms using SNP array signal intensity data
inferredcites →https://doi.org/10.1007/s00122-013-2177-7openalex-snapshot
Copy number polymorphism in plant genomes
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Characterization of a knock-out mutation at the Gc2 locus in wheat
inferredcites →https://doi.org/10.1007/s00438-011-0648-6openalex-snapshot
Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses
inferredcites →https://doi.org/10.1007/s00439-012-1257-0openalex-snapshot
Transmission ratio distortion: review of concept and implications for genetic association studies
inferredcites →https://doi.org/10.1016/j.asr.2013.05.004openalex-snapshot
Differential gene expression patterns in white spruce newly formed tissue on board the International Space Station
inferredcites →https://doi.org/10.1016/j.cell.2012.11.043openalex-snapshot
Gene Copy-Number Alterations: A Cost-Benefit Analysis
inferredcites →https://doi.org/10.1016/j.cub.2009.11.061openalex-snapshot
Transcription-Dependent Cytosine Deamination Is a Novel Mechanism in Ultraviolet Light-Induced Mutagenesis
inferredcites →https://doi.org/10.1016/j.cub.2011.01.026openalex-snapshot
High Spontaneous Rate of Gene Duplication in Caenorhabditis elegans
inferredcites →https://doi.org/10.1016/j.molcel.2014.10.020openalex-snapshot
Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability
inferredcites →https://doi.org/10.1016/j.sbi.2008.02.005openalex-snapshot
The current excitement about copy-number variation: how it relates to gene duplications and protein families
inferredcites →https://doi.org/10.1016/j.semcancer.2010.05.007openalex-snapshot
Genomic rearrangements in inherited disease and cancer
inferredcites →https://doi.org/10.1016/j.ygeno.2012.10.004openalex-snapshot
Molecular methods for genotyping complex copy number polymorphisms
inferredcites →https://doi.org/10.1017/cbo9781107415324.004openalex-snapshot
An Ichthyosaurus (Reptilia, Ichthyosauria) with gastric contents from Charmouth, England:first report of the genus from the Pliensbachian
inferredcites →https://doi.org/10.1023/a:1022308414864openalex-snapshot
Common Features of Segregation Distortion in Plants and Animals
inferredcites →https://doi.org/10.1038/ejhg.2012.188openalex-snapshot
Utilizing extended pedigree information for discovery and confirmation of copy number variable regions among Mexican Americans
inferredcites →https://doi.org/10.1038/embor.2012.165openalex-snapshot
Genomic evidence for elevated mutation rates in highly expressed genes
inferredcites →https://doi.org/10.1038/hdy.1984.78openalex-snapshot
Variation in spontaneous mutation and repair in natural population lines of Drosophila melanogaster
inferredcites →https://doi.org/10.1038/hdy.2011.64openalex-snapshot
Complex genetic nature of sex-independent transmission ratio distortion in Asian rice species: the involvement of unlinked modifiers and sex-specific mechanisms
inferredcites →https://doi.org/10.1038/hdy.2013.34openalex-snapshot
An improvement on the maximum likelihood reconstruction of pedigrees from marker data
inferredcites →https://doi.org/10.1038/nature05329openalex-snapshot
Global variation in copy number in the human genome
inferredcites →https://doi.org/10.1038/nature06742openalex-snapshot
Genotype, haplotype and copy-number variation in worldwide human populations
inferredcites →https://doi.org/10.1038/nature08516openalex-snapshot
Origins and functional impact of copy number variation in the human genome
inferredcites →https://doi.org/10.1038/nature09708openalex-snapshot
Mapping copy number variation by population-scale genome sequencing
inferredcites →https://doi.org/10.1038/nature12211openalex-snapshot
The Norway spruce genome sequence and conifer genome evolution
inferredcites →https://doi.org/10.1038/ng.2007.19openalex-snapshot
Recurrent DNA copy number variation in the laboratory mouse
inferredcites →https://doi.org/10.1038/ng2080openalex-snapshot
Copy-number variation and association studies of human disease
inferredcites →https://doi.org/10.1038/nrg2149openalex-snapshot
Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability
inferredcites →https://doi.org/10.1038/nrg2158openalex-snapshot
Mutation rate variation in multicellular eukaryotes: causes and consequences
inferredcites →https://doi.org/10.1038/sj.hdy.6801066openalex-snapshot
Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus
inferredcites →https://doi.org/10.1046/j.1525-142x.2001.003002073.xopenalex-snapshot
Bias in the introduction of variation as an orienting factor in evolution
inferredcites →https://doi.org/10.1073/pnas.0803466105openalex-snapshot
A genome-wide view of the spectrum of spontaneous mutations in yeast
inferredcites →https://doi.org/10.1093/bfgp/elu016openalex-snapshot
Structural variations in plant genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btm091openalex-snapshot
Enhancements and modifications of primer design program Primer3
inferredcites →https://doi.org/10.1093/bioinformatics/btt178openalex-snapshot
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data
inferredcites →https://doi.org/10.1093/gbe/evq033openalex-snapshot
Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales
inferredcites →https://doi.org/10.1093/gbe/evr066openalex-snapshot
The Lower Bound to the Evolution of Mutation Rates
inferredcites →https://doi.org/10.1093/genetics/153.1.415openalex-snapshot
Meiotic Drive of Chromosomal Knobs Reshaped the Maize Genome
inferredcites →https://doi.org/10.1093/genetics/154.1.333openalex-snapshot
A Genetic Test to Determine the Origin of Maternal Transmission Ratio Distortion: Meiotic Drive at the Mouse Om Locus
inferredcites →https://doi.org/10.1093/hmg/ddp541openalex-snapshot
Population-genetic nature of copy number variations in the human genome
inferredcites →https://doi.org/10.1093/jhered/89.3.197openalex-snapshot
RAPD Genome maps of Douglas-fir
inferredcites →https://doi.org/10.1093/molbev/msw161openalex-snapshot
Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation
inferredcites →https://doi.org/10.1093/nar/30.9.e36openalex-snapshot
Relative expression software tool (REST(C)) for group-wise comparison and statistical analysis of relative expression results in real-time PCR
inferredcites →https://doi.org/10.1093/nar/gkm234openalex-snapshot
OligoCalc: an online oligonucleotide properties calculator
inferredcites →https://doi.org/10.1093/nar/gks596openalex-snapshot
Primer3—new capabilities and interfaces
inferredcites →https://doi.org/10.1093/oso/9780195135848.001.0001openalex-snapshot
Molecular Evolution and Phylogenetics
inferredcites →https://doi.org/10.1098/rspb.2005.3304openalex-snapshot
Mitosis, stature and evolution of plant mating systems: low-Φ and high-Φ plants
inferredcites →https://doi.org/10.1101/gr.107680.110openalex-snapshot
De novo rates and selection of large copy number variation
inferredcites →https://doi.org/10.1101/gr.109165.110openalex-snapshot
Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
inferredcites →https://doi.org/10.1101/gr.122614.111openalex-snapshot
Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
inferredcites →https://doi.org/10.1101/gr.127522.111openalex-snapshot
Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis
inferredcites →https://doi.org/10.1101/gr.177659.114openalex-snapshot
Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations
inferredcites →https://doi.org/10.1104/pp.112.194605openalex-snapshot
Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes
inferredcites →https://doi.org/10.1104/pp.114.248708openalex-snapshot
Insights into Conifer Giga-Genomes
inferredcites →https://doi.org/10.1111/1755-0998.12062openalex-snapshot
Development of high‐density SNP genotyping arrays for white spruce ( P icea glauca) and transferability to subtropical and nordic congeners
inferredcites →https://doi.org/10.1111/j.1365-313x.2012.05087.xopenalex-snapshot
Changes in genome content generated via segregation of non‐allelic homologs
inferredcites →https://doi.org/10.1111/j.1755-0998.2009.02787.xopenalex-snapshot
COLONY: a program for parentage and sibship inference from multilocus genotype data
inferredcites →https://doi.org/10.1111/tpj.12886openalex-snapshot
Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism
inferredcites →https://doi.org/10.1126/science.1098918openalex-snapshot
Large-Scale Copy Number Polymorphism in the Human Genome
inferredcites →https://doi.org/10.1126/science.1136678openalex-snapshot
Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes
inferredcites →https://doi.org/10.1126/science.1180677openalex-snapshot
The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana
inferredcites →https://doi.org/10.1126/science.1193063openalex-snapshot
Hybrid Incompatibility “Snowballs” Between Solanum Species
inferredcites →https://doi.org/10.1146/annurev.ecolsys.37.091305.110215openalex-snapshot
Some Evolutionary Consequences of Being a Tree
inferredcites →https://doi.org/10.1186/1471-2148-12-86openalex-snapshot
Variation of presence/absence genes among Arabidopsis populations
inferredcites →https://doi.org/10.1186/1471-2164-12-372openalex-snapshot
Detection of copy number variations in rice using array-based comparative genomic hybridization
inferredcites →https://doi.org/10.1186/1471-2164-13-434openalex-snapshot
Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression
inferredcites →https://doi.org/10.1186/1471-2164-14-124openalex-snapshot
Massive screening of copy number population-scale variation in Bos taurus genome
inferredcites →https://doi.org/10.1186/1471-2164-15-1048openalex-snapshot
Genomic selection accuracies within and between environments and small breeding groups in white spruce
inferredcites →https://doi.org/10.1186/1472-6750-9-75openalex-snapshot
Evaluation of the impact of single nucleotide polymorphisms and primer mismatches on quantitative PCR
inferredcites →https://doi.org/10.1186/gb-2002-3-2-reviews0003openalex-snapshot
Exploring prokaryotic diversity in the genomic era.
inferredcites →https://doi.org/10.1186/gb-2002-3-7-research0034openalex-snapshot
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
inferredcites →https://doi.org/10.1186/gb-2007-8-10-r228openalex-snapshot
Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization
inferredcites →https://doi.org/10.1186/s12864-016-3458-8openalex-snapshot
CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation
inferredcites →https://doi.org/10.1242/dev.01595openalex-snapshot
Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis
inferredcites →https://doi.org/10.1371/journal.pbio.1001115openalex-snapshot
A Novel Sperm-Delivered Toxin Causes Late-Stage Embryo Lethality and Transmission Ratio Distortion in C. elegans
inferredcites →https://doi.org/10.1371/journal.pgen.1004830openalex-snapshot
Extensive Copy-Number Variation of Young Genes across Stickleback Populations
inferredcites →https://doi.org/10.1371/journal.pgen.1004850openalex-snapshot
A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2
inferredcites →https://doi.org/10.1371/journal.pone.0068822openalex-snapshot
GStream: Improving SNP and CNV Coverage on Genome-Wide Association Studies
inferredcites →https://doi.org/10.1534/g3.113.008714openalex-snapshot
A High-Density Gene Map of Loblolly Pine (Pinus taedaL.) Based on Exome Sequence Capture Genotyping
inferredcites →https://doi.org/10.1534/g3.116.030890openalex-snapshot
Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life
inferredcites →https://doi.org/10.1534/genetics.103.022343openalex-snapshot
Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana
inferredcites →https://doi.org/10.1534/genetics.104.032789openalex-snapshot
A Novel Meiotic Drive Locus Almost Completely Distorts Segregation in Mimulus (Monkeyflower) Hybrids
inferredcites →https://doi.org/10.1534/genetics.105.052977openalex-snapshot
The Hitchhiking Effect of an Autosomal Meiotic Drive Gene
inferredcites →https://doi.org/10.1534/genetics.106.065508openalex-snapshot
Low Impact of Germline Transposition on the Rate of Mildly Deleterious Mutation in Caenorhabditis elegans
inferredcites →https://doi.org/10.1534/genetics.108.090126openalex-snapshot
The Evolution of Sex-Independent Transmission Ratio Distortion Involving Multiple Allelic Interactions at a Single Locus in Rice
inferredcites →https://doi.org/10.1534/genetics.108.100214openalex-snapshot
Parentage and Sibship Inference From Multilocus Genotype Data Under Polygamy
inferredcites →https://doi.org/10.1534/genetics.113.151670openalex-snapshot
Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster
inferredcites →https://doi.org/10.1534/genetics.113.152561openalex-snapshot
Investigating Incipient Speciation in Arabidopsis lyrata from Patterns of Transmission Ratio Distortion
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3389/fgene.2013.00273openalex-snapshot
Copy-number changes in evolution: rates, fitness effects and adaptive significance
inferredcites →https://doi.org/10.3389/fpls.2011.00105openalex-snapshot
Preferential Repair of the Transcribed DNA Strand in Plants
inferredcites →https://doi.org/10.5860/choice.47-2566openalex-snapshot
Conifer reproductive biology
inferredcites →https://doi.org/10.7554/elife.12248openalex-snapshot
RETRACTED: A mathematical model explains saturating axon guidance responses to molecular gradients
inferredcites →https://doi.org/10.7554/elife.13087openalex-snapshot
Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots
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