Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing
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Title
Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing
Authors
Keywords
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Journal
MOLECULAR ECOLOGY
Volume 25, Issue 10, Pages 2117-2129
Publisher
Wiley
Online
2016-03-04
DOI
10.1111/mec.13601
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Note: Only part of the references are listed.- Harnessing the power of RADseq for ecological and evolutionary genomics
- (2016) Kimberly R. Andrews et al. NATURE REVIEWS GENETICS
- Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications
- (2015) Lei Huang et al. Annual Review of Genomics and Human Genetics
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- (2015) Aleksander Siger et al. INDUSTRIAL CROPS AND PRODUCTS
- Effects of Crossovers Between Homeologs on Inheritance and Population Genomics in Polyploid-Derived Salmonid Fishes
- (2015) F. W. Allendorf et al. JOURNAL OF HEREDITY
- Don't throw the baby out with the bathwater: identifying and mapping paralogs in salmonids
- (2015) France Dufresne Molecular Ecology Resources
- Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)
- (2015) R. K. Waples et al. Molecular Ecology Resources
- An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)
- (2015) G. J. McKinney et al. Molecular Ecology Resources
- Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids
- (2015) Paul D. Blischak et al. Molecular Ecology Resources
- Polyploidy can drive rapid adaptation in yeast
- (2015) Anna M. Selmecki et al. NATURE
- Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data
- (2015) Morten T. Limborg et al. G3-Genes Genomes Genetics
- SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops
- (2015) Josh P. Clevenger et al. G3-Genes Genomes Genetics
- Conservation Genetics and Genomics of Amphibians and Reptiles
- (2015) H. Bradley Shaffer et al. Annual Review of Animal Biosciences
- A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
- (2015) Jarrod A Chapman et al. GENOME BIOLOGY
- SNP Discovery in Complex Allotetraploid Genomes (Gossypiumspp., Malvaceae) Using Genotyping by Sequencing
- (2015) Carla Jo Logan-Young et al. Applications in Plant Sciences
- Advances in plant chromosome genomics
- (2014) Jaroslav Doležel et al. BIOTECHNOLOGY ADVANCES
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- Extensive Local Gene Duplication and Functional Divergence among Paralogs in Atlantic Salmon
- (2014) Ian A. Warren et al. Genome Biology and Evolution
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- (2014) Alicia Mastretta-Yanes et al. Genome Biology and Evolution
- Genome-Wide Patterns of Genetic Polymorphism and Signatures of Selection in Plasmodium vivax
- (2014) Omar E. Cornejo et al. Genome Biology and Evolution
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- (2014) Morten T. Limborg et al. JOURNAL OF HEREDITY
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- First Haploid Genetic Map Based on Microsatellite Markers in Senegalese Sole (Solea senegalensis, Kaup 1858)
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- The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout
- (2014) Y. Palti et al. Molecular Ecology Resources
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- (2014) Peng Xu et al. NATURE GENETICS
- The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei
- (2014) Eric B. Rondeau et al. PLoS One
- A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification
- (2014) D. J. Macqueen et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
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- (2014) Marine S. O. Brieuc et al. G3-Genes Genomes Genetics
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- (2012) Pierre-Alexandre Gagnaire et al. MOLECULAR ECOLOGY
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- (2012) Benjamin C. Hecht et al. MOLECULAR ECOLOGY
- Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach
- (2012) Jesse A. Poland et al. PLoS One
- A RAD Tag Derived Marker Based Eggplant Linkage Map and the Location of QTLs Determining Anthocyanin Pigmentation
- (2012) Lorenzo Barchi et al. PLoS One
- Genotyping-by-Sequencing for Plant Breeding and Genetics
- (2012) Jesse A. Poland et al. Plant Genome
- Methods for generating triploid green sea urchin embryos: An initial step in producing triploid adults for land-based and near-shore aquaculture
- (2011) S. Anne Böttger et al. AQUACULTURE
- Genotype calling in tetraploid species from bi-allelic marker data using mixture models
- (2011) Roeland E Voorrips et al. BMC BIOINFORMATICS
- Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley
- (2011) Yada Chutimanitsakun et al. BMC GENOMICS
- A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns
- (2011) Sigbjørn Lien et al. BMC GENOMICS
- Extent and scale of local adaptation in salmonid fishes: review and meta-analysis
- (2011) D J Fraser et al. HEREDITY
- Genome duplication in amphibians and fish: an extended synthesis
- (2011) B. K. Mable et al. JOURNAL OF ZOOLOGY
- Genome-wide genetic marker discovery and genotyping using next-generation sequencing
- (2011) John W. Davey et al. NATURE REVIEWS GENETICS
- Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism
- (2011) Simon W. Baxter et al. PLoS One
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- (2011) I. Mayrose et al. SCIENCE
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- (2010) Lars Gidskehaug et al. BIOINFORMATICS
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- Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids
- (2010) J. E. SEEB et al. Molecular Ecology Resources
- Evolutionary consequences of autopolyploidy
- (2010) Christian Parisod et al. NEW PHYTOLOGIST
- Rapid spread of invasive genes into a threatened native species
- (2010) Benjamin M. Fitzpatrick et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
- (2010) Paul A. Hohenlohe et al. PLoS Genetics
- Light-Dependent Transcriptional Regulation of Genes of Biogeochemical Interest in the Diploid and Haploid Life Cycle Stages of Emiliania huxleyi
- (2009) S. Richier et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Hybridization rapidly reduces fitness of a native trout in the wild
- (2009) C. C. Muhlfeld et al. Biology Letters
- A review of the need and possible uses for genetically standardized Atlantic salmon (Salmo salar) in research
- (2009) U Grimholt et al. LABORATORY ANIMALS
- Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation
- (2009) JÜRGEN TOMIUK et al. Molecular Ecology Resources
- Effective population size and patterns of molecular evolution and variation
- (2009) Brian Charlesworth NATURE REVIEWS GENETICS
- Introgression of fitness genes across a ploidy barrier
- (2009) Mark A. Chapman et al. NEW PHYTOLOGIST
- Homoeologous recombination in allopolyploids: the polyploid ratchet
- (2009) Robert T. Gaeta et al. NEW PHYTOLOGIST
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