Copy number variation and disease resistance in plants

Copy number variations ofCBFgenes at theFr-A2locus are essential components of winter hardiness in wheat

(2017) Tobias Würschum et al.   PLANT JOURNAL

Copy Number Variation in Acetolactate Synthase Genes of Thifensulfuron-Methyl Resistant Alopecurus aequalis (Shortawn Foxtail) Accessions in Japan

(2017) Satoshi Iwakami et al.   Frontiers in Plant Science

MLPA-Based Analysis of Copy Number Variation in Plant Populations

(2017) Anna Samelak-Czajka et al.   Frontiers in Plant Science

The impact and origin of copy number variations in the Oryza species

(2016) Zetao Bai et al.   BMC GENOMICS

Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location

(2016) Agnieszka Zmienko et al.   BMC GENOMICS

Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation

(2016) Sara Pinosio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

(2016) Michael A. Hardigan et al.   PLANT CELL

Copy number variation of CBF-A14 at the Fr-A2 locus determines frost tolerance in winter durum wheat

(2016) Alisa-Naomi Sieber et al.   THEORETICAL AND APPLIED GENETICS

The pangenome of an agronomically important crop plant Brassica oleracea

(2016) Agnieszka A. Golicz et al.   Nature Communications

Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies

(2016) Chunhua Wei et al.   PLoS One

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat

(2015) Tobias Würschum et al.   BMC GENETICS

The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh

(2015) James Boocock et al.   BMC GENOMICS

Virus disease in wheat predicted to increase with a changing climate

(2015) Piotr Trębicki et al.   GLOBAL CHANGE BIOLOGY

Evolution and selection ofRhg1,a copy-number variant nematode-resistance locus

(2015) Tong Geon Lee et al.   MOLECULAR ECOLOGY

High-throughput genotyping for species identification and diversity assessment in germplasm collections

(2015) Annaliese S. Mason et al.   Molecular Ecology Resources

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

(2015) María Muñoz-Amatriaín et al.   PLANT JOURNAL

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

(2015) Philipp E. Bayer et al.   THEORETICAL AND APPLIED GENETICS

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

Whole-genome CNV analysis: advances in computational approaches

(2015) Mehdi Pirooznia et al.   Frontiers in Genetics

Changes in Variable Number of Tandem Repeats in ‘Candidatus Liberibacter asiaticus’ through Insect Transmission

(2015) Hiroshi Katoh et al.   PLoS One

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries

(2014) Alexandre Gillet-Markowska et al.   BIOINFORMATICS

Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone

(2014) K. Trappe et al.   BIOINFORMATICS

Copy number variation detection using next generation sequencing read counts

(2014) Heng Wang et al.   BMC BIOINFORMATICS

Paleo-evolutionary plasticity of plant disease resistance genes

(2014) Rongzhi Zhang et al.   BMC GENOMICS

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage

(2014) Ke Lin et al.   BMC GENOMICS

Structural variations in plant genomes

(2014) R. K. Saxena et al.   Briefings in Functional Genomics

A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes

(2014) Jessica Dalton-Morgan et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Unraveling Genomic Complexity at a Quantitative Disease Resistance Locus in Maize

(2014) Tiffany M. Jamann et al.   GENETICS

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Glyphosate resistance: state of knowledge

(2014) Robert Douglas Sammons et al.   PEST MANAGEMENT SCIENCE

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data

(2014) Hoang T. Nguyen et al.   Frontiers in Genetics

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels

(2013) Tobias Marschall et al.   BIOINFORMATICS

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

Genome-wide copy number variations in Oryza sativa L.

(2013) Ping Yu et al.   BMC GENOMICS

Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae

(2013) Xiao Lin et al.   BMC GENOMICS

The Standing Pool of Genomic Structural Variation in a Natural Population of Mimulus guttatus

(2013) Lex E. Flagel et al.   Genome Biology and Evolution

An MLPA-Based Strategy for Discrete CNV Genotyping: CNV-miRNAs as an Example

(2013) Malgorzata Marcinkowska-Swojak et al.   HUMAN MUTATION

Identifying the Genome-Wide Sequence Variations and Developing New Molecular Markers for Genetics Research by Re-Sequencing a Landrace Cultivar of Foxtail Millet

(2013) Hui Bai et al.   PLoS One

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

(2013) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Copy number polymorphism in plant genomes

(2013) Agnieszka Żmieńko et al.   THEORETICAL AND APPLIED GENETICS

Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches

(2013) Haley J. Abel et al.   Cancer Genetics

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

Hard Selective Sweep and Ectopic Gene Conversion in a Gene Cluster Affording Environmental Adaptation

(2013) Marc Hanikenne et al.   PLoS Genetics

Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes

(2012) Mingfu Zhu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants

(2012) Yue Jiang et al.   BIOINFORMATICS

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo et al.   BIOINFORMATICS

De novo detection of copy number variation by co-assembly

(2012) Jurgen F. Nijkamp et al.   BIOINFORMATICS

Copy number variation of individual cattle genomes using next-generation sequencing

(2012) D. M. Bickhart et al.   GENOME RESEARCH

Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time

(2012) Hidetaka Nishida et al.   MOLECULAR BREEDING

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

De novo mutations in human genetic disease

(2012) Joris A. Veltman et al.   NATURE REVIEWS GENETICS

A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation

(2012) Yiyuan Li et al.   NEW PHYTOLOGIST

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Plant disease resistance genes: Current status and future directions

(2012) Mayank Anand Gururani et al.   PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY

Current analysis platforms and methods for detecting copy number variation

(2012) Wenli Li et al.   PHYSIOLOGICAL GENOMICS

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

Copy Number Variation Affecting the Photoperiod-B1 and Vernalization-A1 Genes Is Associated with Altered Flowering Time in Wheat (Triticum aestivum)

(2012) Aurora Díaz et al.   PLoS One

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

RNA-Seq methods for imperfect samples: development, evaluation and applications

(2012)   GENOME BIOLOGY

Novel origins of copy number variation in the dog genome

(2012) Jonas Berglund et al.   GENOME BIOLOGY

Human Copy Number Variation and Complex Genetic Disease

(2011) Santhosh Girirajan et al.   Annual Review of Genetics

Detection of copy number variations in rice using array-based comparative genomic hybridization

(2011) Ping Yu et al.   BMC GENOMICS

A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog

(2011) Thomas J Nicholas et al.   BMC GENOMICS

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

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

(2011) P. Lu et al.   GENOME RESEARCH

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

(2011) E. Gazave et al.   GENOME RESEARCH

Mechanism of Resistance of Evolved Glyphosate-Resistant Palmer Amaranth (Amaranthus palmeri)

(2011) Todd A. Gaines et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

(2011) Y.-L. Guo et al.   PLANT PHYSIOLOGY

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

Copy number variation in the bovine genome

(2010) João Fadista et al.   BMC GENOMICS

Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales

(2010) Seth DeBolt   Genome Biology and Evolution

Analysis of copy number variations among diverse cattle breeds

(2010) G. E. Liu et al.   GENOME RESEARCH

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene–loci expression

(2010) M. Ortiz-Estevez et al.   GENOMICS

Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution

(2010) Suzanne Weaver et al.   METHODS

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

Copy number variation influences gene expression and metabolic traits in mice

(2009) Luz D. Orozco et al.   HUMAN MOLECULAR GENETICS

Higher Copy Numbers of the Potato RB Transgene Correspond to Enhanced Transcript and Late Blight Resistance Levels

(2009) James M. Bradeen et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Impact of segmental chromosomal duplications on leaf size in thegrandifolia-Dmutants ofArabidopsis thaliana

(2009) Gorou Horiguchi et al.   PLANT JOURNAL

A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean

(2009) P. David et al.   PLANT PHYSIOLOGY

Gene amplification confers glyphosate resistance in Amaranthus palmeri

(2009) T. A. Gaines et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

(2008) Marc Hanikenne et al.   NATURE

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication

(2008) Bin Cong et al.   NATURE GENETICS

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE