A comprehensive analysis of copy number variations in diverse apple populations

[1]  Shizhong Xu,et al.  Graph pangenome captures missing heritability and empowers tomato breeding , 2022, Nature.

[2]  Maojun Wang,et al.  Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton , 2022, Communications Biology.

[3]  Z. Fei,et al.  Unraveling a Genetic Roadmap for Improved Taste in the Domesticated Apple. , 2021, Molecular Plant.

[4]  A. J. Higgins,et al.  Author Correction: Cycloalkane-modified amphiphilic polymers provide direct extraction of membrane proteins for CryoEM analysis , 2021, Communications biology.

[5]  Dong Zhang,et al.  Genome-wide identification of the 14–3-3 gene family and its participation in floral transition by interacting with TFL1/FT in apple , 2020, BMC Genomics.

[6]  W. Karłowski,et al.  AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome[OPEN] , 2020, Plant Cell.

[7]  B. Rosen,et al.  Detection of copy number variants in African goats using whole genome sequence data , 2020, BMC Genomics.

[8]  Ryan E. Mills,et al.  Structural variation in the sequencing era , 2019, Nature Reviews Genetics.

[9]  Y. Gibon,et al.  Regulation of Pyridine Nucleotide Metabolism During Tomato Fruit Development Through Transcript and Protein Profiling , 2019, Front. Plant Sci..

[10]  E. Mullaart,et al.  Functional and population genetic features of copy number variations in two dairy cattle populations , 2019, BMC Genomics.

[11]  P. Green,et al.  RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4 , 2019, Nucleic acids research.

[12]  C. Vernesi,et al.  A Multifaceted Overview of Apple Tree Domestication. , 2019, Trends in plant science.

[13]  Y. Kamatani,et al.  Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing , 2019, Genome Biology.

[14]  Xiaojia Hu,et al.  UV-C treatment promotes quality of early ripening apple fruit by regulating malate metabolizing genes during postharvest storage , 2019, PloS one.

[15]  C. Richards,et al.  A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour , 2019, Nature Communications.

[16]  C. Richards,et al.  A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour , 2019, Nature Communications.

[17]  M. Purugganan,et al.  Copy Number Variation in Domestication. , 2019, Trends in plant science.

[18]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v4: recent updates and new developments , 2019, Nucleic Acids Res..

[19]  Sanzhen Liu,et al.  Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize , 2018, Front. Plant Sci..

[20]  Z. Fei,et al.  Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement , 2017, Nature Communications.

[21]  E. van der Knaap,et al.  Fruit weight is controlled by Cell Size Regulator encoding a novel protein that is expressed in maturing tomato fruits , 2017, PLoS genetics.

[22]  J. Gouzy,et al.  High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development , 2017, Nature Genetics.

[23]  Q. Qian,et al.  Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice. , 2017, Molecular plant.

[24]  C. Cañestro,et al.  Evolution by gene loss , 2016, Nature Reviews Genetics.

[25]  Yuliya V. Karpievitch,et al.  Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation , 2016, bioRxiv.

[26]  Anil Kumar Singh,et al.  Comparative phylogenetic analysis and transcriptional profiling of MADS-box gene family identified DAM and FLC-like genes in apple (Malusx domestica) , 2016, Scientific Reports.

[27]  H. Kuang,et al.  Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies , 2016, PloS one.

[28]  T. Giraud,et al.  A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. , 2015, The Plant journal : for cell and molecular biology.

[29]  B. Stranger,et al.  The impact of human copy number variation on gene expression. , 2015, Briefings in functional genomics.

[30]  E. Septiningsih,et al.  A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice , 2015, Nature Plants.

[31]  T. Merriman,et al.  The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh , 2015, bioRxiv.

[32]  Q. Qian,et al.  Copy number variation at the GL7 locus contributes to grain size diversity in rice , 2015, Nature Genetics.

[33]  Shuai Li,et al.  Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber , 2015, Plant Cell.

[34]  Yuepeng Han,et al.  Comparative assessment of sugar and malic acid composition in cultivated and wild apples. , 2015, Food chemistry.

[35]  J. R. MacDonald,et al.  A copy number variation map of the human genome , 2015, Nature Reviews Genetics.

[36]  Ryan M. Layer,et al.  SpeedSeq: Ultra-fast personal genome analysis and interpretation , 2014, Nature Methods.

[37]  Rajeev K. Varshney,et al.  Structural variations in plant genomes , 2014, Briefings in functional genomics.

[38]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[39]  D. Skinner,et al.  Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat , 2014, Theoretical and Applied Genetics.

[40]  Lars Feuk,et al.  The Database of Genomic Variants: a curated collection of structural variation in the human genome , 2013, Nucleic Acids Res..

[41]  Qingguo Wang,et al.  Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives , 2013, BMC Bioinformatics.

[42]  Martin Dugas,et al.  RSVSim: an R/Bioconductor package for the simulation of structural variations , 2013, Bioinform..

[43]  Rod A Wing,et al.  Aluminum tolerance in maize is associated with higher MATE1 gene copy number , 2013, Proceedings of the National Academy of Sciences.

[44]  D. K. Willis,et al.  Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean , 2012, Science.

[45]  Riccardo Velasco,et al.  An Ancient Duplication of Apple MYB Transcription Factors Is Responsible for Novel Red Fruit-Flesh Phenotypes1[C][W] , 2012, Plant Physiology.

[46]  Ryan M. Layer,et al.  LUMPY: a probabilistic framework for structural variant discovery , 2012, Genome Biology.

[47]  T. Giraud,et al.  New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties , 2012, PLoS genetics.

[48]  Santhosh Girirajan,et al.  Human copy number variation and complex genetic disease. , 2011, Annual review of genetics.

[49]  M. Gerstein,et al.  CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. , 2011, Genome research.

[50]  Joshua M. Korn,et al.  Mapping copy number variation by population scale genome sequencing , 2010, Nature.

[51]  Tomas W. Fitzgerald,et al.  Origins and functional impact of copy number variation in the human genome , 2010, Nature.

[52]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[53]  Yusuke Nakamura,et al.  Population-genetic nature of copy number variations in the human genome , 2009, Human molecular genetics.

[54]  Judy H. Cho,et al.  Finding the missing heritability of complex diseases , 2009, Nature.

[55]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[56]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[57]  Faxing Chen,et al.  Developmental changes in pulp organic acid concentration and activities of acid-metabolising enzymes during the fruit development of two loquat (Eriobotrya japonica Lindl.) cultivars differing in fruit acidity , 2009 .

[58]  Joshua M. Korn,et al.  Integrated detection and population-genetic analysis of SNPs and copy number variation , 2008, Nature Genetics.

[59]  E. Eichler,et al.  Systematic assessment of copy number variant detection via genome-wide SNP genotyping , 2008, Nature Genetics.

[60]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[61]  R. Hellens,et al.  Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10 , 2007, The Plant journal : for cell and molecular biology.

[62]  D. Conrad,et al.  Global variation in copy number in the human genome , 2006, Nature.

[63]  J. Bailey-Serres,et al.  Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice , 2006, Nature.

[64]  D. Reich,et al.  Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.

[65]  N. Wray Allele Frequencies and the r2 Measure of Linkage Disequilibrium: Impact on Design and Interpretation of Association Studies , 2005, Twin Research and Human Genetics.

[66]  Yi Tian,et al.  Genome-wide identification and analysis of the MADS-box gene family in apple. , 2015, Gene.

[67]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..