Genome reduction uncovers a large dispensable genome and adaptive role for 2 copy number variation in asexually propagated Solanum tuberosum 3 4 SHORT TITLE: 5 Unique structural variation in clonal potato. 6

[1]  S. Mirarab,et al.  Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.

[2]  Yuehua Cui,et al.  Genetic Map and QTL Analysis of Agronomic Traits in a Diploid Potato Population using Single Nucleotide Polymorphism Markers , 2015 .

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

[4]  M. Hardigan,et al.  Taxonomy and Genetic Differentiation among Wild and Cultivated Germplasm of Solanum sect. Petota , 2015, The plant genome.

[5]  D. Moazed,et al.  RNA-mediated epigenetic regulation of gene expression , 2015, Nature Reviews Genetics.

[6]  Ruiqiang Li,et al.  De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits , 2014, Nature Biotechnology.

[7]  M. A. Pedraza,et al.  Insights into the Maize Pan-Genome and Pan-Transcriptome[W][OPEN] , 2014, Plant Cell.

[8]  David M. A. Martin,et al.  Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps , 2013, G3: Genes, Genomes, Genetics.

[9]  M. Figlerowicz,et al.  Copy number polymorphism in plant genomes , 2013, Theoretical and Applied Genetics.

[10]  A. Aharoni,et al.  Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes , 2013, Science.

[11]  Jiming Jiang,et al.  Copy number variation in potato - an asexually propagated autotetraploid species. , 2013, The Plant journal : for cell and molecular biology.

[12]  R. Veilleux,et al.  Retrospective View of North American Potato (Solanum tuberosum L.) Breeding in the 20th and 21st Centuries , 2013, G3: Genes, Genomes, Genetics.

[13]  R. Visser,et al.  A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato , 2013, PloS one.

[14]  D. Spooner,et al.  Genetic diversity and origin of cultivated potatoes based on plastid microsatellite polymorphism , 2013, Genetic Resources and Crop Evolution.

[15]  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.

[16]  Jan O. Korbel,et al.  Phenotypic impact of genomic structural variation: insights from and for human disease , 2013, Nature Reviews Genetics.

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

[18]  Jian Wu,et al.  Genome-wide analysis of SAUR gene family in Solanaceae species. , 2012, Gene.

[19]  D. Ding,et al.  MicroRNA Transcriptomic Analysis of Heterosis during Maize Seed Germination , 2012, PloS one.

[20]  Peter J. Bradbury,et al.  Maize HapMap2 identifies extant variation from a genome in flux , 2012, Nature Genetics.

[21]  T. E. Wilson,et al.  Replication stress and mechanisms of CNV formation. , 2012, Current opinion in genetics & development.

[22]  R. Veilleux,et al.  Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence , 2012, PloS one.

[23]  D. Laurie,et al.  Copy Number Variation Affecting the Photoperiod-B1 and Vernalization-A1 Genes Is Associated with Altered Flowering Time in Wheat (Triticum aestivum) , 2012, PloS one.

[24]  C. Robin Buell,et al.  Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing , 2012, PloS one.

[25]  Hong Ma,et al.  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. , 2012, Genome research.

[26]  Edward S. Buckler,et al.  Crop genomics: advances and applications , 2011, Nature Reviews Genetics.

[27]  Lin Fang,et al.  Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes , 2011, Nature Biotechnology.

[28]  L. Holm,et al.  The Pfam protein families database , 2011, Nucleic Acids Res..

[29]  Karsten M. Borgwardt,et al.  Whole-genome sequencing of multiple Arabidopsis thaliana populations , 2011, Nature Genetics.

[30]  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.

[31]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[32]  J. Jez,et al.  Modulating plant hormones by enzyme action , 2010, Plant signaling & behavior.

[33]  N. Tuteja,et al.  Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. , 2010, Plant physiology and biochemistry : PPB.

[34]  B. Langmead,et al.  Aligning Short Sequencing Reads with Bowtie , 2010, Current protocols in bioinformatics.

[35]  Jian Wang,et al.  Genome-wide patterns of genetic variation among elite maize inbred lines , 2010, Nature Genetics.

[36]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[37]  J. Noel,et al.  Enzymatic Functions of Wild Tomato Methylketone Synthases 1 and 21[W][OA] , 2010, Plant Physiology.

[38]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[39]  Seth Debolt,et al.  Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales , 2010, Genome biology and evolution.

[40]  Nicola Pecchioni,et al.  CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals , 2010, Theoretical and Applied Genetics.

[41]  P. Stankiewicz,et al.  Structural variation in the human genome and its role in disease. , 2010, Annual review of medicine.

[42]  Lars Bolund,et al.  Building the sequence map of the human pan-genome , 2010, Nature Biotechnology.

[43]  Jiming Jiang,et al.  Gene amplification confers glyphosate resistance in Amaranthus palmeri , 2009, Proceedings of the National Academy of Sciences.

[44]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[45]  Patrick S. Schnable,et al.  Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content , 2009, PLoS genetics.

[46]  Jung Sun Kim,et al.  Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication , 2009, Genome Biology.

[47]  J. Salojärvi,et al.  Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. , 2009, The Plant journal : for cell and molecular biology.

[48]  Xian-Jun Song,et al.  The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water , 2009, Nature.

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

[50]  M. Nei,et al.  Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification , 2009, Proceedings of the National Academy of Sciences.

[51]  S. Henikoff,et al.  Intergenic Locations of Rice Centromeric Chromatin , 2008, PLoS biology.

[52]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[53]  Andrew H. Paterson,et al.  Synteny and Collinearity in Plant Genomes , 2008, Science.

[54]  Cai-guo Xu,et al.  Activation of the Indole-3-Acetic Acid–Amido Synthetase GH3-8 Suppresses Expansin Expression and Promotes Salicylate- and Jasmonate-Independent Basal Immunity in Rice[W] , 2008, The Plant Cell Online.

[55]  D. Spooner,et al.  Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification , 2007, Proceedings of the National Academy of Sciences.

[56]  Sofia M. C. Robb,et al.  MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.

[57]  P. Langridge,et al.  Boron-Toxicity Tolerance in Barley Arising from Efflux Transporter Amplification , 2007, Science.

[58]  Michele Morgante,et al.  Transposable elements and the plant pan-genomes. , 2007, Current opinion in plant biology.

[59]  R. Martienssen,et al.  Transposable elements and the epigenetic regulation of the genome , 2007, Nature Reviews Genetics.

[60]  Mukesh Jain,et al.  Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa). , 2006, Genomics.

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

[62]  Richard W. Jones,et al.  Assessment of Linkage Disequilibrium in Potato Genome With Single Nucleotide Polymorphism Markers , 2006, Genetics.

[63]  Jun Wang,et al.  High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes[W] , 2006, The Plant Cell Online.

[64]  Steven Maere,et al.  Genome duplication and the origin of angiosperms. , 2005, Trends in ecology & evolution.

[65]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[66]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[67]  J. Ohlrogge,et al.  Metabolic, Genomic, and Biochemical Analyses of Glandular Trichomes from the Wild Tomato Species Lycopersicon hirsutum Identify a Key Enzyme in the Biosynthesis of Methylketonesw⃞ , 2005, The Plant Cell Online.

[68]  Michele Morgante,et al.  Evolution of DNA Sequence Nonhomologies among Maize Inbredsw⃞ , 2005, The Plant Cell Online.

[69]  Jutta Papenbrock,et al.  The multi-protein family of Arabidopsis sulphotransferases and their relatives in other plant species. , 2004, Journal of experimental botany.

[70]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[71]  Julie D Thompson,et al.  Multiple Sequence Alignment Using ClustalW and ClustalX , 2003, Current protocols in bioinformatics.

[72]  H. Fu,et al.  Intraspecific violation of genetic colinearity and its implications in maize , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[73]  G. Antonious.  PRODUCTION AND QUANTIFICATION OF METHYL KETONES IN WILD TOMATO ACCESSIONS , 2001, Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes.

[74]  E. Stahl,et al.  Evolutionary Dynamics of Plant R-Genes , 2001, Science.

[75]  P. Dodds,et al.  Structure, function and evolution of plant disease resistance genes. , 2000, Current opinion in plant biology.

[76]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[77]  De Luca V,et al.  Developmental and light regulation of desacetoxyvindoline 4-hydroxylase in catharanthus roseus (L.) G. Don. . Evidence Of a multilevel regulatory mechanism , 1998, Plant physiology.

[78]  M. G. Kidwell,et al.  Transposable elements as sources of variation in animals and plants. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[79]  F. Marsolais,et al.  Biochemistry and molecular biology of plant sulfotransferases , 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[80]  S. Tanksley,et al.  QTL analysis of trichome-mediated insect resistance in potato , 1994, Theoretical and Applied Genetics.

[81]  A. Chakravarti.  A graphical representation of genetic and physical maps: the Marey map. , 1991, Genomics.

[82]  J. G. Hawkes,et al.  The potato: evolution, biodiversity and genetic resources , 1990 .

[83]  G. Wenzel,et al.  Comparison of single cell culture derived Solanum tuberosum L. plants and a model for their application in breeding programs , 1979, Theoretical and Applied Genetics.

[84]  H. D. Jong,et al.  Inbreeding in cultivated diploid potatoes , 1971, Potato Research.

[85]  G. Glevarec,et al.  Deciphering the Evolution, Cell Biology and Regulation of Monoterpene Indole Alkaloids , 2013 .

[86]  R. Wing,et al.  Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers , 2004, Chromosome Research.

[87]  J. Valkonen,et al.  Organization of genes controlling disease resistance in the potato genome. , 2001, Annual review of phytopathology.

[88]  L. Pachter,et al.  TopHat: discovering splice junctions with RNA-Seq , 2009, Bioinform..

[89]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[90]  Jian Wang,et al.  Nature Genetics Advance Online Publication Resequencing of 31 Wild and Cultivated Soybean Genomes Identifies Patterns of Genetic Diversity and Selection , 2022 .