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

Keywords

Biology, Genome, Gene, Gene duplication, Solanum tuberosum

References

• Copy number variation in potato - an asexually propagated autotetraploid species.Arturo Flores — 2013
• Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibersZhukuan Cheng, C. Robin Buell, Rod A. Wing — 2004
• Aligning short sequencing reads with BowtieBen Langmead — 2010
• Multiple Sequence Alignment Using ClustalW and ClustalXJulie Thompson, Toby J. Gibson, Desmond G. Higgins — 2003
• Biochemistry and molecular biology of plant sulfotransferasesLuc Varin, Frédéric Marsolais, Martine Richard — 1997
• Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in CucumberZhonghua Zhang, Linyong Mao, Huiming Chen — 2015
• The potato: evolution, biodiversity and genetic resourcesJ. Hawkes — 1990
• De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traitsYinghui Li, Guangyu Zhou, Jianxin Ma — 2014
• Comparison of single cell culture derived Solanum tuberosum L. plants and a model for their application in breeding programsG. Wenzel, O. Schieder, T. Przewoźny — 1979
• A graphical representation of genetic and physical maps: the Marey map.Aravinda Chakravarti — 1991
• Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered GenesMaxim Itkin, Uwe Heinig, Oren Tzfadia — 2013
• Modulating plant hormones by enzyme actionCorey S. Westfall, Jonathan Herrmann, Qing-Feng Chen — 2010
• Phenotypic impact of genomic structural variation: insights from and for human diseaseJoachim Weischenfeldt, Orsolya Symmons, François Spitz — 2013
• Evolutionary Dynamics of Plant R-GenesJoy Bergelson, Martin Kreitman, Eli A. Stahl — 2001
• Intergenic Locations of Rice Centromeric ChromatinHuihuang Yan, Paul B. Talbert, Hye Ran Lee — 2008
• Replication Stress and Mechanisms of CNV FormationMartin F. Arlt, Thomas E. Wilson, Thomas W. Glover — 2012
• Genome-wide analysis of SAUR gene family in Solanaceae species.Jian Wu, Songyu Liu, Yanjun He — 2012
• MicroRNA Transcriptomic Analysis of Heterosis during Maize Seed GerminationDong Ding, Yinju Wang, Mingshui Han — 2012
• ANNOVAR: functional annotation of genetic variants from high-throughput sequencing dataKai Wang, Man Li, Håkon Håkonarson — 2010
• Structure, function and evolution of plant disease resistance genes.Jeff Ellis, Peter N. Dodds, Tony Pryor — 2000

Cited by

• Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA) Genes in Flax (Linum usitatissimum L.)Gerardo Pereira Menaut — 2017
• Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid PotatoConnie S. Rosati — 2019
• Transcriptome profiling of transgenic potato plants provides insights into variability caused by plant transformationIván Silén — 2018
• Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences[OPEN]Elisabeth Veeckman, Tom Ruttink, Klaas Vandepoele — 2016
• Self‐Fertility in a Cultivated Diploid Potato Population Examined with the Infinium 8303 Potato Single‐Nucleotide Polymorphism ArrayBrenda A. Peterson, Sarah H. Holt, F. Parker E. Laimbeer — 2016
• Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize[OPEN]Candice N. Hirsch, Cory D. Hirsch, Alex B. Brohammer — 2016
• Understanding potato with the help of genomicsJosé Héctor Gálvez, Helen H. Tai, Noelle A. Barkley — 2017
• Effectoromics-Based Identification of Cell Surface Receptors in Potato.Emmanouil Domazakis, Xiao Lin, Carolina Aguilera-Gálvez — 2017
• Plant Pattern Recognition ReceptorsLibo Shan, Ping He — 2017
• The pangenome of hexaploid bread wheatJuan D. Montenegro, Agnieszka A. Golicz, Philipp E. Bayer — 2017
• Overexpression of StNF-YB3.1 reduces photosynthetic capacity and tuber production, and promotes ABA-mediated stomatal closure in potato (Solanum tuberosum L.).Guochao Xuanyuan, Congming Lu, Ruofang Zhang — 2017
• Genome-wide survey of B-box proteins in potato (Solanum tuberosum)—Identification, characterization and expression patterns during diurnal cycle, etiolation and de-etiolationUrszula Talar, Agnieszka Kiełbowicz‐Matuk, Jagoda Czarnecka — 2017
• De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecinDongyan Zhao, John P. Hamilton, Gina M. Pham — 2017
• Extensive genome heterogeneity leads to preferential allele expression and copy number‐dependent expression in cultivated potatoGina M. Pham, Linsey Newton, Krystle Wiegert‐Rininger — 2017
• A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana AccessionsKazumasa Shirai, Fumio Matsuda, Ryo Nakabayashi — 2017
• Glyphosate Resistance and EPSPS Gene Duplication: Convergent Evolution in Multiple Plant Species.Eric L. Patterson, Dean Pettinga, Karl Ravet — 2018
• A critical comparison of technologies for a plant genome sequencing projectPirita Paajanen, George Kettleborough, Elena López‐Girona — 2017
• Copy number variation and disease resistance in plantsAria Dolatabadian, Dhwani A. Patel, David Edwards — 2017
• Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potatoMichael A. Hardigan, F. Parker E. Laimbeer, Linsey Newton — 2017
• Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potatoAlexandre P. Marand, Shelley Jansky, Hainan Zhao — 2017

Related papers

• Copy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogasterJun Zhou, Bernardo Lemos, Erik B. Dopman — 2011
• Dosage Sensitivity Shapes the Evolution of Copy-Number Varied RegionsBenjamin Schuster‐Böckler, Donald F. Conrad, Alex Bateman — 2010
• Genome-wide investigation identifies a rare copy-number variant burden associated with human spina bifidaPaul Wolujewicz, Vanessa Aguiar‐Pulido, Alice AbdelAleem — 2021
• Global copy number analyses by next generation sequencing provide insight into pig genome variationJicai Jiang, Jiying Wang, Haifei Wang — 2014
• Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genomeViolaine Goidts, D.N. Cooper, Lluı́s Armengol — 2006
• Copy Number Variation in Chickens: A Review and Future ProspectsXiaofei Wang, Mary Shannon Byers — 2014
• Research Progress on Gene Copy Number VariationsJian Wu — 2012