<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Alonge, Michael</style></author><author><style face="normal" font="default" size="100%">Wang, Xingang</style></author><author><style face="normal" font="default" size="100%">Benoit, Matthias</style></author><author><style face="normal" font="default" size="100%">Soyk, Sebastian</style></author><author><style face="normal" font="default" size="100%">Pereira, Lara</style></author><author><style face="normal" font="default" size="100%">Zhang, Lei</style></author><author><style face="normal" font="default" size="100%">Suresh, Hamsini</style></author><author><style face="normal" font="default" size="100%">Ramakrishnan, Srividya</style></author><author><style face="normal" font="default" size="100%">Maumus, Florian</style></author><author><style face="normal" font="default" size="100%">Ciren, Danielle</style></author><author><style face="normal" font="default" size="100%">Levy, Yuval</style></author><author><style face="normal" font="default" size="100%">Harel, Tom Hai</style></author><author><style face="normal" font="default" size="100%">Shalev-Schlosser, Gili</style></author><author><style face="normal" font="default" size="100%">Amsellem, Ziva</style></author><author><style face="normal" font="default" size="100%">Razifard, Hamid</style></author><author><style face="normal" font="default" size="100%">Caicedo, Ana L</style></author><author><style face="normal" font="default" size="100%">Tieman, Denise M</style></author><author><style face="normal" font="default" size="100%">Klee, Harry</style></author><author><style face="normal" font="default" size="100%">Kirsche, Melanie</style></author><author><style face="normal" font="default" size="100%">Aganezov, Sergey</style></author><author><style face="normal" font="default" size="100%">Ranallo-Benavidez, T Rhyker</style></author><author><style face="normal" font="default" size="100%">Lemmon, Zachary H</style></author><author><style face="normal" font="default" size="100%">Kim, Jennifer</style></author><author><style face="normal" font="default" size="100%">Robitaille, Gina</style></author><author><style face="normal" font="default" size="100%">Kramer, Melissa</style></author><author><style face="normal" font="default" size="100%">Goodwin, Sara</style></author><author><style face="normal" font="default" size="100%">McCombie, W Richard</style></author><author><style face="normal" font="default" size="100%">Hutton, Samuel</style></author><author><style face="normal" font="default" size="100%">Van Eck, Joyce</style></author><author><style face="normal" font="default" size="100%">Gillis, Jesse</style></author><author><style face="normal" font="default" size="100%">Eshed, Yuval</style></author><author><style face="normal" font="default" size="100%">Sedlazeck, Fritz J</style></author><author><style face="normal" font="default" size="100%">van der Knaap, Esther</style></author><author><style face="normal" font="default" size="100%">Schatz, Michael C</style></author><author><style face="normal" font="default" size="100%">Lippman, Zachary B</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.</style></title><secondary-title><style face="normal" font="default" size="100%">Cell</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Cell</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Alleles</style></keyword><keyword><style  face="normal" font="default" size="100%">Crops, Agricultural</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome P-450 Enzyme System</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Epistasis, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Fruit</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Duplication</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomic Structural Variation</style></keyword><keyword><style  face="normal" font="default" size="100%">Genotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Inbreeding</style></keyword><keyword><style  face="normal" font="default" size="100%">Lycopersicon esculentum</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Annotation</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Breeding</style></keyword><keyword><style  face="normal" font="default" size="100%">Quantitative Trait Loci</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 07 09</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">182</style></volume><pages><style face="normal" font="default" size="100%">145-161.e23</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32553272?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wenger, Aaron M</style></author><author><style face="normal" font="default" size="100%">Peluso, Paul</style></author><author><style face="normal" font="default" size="100%">Rowell, William J</style></author><author><style face="normal" font="default" size="100%">Chang, Pi-Chuan</style></author><author><style face="normal" font="default" size="100%">Hall, Richard J</style></author><author><style face="normal" font="default" size="100%">Concepcion, Gregory T</style></author><author><style face="normal" font="default" size="100%">Ebler, Jana</style></author><author><style face="normal" font="default" size="100%">Fungtammasan, Arkarachai</style></author><author><style face="normal" font="default" size="100%">Kolesnikov, Alexey</style></author><author><style face="normal" font="default" size="100%">Olson, Nathan D</style></author><author><style face="normal" font="default" size="100%">Töpfer, Armin</style></author><author><style face="normal" font="default" size="100%">Alonge, Michael</style></author><author><style face="normal" font="default" size="100%">Mahmoud, Medhat</style></author><author><style face="normal" font="default" size="100%">Qian, Yufeng</style></author><author><style face="normal" font="default" size="100%">Chin, Chen-Shan</style></author><author><style face="normal" font="default" size="100%">Phillippy, Adam M</style></author><author><style face="normal" font="default" size="100%">Schatz, Michael C</style></author><author><style face="normal" font="default" size="100%">Myers, Gene</style></author><author><style face="normal" font="default" size="100%">DePristo, Mark A</style></author><author><style face="normal" font="default" size="100%">Ruan, Jue</style></author><author><style face="normal" font="default" size="100%">Marschall, Tobias</style></author><author><style face="normal" font="default" size="100%">Sedlazeck, Fritz J</style></author><author><style face="normal" font="default" size="100%">Zook, Justin M</style></author><author><style face="normal" font="default" size="100%">Li, Heng</style></author><author><style face="normal" font="default" size="100%">Koren, Sergey</style></author><author><style face="normal" font="default" size="100%">Carroll, Andrew</style></author><author><style face="normal" font="default" size="100%">Rank, David R</style></author><author><style face="normal" font="default" size="100%">Hunkapiller, Michael W</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Biotechnol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">37</style></volume><pages><style face="normal" font="default" size="100%">1155-1162</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions &lt;50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of &gt;15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31406327?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Alonge, Michael</style></author><author><style face="normal" font="default" size="100%">Soyk, Sebastian</style></author><author><style face="normal" font="default" size="100%">Ramakrishnan, Srividya</style></author><author><style face="normal" font="default" size="100%">Wang, Xingang</style></author><author><style face="normal" font="default" size="100%">Goodwin, Sara</style></author><author><style face="normal" font="default" size="100%">Sedlazeck, Fritz J</style></author><author><style face="normal" font="default" size="100%">Lippman, Zachary B</style></author><author><style face="normal" font="default" size="100%">Schatz, Michael C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">RaGOO: fast and accurate reference-guided scaffolding of draft genomes.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019 Oct 28</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">224</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps. We show that RaGOO accurately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open source at https://github.com/malonge/RaGOO .&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31661016?dopt=Abstract</style></custom1></record></records></xml>