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dc.contributor.authorThind, Anupriya Kaur
dc.contributor.authorInternational Wheat Genome Sequencing Consortium
dc.contributor.authorWicker, Thomas
dc.contributor.authorMüller, Thomas
dc.contributor.authorAckermann, Patrick M.
dc.contributor.authorSteuernagel, Burkhard
dc.contributor.authorWulff, Brande B. H.
dc.contributor.authorSpannagl, Manuel
dc.contributor.authorTwardziok, Sven O.
dc.contributor.authorFelder, Marius
dc.contributor.authorLux, Thomas
dc.contributor.authorMayer, Klaus F. X.
dc.contributor.authorKeller, Beat
dc.contributor.authorKrattinger, Simon G.
dc.date.accessioned2018-09-03T13:26:44Z
dc.date.available2018-09-03T13:26:44Z
dc.date.issued2018-08-17
dc.identifier.citationThind AK, Wicker T, Müller T, Ackermann PM, et al. (2018) Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biology 19. Available: http://dx.doi.org/10.1186/s13059-018-1477-2.
dc.identifier.issn1474-760X
dc.identifier.doi10.1186/s13059-018-1477-2
dc.identifier.urihttp://hdl.handle.net/10754/628478
dc.description.abstractRecent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the dynamics of wheat genomes on a megabase scale.Here, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes-the old landrace Chinese Spring and the elite Swiss spring wheat line 'CH Campala Lr22a'. Both chromosomes were assembled into megabase-sized scaffolds. There is a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations reveals four large indels of more than 100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the molecular mechanisms that caused these indels. Three of the large indels affect copy number of NLRs, a gene family involved in plant immunity. Analysis of SNP density reveals four haploblocks of 4, 8, 9 and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Gene content across the two chromosomes was highly conserved. Ninety-nine percent of the genic sequences were present in both genotypes and the fraction of unique genes ranged from 0.4 to 0.7%.This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.
dc.description.sponsorshipThis study was supported by an Ambizione grant of the Swiss National Science Foundation, the University of Zurich, the BMEL Research grant WheatSeq and by the King Abdullah University of Science and Technology (KAUST).
dc.publisherSpringer Nature
dc.relation.urlhttps://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1477-2
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectWheat
dc.subjectStructural Variation
dc.subjectGenome Diversity
dc.subjectHigh-quality Assembly
dc.titleChromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentPlant Science
dc.identifier.journalGenome Biology
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland.
dc.contributor.institutionInternational Wheat Genome Sequencing Consortium (IWGSC), 2841 NE Marywood Ct, Lee’s Summit, MO 64086, USA.
dc.contributor.institutionJohn Innes Centre, Norwich Research Park, Norwich, UK.
dc.contributor.institutionHelmholtz Zentrum Munich, Munich, Germany.
dc.contributor.institutionCollege of Science, King Saud University, Riad, Kingdom of Saudi Arabia.
dc.contributor.institutionSchool of Life Sciences, Technical University Munich, Munich, Germany.
kaust.personKrattinger, Simon G.
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.6978293
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.6978275.v1
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.6978260.v1
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.c.4201652
refterms.dateFOA2018-09-04T12:01:12Z
display.relations<b> Is Supplemented By:</b> <br/> <ul> <li><i>[Dataset]</i> <br/> . DOI: <a href="https://doi.org/10.6084/m9.figshare.6978293">10.6084/m9.figshare.6978293</a> HANDLE: <a href="http://hdl.handle.net/10754/664150">10754/664150</a></li></ul><b> Is Supplemented By:</b> <br/> <ul> <li><i>[Dataset]</i> <br/> . DOI: <a href="https://doi.org/10.6084/m9.figshare.6978275.v1">10.6084/m9.figshare.6978275.v1</a> HANDLE: <a href="http://hdl.handle.net/10754/664151">10754/664151</a></li></ul><b> Is Supplemented By:</b> <br/> <ul> <li><i>[Dataset]</i> <br/> . DOI: <a href="https://doi.org/10.6084/m9.figshare.6978260.v1">10.6084/m9.figshare.6978260.v1</a> HANDLE: <a href="http://hdl.handle.net/10754/664152">10754/664152</a></li></ul><b> Is Supplemented By:</b> <br/> <ul> <li><i>[Dataset]</i> <br/> . DOI: <a href="https://doi.org/10.6084/m9.figshare.c.4201652">10.6084/m9.figshare.c.4201652</a> HANDLE: <a href="http://hdl.handle.net/10754/664154">10754/664154</a></li></ul>
dc.date.published-online2018-08-17
dc.date.published-print2018-12


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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.