Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat

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DOI

  • Tatiana Belova, Department of Plant and Environmental Sciences, University of Life Sciences, Norge
  • Bujie Zhan, Department of Plant and Environmental Sciences, University of Life Sciences, Norge
  • Jonathan Wright, 2 The Genome Analysis Centre (TGAC), Norwich Research Park, Storbritannien
  • Mario Caccamo, 2 The Genome Analysis Centre (TGAC), Norwich Research Park, Storbritannien
  • Torben Asp
  • Hana Simková, Center of the Region Haná, Institute of Experimental Botany, Tjekkiet
  • Matthew Kent, 5 Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Norge
  • Christian Bendixen
  • Frank Panitz
  • Sigbjørn Lien, 5 Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Norge
  • Jaroslav Doležel, Center of the Region Haná, Institute of Experimental Botany, Tjekkiet
  • Odd-Arne Olsen, Department of Plant and Environmental Sciences, University of Life Sciences, Norge
  • Simen R Sandve, Department of Plant and Environmental Sciences, University of Life Sciences, Norge
The assembly of the bread wheat genome sequence is challenging due to allohexaploidy and extreme repeat content (>80%). Isolation of single chromosome arms by flow sorting can be used to overcome the polyploidy problem, but the repeat content cause extreme assembly fragmentation even at a single chromosome level. Long jump paired sequencing data (mate pairs) can help reduce assembly fragmentation by joining multiple contigs into single scaffolds. The aim of this work was to assess how mate pair data generated from multiple displacement amplified DNA of flow-sorted chromosomes affect assembly fragmentation of shotgun assemblies of the wheat chromosomes.
OriginalsprogEngelsk
TidsskriftB M C Genomics
Vol/bind14
Sider (fra-til)222
ISSN1471-2164
DOI
StatusUdgivet - 2013

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