title: Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  Three mate pair (MP) libraries (2 Kb, 3 Kb, and 5 Kb) were sequenced to a total coverage of 89x and 64x for the short and long arm of chromosome 7B, respectively. Scaffolding using SSPACE improved the 7B assembly contiguity and decreased gene space fragmentation, but the degree of improvement was greatly affected by scaffolding stringency applied. At the lowest stringency the assembly N50 increased by ~7 fold, while at the highest stringency N50 was only increased by ~1.5 fold. Furthermore, a strong positive correlation between estimated scaffold reliability and scaffold assembly stringency was observed. A 7BS scaffold assembly with reduced MP coverage proved that assembly contiguity was affected only to a small degree down to ~50% of the original coverage.
  
  
  CONCLUSIONS
  The effect of MP data integration into pair end shotgun assemblies of wheat chromosome was moderate; possibly due to poor contig assembly contiguity, the extreme repeat content of wheat, and the use of amplified chromosomal DNA for MP library construction.
authors.affiliation: Department of Plant and Environmental Sciences, University of Life Sciences, Ås, Norway.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Belova
authors.forename: Bujie
authors.initials: B
authors.lastname: Zhan
authors.forename: Jonathan
authors.initials: J
authors.lastname: Wright
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
authors.forename: Torben
authors.initials: T
authors.lastname: Asp
authors.forename: Hana
authors.initials: H
authors.lastname: Simková
authors.forename: Matthew
authors.initials: M
authors.lastname: Kent
authors.forename: Christian
authors.initials: C
authors.lastname: Bendixen
authors.forename: Frank
authors.initials: F
authors.lastname: Panitz
authors.forename: Sigbjørn
authors.initials: S
authors.lastname: Lien
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.forename: Odd-Arne
authors.initials: OA
authors.lastname: Olsen
authors.forename: Simen R
authors.initials: SR
authors.lastname: Sandve
mesh_terms: D032461:Chromosomes, Plant / Q000737:chemistry / Q000235:genetics*; D020451:Contig Mapping; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D015723:Gene Library; D011123:Polyploidy; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics*
chemical_list: D018744:DNA, Plant
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