title: Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin.
abstract: BACKGROUND
  In flowering plants it has been shown that de novo genome assemblies of different species and genera show a significant drop in the proportion of alignable sequence. Within a plant species, however, it is assumed that different haplotypes of the same chromosome align well. In this paper we have compared three de novo assemblies of potato chromosome 5 and report on the sequence variation and the proportion of sequence that can be aligned.
  
  
  RESULTS
  For the diploid potato clone RH89-039-16 (RH) we produced two linkage phase controlled and haplotype-specific assemblies of chromosome 5 based on BAC-by-BAC sequencing, which were aligned to each other and compared to the 52 Mb chromosome 5 reference sequence of the doubled monoploid clone DM 1-3 516 R44 (DM). We identified 17.0 Mb of non-redundant sequence scaffolds derived from euchromatic regions of RH and 38.4 Mb from the pericentromeric heterochromatin. For 32.7 Mb of the RH sequences the correct position and order on chromosome 5 was determined, using genetic markers, fluorescence in situ hybridisation and alignment to the DM reference genome. This ordered fraction of the RH sequences is situated in the euchromatic arms and in the heterochromatin borders. In the euchromatic regions, the sequence collinearity between the three chromosomal homologs is good, but interruption of collinearity occurs at nine gene clusters. Towards and into the heterochromatin borders, absence of collinearity due to structural variation was more extensive and was caused by hemizygous and poorly aligning regions of up to 450 kb in length. In the most central heterochromatin, a total of 22.7 Mb sequence from both RH haplotypes remained unordered. These RH sequences have very few syntenic regions and represent a non-alignable region between the RH and DM heterochromatin haplotypes of chromosome 5.
  
  
  CONCLUSIONS
  Our results show that among homologous potato chromosomes large regions are present with dramatic loss of sequence collinearity. This stresses the need for more de novo reference assemblies in order to capture genome diversity in this crop. The discovery of three highly diverged pericentric heterochromatin haplotypes within one species is a novelty in plant genome analysis. The possible origin and cytogenetic implication of this heterochromatin haplotype diversity are discussed.
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. Jan.de.Boer@AVEBE.COM.|Current address: Averis Seeds B.V., Valtherblokken Zuid 40, 7876 TC, Valthermond, The Netherlands. Jan.de.Boer@AVEBE.COM.
authors.forename: Jan M
authors.initials: JM
authors.lastname: de Boer
authors.affiliation: Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. erwin.datema@keygene.com.|Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands. erwin.datema@keygene.com.
authors.forename: Erwin
authors.initials: E
authors.lastname: Datema
authors.affiliation: Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. xiaomintang2013@hotmail.com.|Current address: Department of Biology, Colorado State University, Fort Collins, USA. xiaomintang2013@hotmail.com.
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Tang
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. theo@borm.org.
authors.forename: Theo J A
authors.initials: TJ
authors.lastname: Borm
authors.affiliation: Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. erin_bakker@borm.org.
authors.forename: Erin H
authors.initials: EH
authors.lastname: Bakker
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. Herman.vanEck@wur.nl.
authors.forename: Herman J
authors.initials: HJ
authors.lastname: van Eck
authors.affiliation: Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. roeland.van-ham@keygene.com.|Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands. roeland.van-ham@keygene.com.
authors.forename: Roeland C H J
authors.initials: RC
authors.lastname: van Ham
authors.affiliation: Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. hans.dejong@wur.nl.
authors.forename: Hans
authors.initials: H
authors.lastname: de Jong
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. Richard.Visser@wur.nl.
authors.forename: Richard G F
authors.initials: RG
authors.lastname: Visser
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. christian.bachem@wur.nl.
authors.forename: Christian W B
authors.initials: CW
authors.lastname: Bachem
mesh_terms: D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant; D022041:Euchromatin / Q000235:genetics* / Q000378:metabolism; D008040:Genetic Linkage; D005838:Genotype; D006239:Haplotypes; D006570:Heterochromatin / Q000235:genetics* / Q000378:metabolism; D017404:In Situ Hybridization, Fluorescence; D011110:Polymorphism, Genetic; D011198:Solanum tuberosum / Q000235:genetics*
chemical_list: D022041:Euchromatin; D006570:Heterochromatin