title: Next-generation sequencing and genome evolution in allopolyploids.
abstract: OBJECTIVE
  Hybridization and polyploidization (allopolyploidy) are ubiquitous in the evolution of plants, but tracing the origins and subsequent evolution of the constituent genomes of allopolyploids has been challenging. Genome doubling greatly complicates genetic analyses, and this has long hindered investigation in that most allopolyploid species are "nonmodel" organisms. However, recent advances in sequencing and genomics technologies now provide unprecedented opportunities to analyze numerous genetic markers in multiple individuals in any organism.
  
  
  METHODS
  Here we review the application of next-generation sequencing technologies to the study of three aspects of allopolyploid genome evolution: duplicated gene loss and expression in two recently formed Tragopogon allopolyploids, intergenomic interactions and chromosomal evolution in Tragopogon miscellus, and repetitive DNA evolution in Nicotiana allopolyploids.
  
  
  RESULTS
  For the first time, we can explore on a genomic scale the evolutionary processes that are ongoing in natural allopolyploids and not be restricted to well-studied crops and genetic models.
  
  
  CONCLUSIONS
  These approaches can be easily and inexpensively applied to many other plant species-making any evolutionarily provocative system a new "model" system.
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
authors.forename: Richard J A
authors.initials: RJ
authors.lastname: Buggs
authors.forename: Simon
authors.initials: S
authors.lastname: Renny-Byfield
authors.forename: Michael
authors.initials: M
authors.lastname: Chester
authors.forename: Ingrid E
authors.initials: IE
authors.lastname: Jordon-Thaden
authors.forename: Lyderson Facio
authors.initials: LF
authors.lastname: Viccini
authors.forename: Srikar
authors.initials: S
authors.lastname: Chamala
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Leitch
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Schnable
authors.forename: W Bradley
authors.initials: WB
authors.lastname: Barbazuk
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
mesh_terms: D000483:Alleles; D032461:Chromosomes, Plant / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D011123:Polyploidy; D012091:Repetitive Sequences, Nucleic Acid; D014026:Nicotiana / Q000235:genetics; D031188:Tragopogon / Q000235:genetics
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers