title: Evolution of genome size and complexity in Pinus.
abstract: BACKGROUND
  Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood.
  
  
  RESULTS
  Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA.
  
  
  CONCLUSIONS
  Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.
authors.affiliation: School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Alison M
authors.initials: AM
authors.lastname: Morse
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Peterson
authors.forename: M Nurul
authors.initials: MN
authors.lastname: Islam-Faridi
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Smith
authors.forename: Zenaida
authors.initials: Z
authors.lastname: Magbanua
authors.forename: Saul A
authors.initials: SA
authors.lastname: Garcia
authors.forename: Thomas L
authors.initials: TL
authors.lastname: Kubisiak
authors.forename: Henry V
authors.initials: HV
authors.lastname: Amerson
authors.forename: John E
authors.initials: JE
authors.lastname: Carlson
authors.forename: C Dana
authors.initials: CD
authors.lastname: Nelson
authors.forename: John M
authors.initials: JM
authors.lastname: Davis
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D015139:Blotting, Southern; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D018628:Gene Dosage; D018745:Genome, Plant / Q000235:genetics*; D006824:Hybridization, Genetic; D017404:In Situ Hybridization, Fluorescence; D010802:Phylogeny; D028223:Pinus / Q000235:genetics*; D018626:Retroelements / Q000235:genetics
chemical_list: D018626:Retroelements