title: Early genome duplications in conifers and other seed plants.
abstract: Polyploidy is a common mode of speciation and evolution in angiosperms (flowering plants). In contrast, there is little evidence to date that whole genome duplication (WGD) has played a significant role in the evolution of their putative extant sister lineage, the gymnosperms. Recent analyses of the spruce genome, the first published conifer genome, failed to detect evidence of WGDs in gene age distributions and attributed many aspects of conifer biology to a lack of WGDs. We present evidence for three ancient genome duplications during the evolution of gymnosperms, based on phylogenomic analyses of transcriptomes from 24 gymnosperms and 3 outgroups. We use a new algorithm to place these WGD events in phylogenetic context: two in the ancestry of major conifer clades (Pinaceae and cupressophyte conifers) and one in Welwitschia (Gnetales). We also confirm that a WGD hypothesized to be restricted to seed plants is indeed not shared with ferns and relatives (monilophytes), a result that was unclear in earlier studies. Contrary to previous genomic research that reported an absence of polyploidy in the ancestry of contemporary gymnosperms, our analyses indicate that polyploidy has contributed to the evolution of conifers and other gymnosperms. As in the flowering plants, the evolution of the large genome sizes of gymnosperms involved both polyploidy and repetitive element activity.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Anthony E
authors.initials: AE
authors.lastname: Baniaga
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Emily B
authors.initials: EB
authors.lastname: Sessa
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Moira
authors.initials: M
authors.lastname: Scascitelli
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Sean W
authors.identifier: 0000-0001-8209-5231
authors.initials: SW
authors.lastname: Graham
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. ; Department of Biology, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Loren H
authors.initials: LH
authors.lastname: Rieseberg
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Barker
keywords: Phylogenomics; conifers; genome duplication; genome evolution; gymnosperms; plant evolution; polyploidy