title: A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales.
abstract: Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification.
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri Department of Plant Biology, University of Georgia mrmckain@gmail.com.
authors.forename: Michael R
authors.initials: MR
authors.lastname: McKain
authors.affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University Department of Plant Biology, University of Georgia.
authors.forename: Joel R
authors.initials: JR
authors.lastname: McNeal
authors.affiliation: Department of Plant Biology, University of Georgia.
authors.forename: Saravanaraj
authors.initials: S
authors.lastname: Ayyampalayam
authors.affiliation: L. H. Bailey Hortorium and Department of Plant Biology, Cornell University.
authors.forename: Jerrold I
authors.initials: JI
authors.lastname: Davis
authors.affiliation: Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, Pennsylvania.
authors.forename: Claude W
authors.initials: CW
authors.lastname: dePamphilis
authors.affiliation: Department of Botany, University of Wisconsin-Madison.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Givnish
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia.
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.affiliation: New York Botanical Garden, Bronx, New York.
authors.forename: Dennis Wm
authors.initials: DW
authors.lastname: Stevenson
authors.affiliation: Department of Plant Biology, University of Georgia.
authors.forename: James H
authors.initials: JH
authors.lastname: Leebens-Mack
mesh_terms: D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D006109:Poaceae / Q000235:genetics; D011123:Polyploidy; D018749:RNA, Plant / Q000235:genetics; D045868:Sorghum / Q000235:genetics; D059467:Transcriptome
chemical_list: D018749:RNA, Plant
keywords: GC content; grasses; monocots; whole-genome duplication