title: Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes.
abstract: Unresolved questions about evolution of the large and diverse legume family include the timing of polyploidy (whole-genome duplication; WGDs) relative to the origin of the major lineages within the Fabaceae and to the origin of symbiotic nitrogen fixation. Previous work has established that a WGD affects most lineages in the Papilionoideae and occurred sometime after the divergence of the papilionoid and mimosoid clades, but the exact timing has been unknown. The history of WGD has also not been established for legume lineages outside the Papilionoideae. We investigated the presence and timing of WGDs in the legumes by querying thousands of phylogenetic trees constructed from transcriptome and genome data from 20 diverse legumes and 17 outgroup species. The timing of duplications in the gene trees indicates that the papilionoid WGD occurred in the common ancestor of all papilionoids. The earliest diverging lineages of the Papilionoideae include both nodulating taxa, such as the genistoids (e.g., lupin), dalbergioids (e.g., peanut), phaseoloids (e.g., beans), and galegoids (=Hologalegina, e.g., clovers), and clades with nonnodulating taxa including Xanthocercis and Cladrastis (evaluated in this study). We also found evidence for several independent WGDs near the base of other major legume lineages, including the Mimosoideae-Cassiinae-Caesalpinieae (MCC), Detarieae, and Cercideae clades. Nodulation is found in the MCC and papilionoid clades, both of which experienced ancestral WGDs. However, there are numerous nonnodulating lineages in both clades, making it unclear whether the phylogenetic distribution of nodulation is due to independent gains or a single origin followed by multiple losses.
authors.affiliation: USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA steven.cannon@ars.usda.gov.
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
authors.affiliation: Department of Plant Biology, University of Georgia Donald Danforth Plant Sciences Center, St Louis, MO.
authors.forename: Michael R
authors.initials: MR
authors.lastname: McKain
authors.affiliation: Department of Plant Biology, University of Georgia.
authors.forename: Alex
authors.initials: A
authors.lastname: Harkess
authors.affiliation: The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia The School of Plant Biology, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Matthew N
authors.initials: MN
authors.lastname: Nelson
authors.affiliation: Virtual Reality Application Center, Iowa State University.
authors.forename: Sudhansu
authors.initials: S
authors.lastname: Dash
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Deyholos
authors.affiliation: Department of Plant Sciences, The University of Tennessee.
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Department of Plant Sciences, The University of Tennessee.
authors.forename: Blake
authors.initials: B
authors.lastname: Joyce
authors.affiliation: Department of Plant Sciences, The University of Tennessee.
authors.forename: Charles N
authors.initials: CN
authors.lastname: Stewart
authors.affiliation: Donald Danforth Plant Sciences Center, St Louis, MO.
authors.forename: Megan
authors.initials: M
authors.lastname: Rolf
authors.affiliation: Donald Danforth Plant Sciences Center, St Louis, MO.
authors.forename: Toni
authors.initials: T
authors.lastname: Kutchan
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Tan
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Cui
authors.initials: C
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
authors.forename: Eric
authors.initials: E
authors.lastname: Carpenter
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China Department of Medicine, University of Alberta, Edmonton, AB, Canada.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.affiliation: L. H. Bailey Hortorium, Department of Plant Biology, Cornell University.
authors.forename: Jeff J
authors.initials: JJ
authors.lastname: Doyle
authors.affiliation: Department of Plant Biology, University of Georgia.
authors.forename: Jim
authors.initials: J
authors.lastname: Leebens-Mack
mesh_terms: D019143:Evolution, Molecular; D007887:Fabaceae / Q000145:classification* / Q000235:genetics* / Q000502:physiology; D018745:Genome, Plant; D005810:Multigene Family; D009154:Mutation; D009586:Nitrogen Fixation; D010802:Phylogeny; D013559:Symbiosis; D057891:Tetraploidy
keywords: Mimosoideae; Papilionoideae; legume; nodulation; polyploidy; symbiotic nitrogen fixation