Plant Paleopolyploidy James C. Schnable1 and Eric Lyons3,4 1Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA 2Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA 3School of Plant Sciences, University of Arizona, Tucson, AZ, USA 4iPlant Collaborative, Bio5 Institute, University of Arizona, Tucson, AZ, USA ABSTRACT Identifying and characterizing plant paleopolyploidies is remains an ongoing area of investigation. Ancient whole genome duplications can be identified through whole genome comparisons using a combination of the data derived from genomic structure (e.g. syntenic dotplots) and evolutionary distances (e.g. synonymous mutation rates). These methods require large genomic and/or transcriptomic datasets, and our understanding identity, placement, and timing of these ancient events continues to change as new datasets become available. The images and texzt presented here represent our best estimates using the data available at this time, but, like many things, must be seen as tentative and subject to revision as new datasets and types of analyses become available. Keywords: Comparative Genomics, Plant Comparative Genomics, Whole Genome Duplication, Plant Paleopolyploidy INTRODUCTION Figure 1. Phylogenetic tree of plant species, predominantly those with published genome sequences with known ancient whole genome duplications marked. Tree is current as of April 2013. 1 EUDICOT HEXAPLOIDY Synonyms: Arabidopsis Gamm This hexaploidy (genome tripling) is shared by the core eudicots (the rosids and asterids), and may be present in additional, basal eudicots, although it will not be possible to reach this conclusion until the genomes of species from basal lineages are sequenced and assembled to the pseudomolecule level. This whole genome duplication was first identified as the most ancient of three whole genome duplication present in the genome of Arabidopsis thaliana, and assigned the name ”gamma” by in 2003 by (Bowers et al., 2003). In this paper, hampered by the fact that only two plant genomes had yet been sequenced, and the ridiculously accelerated rate of base pair substitution in arabidopsis the authors concluded the gamma event was likely shared by both monocots and eudicots and could potentially be as old as the split between gymnosperms and flowering plants 300 million years ago. With the publication of the grape genome in 2007 (Jaillon et al., 2007) which has not experienced any duplications since the eudicot hexaploidy and doesn’t show the same acceleration of nucleotide substitutions, it became possible to conclude that the eudicot hexaploidy was NOT shared with monocots and was shared by all rosids. More recent work in the asterids (Cenci et al., 2010) indicate that this evolutionary successful eudicot clade shares the same ancient whole genome duplication. Based on patterns of fractionation the eudicot hexaploidy is believed to have been a two-step event. citeplyons2008value It is possible – although not confirmed – that the tetraploidy seen in columbine (WGD #10) comes from the tetraploid intermediate of this process. 2 ARABIDOPSIS ALPHA The alpha tetraploidy of arabidopsis was first given that name in (Bowers et al., 2003). It is shared by most or all of the crucifers (family Brassicaceae). 3 ARABIDOPSIS BETA As of yet not a single lineage has been identified in which the beta tetraploidy (naming conventions from (Bowers et al., 2003)) is the most recent whole genome duplication. Despite what the image above might indicate, this duplication is significantly older than arabidopsis alpha, however precise dating is difficult given the acceleration of synonymous substitution rate in the arabidopsis lineage. 4 BRASSICA HEXAPLOIDY The first explanation the base Brassica genomes (B. rapa, B. oleracea, and B. nigra) may be comprised of three ancestral genomes that were Arabidopsis like in structure was based on mapping studies (Lagercrantz, 1998); but remained controversial (LUKENS et al., 2004). Studies based on comparative chromosome painting (Lysak et al., 2005) and BAC-sequencing (Yang et al., 2006) (Cheung et al., 2009) further established the Brassica triplication hypothesis, which was confirmed by the genome sequence of Brassica rapa citepwang2011genome. Ongoing studies are attempting to confirm if the Brassica hexaploidy event occurred in one or two steps, and the (allo)polyploidy origin of the event(s). An analysis of fractionation patterns in Brassica rapa supports the two-step model for this hexaploidy (Tang et al., 2012). 5 POPLAR TETRAPLOIDY When the genome of poplar was released in 2006, researchers identified a new ancient whole genome duplication (Tuskan et al., 2006). Poplar retains around 8000 pairs of duplicated genes, which is an unexpectedly high rate of retention given the age of this duplication. 6 FLAX TETRAPLOIDY Occurred within the genus Linum. Domesticated flax (L usitatissimim) and its close relative Linum bienne both share this event. 7 APPLE TETRAPLOIDY The genome paper of apple discussed an ancient whole genome duplication identified in that linage which is estimated to be ¿50 million years old (Velasco et al., 2010) 2/7 8 SOYBEAN TETRAPLOIDY The relatively recent whole genome duplication in soybean was long suspected based a number of different forms of analysis, from chromosome number and early linkage mapping studies (Shoemaker et al., 1996), analysis of Ks peaks (Schlueter et al., 2004), phylogenies of individual gene families (Pfeil et al., 2005) and analyzing the fractionation of individual sequenced regions (Schlueter et al., 2008). As expected, when the genome of soybean was published in 2010, researchers did identify a recent whole genome duplication (peak ks=0.13, estimated age of divergence between whole genome duplicates 13 million years). The minimum age of the event has been fixed at five million years based on the divergence of Glycine species carrying the duplication (Doyle and Egan, 2010). 9 PANILIONOID TETRAPLOIDY Synonym: Legume tetraploidy ¡– note that this name is misleading as this duplication is not shared by many clades within the legumes Linkage mapping studies in soybean led to the hypothesis of a second, older polyploidy event in that lineage (Shoemaker et al., 1996). This hypothesis was corroborated by evidence from Ks studies (Blanc and Wolfe, 2004) (Schlueter et al., 2008) for an ancient polyploidy event in the Medicago truncatula genome. Phylogenomic studies (Pfeil et al., 2005) provided evidence that the soybean and Medicago Ks peaks were due to a single event that occurred in their common ancestor (also shared by Lotus). Subsequently the event was also shown to be shared by peanut (Arachis hypogaea), a member of the clade sister to the Glycine-Medicago-Lotus clade (Bertioli et al., 2009). Unpublished information suggests that this WGD is also found in lupin (Lupinus) in the clade sister to the Arachis-Glycine et al. clade. Phylogenomic studies in a caesalpinioid legume, Chamaecrista fasciculata showed that this species—and thus all caesalpinioid and mimosoid legumes—lacks this polyploidy event, indicating the duplication occurred at the base of (or within) the papilionoid subfamily (Cannon et al., 2010). It is unknown whether the “papilionoid WGD” occurred in the ancestor of all papilionoid legumes, because there is not yet any data for early diverging lineages within the subfamily. The “papilionoid” WGD is estimated to have occurred between 50-60 million years ago, early in the evolution of the legume family. 10 COLUMBINE TETRAPLOIDY Determined from SynMap analysis (Lyons et al., 2008). 11 FLOWERING PLANT TETRAPLOIDY An analysis of conserved orthologous gene groups (COGs) and huge numbers of ESTs identified evidence of two ancient whole genome duplications shared by both monocots and eudicots (Jiao et al., 2011). The more recent of the two, placed at 192 million years ago, occurred after the split of gymnosperms (non-flowering seed plants) but is shared by all extant flowering plant species including Amborella trichopoda. 12 SEED PLANT TETRAPLOIDY The more ancient of the two events identified in (Jiao et al., 2011) is shared by all flowering plants as well as gymnosperms, but after the divergence from Selaginella, a basal vascular plant. 13 MAIZE TETRAPLOIDY The suspicion that maize is an ancient polyploid can be traced back through at least a generation of maize geneticists, and finds its earlier roots in the large number of duplicate mutant loci found in maize, sometimes found in parallel orders along different chromosomes. Perhaps the most famous of these are the pairs of duplicate regulators of anthocyanin biosynthesis: aleurone1 and Purple plant1. Brandon Gaut and John Doebley concluded maize was an allopolyploid in the late 1990s (Gaut and Doebley, 1997). While whether maize is an allo- or auto- polyploid has been argued back and forth over the years, the polyploidy question was settled more than a decade before the publication of the first draft of the maize genome. 3/7 The two subgenomes of maize are estimated to have diverged 12 million years ago (Swigonovˇ a´ et al., 2004). If maize is an autopolyploid, the two genomes also merged into a single genome 12 million years ago, but if maize is an allopolyploid the two genomes could have evolved as separate species for several million years before the wide cross that created the polyploid ancestor of modern maize. In either case, the two ancestral genomes of maize have been contained in the same nucleus for at least five million years (Swigonovˇ a´ et