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As testified by the many papers in this volume, polyploidy, or whole genome duplication, is a prevalent feature among angiosperm species (Wendel, 2000; Comai, 2005; Leitch & Leitch, 2008). Emerging genomic data have shed light on the ancient and recurrent history of polyploidy among the angiosperms (Barker et al., 2008; Tang et al., 2008; Soltis et al., 2009). Because polyploidy involves the duplication of the entire genome, its effect on genomic organization can be extensive (Comai, 2005), including well-documented cases of structural and epigenetic modifications (Shaked et al., 2001; Gaeta et al., 2007; Buggs et al., 2009; Ni et al., 2009; Tate et al., 2009), as well as changes in gene expression patterns (Bottley et al., 2006; Hegarty et al., 2006; Wang et al., 2006; Flagel et al., 2008; Hovav et al., 2008; Rapp et al., 2009). Furthermore, some of these genome-wide changes have been linked to phenotypic variation (Pires et al., 2004; Gaeta et al., 2007; Ni et al., 2009), providing direct support for the long-held notion that polyploidy can be an important driver of phenotypic evolution.
The establishment of a new allopolyploid species is not a trivial feat. First, all allopolyploids face several immediate genomic challenges, including the merger of divergent genomes, the resolution of potentially conflicting developmental signals and new or possibly accidental interactions with organellar genomes, in addition to overcoming the reproductive barriers associated with polyploidy (Wendel, 2000; Comai, 2005). Following this, and owing to their redundant genomic architecture, allopolyploid genomes then face several interesting and potentially dramatic evolutionary resolutions. These include the genomic decay of duplicate genes either in the form of genomic fragment loss (Shaked et al., 2001; Tate et al., 2009) or mutational obliteration (pseudogenization), genomic partitioning of ancestral functions (subfunctionalization; Force et al., 1999) or the possibility of a chance beneficial mutation conferring new functionality (neofunctionalization; Ohno, 1970). These outcomes are not mutually exclusive (Conant & Wolfe, 2008), and most probably require evolutionary time-scales, and can be distorted by additional genomic disruptions, such as further hybridization and/or polyploidization leading to the accumulation of additional genomic content, yielding higher ploidies and additional genomic complexity [e.g. Spartina anglica, sugarcane (Saccharum officinarum) or wheat (Triticum aestivum)]. In the absence of hybridization or additional rounds of polyploidization, nascent polyploids can undergo divergence and spawn cladogenesis, as has happened in hundreds of genera throughout the angiosperms. As this special edition of New Phytologist demonstrates, the polyploid research community has made major inroads into the study of the genomic consequences of polyploidy. Despite this progress, many important questions remain. The study presented here addresses one of these questions using a model system from the cotton genus, namely, how is gene expression among newly co-resident genomes affected during the lengthy process of allopolyploid diversification?
The organismal context for this analysis is as follows: 1–2 million years ago, allopolyploidization within the genus Gossypium resulted in a new allotetraploid lineage containing diploid genomes from both the Old World A genome and New World D genome (Senchina et al., 2003; Wendel & Cronn, 2003). Since that time, species containing this favorable genomic combination have spread throughout the tropical and subtropical portions of the New World and have diversified into five extant allotetraploid species (Wendel & Cronn, 2003), although a sixth species, G. ekmanianum, has been proposed recently (Krapovickas & Seijo, 2008). The presence of shared allopolyploid-specific nucleotide polymorphisms within these species indicates that they probably evolved from a single polyploidy event and, as a consequence, have left a traceable phylogenetic history which has been revealed by previous studies (Wendel et al., 1994; Small et al., 1998) (Fig. 1a).
Figure 1. Gossypium allotetraploid phylogeny and ‘expression phylogram’. (a) The phylogeny of the five Gossypium allotetraploids, including an image of their flowers at maturity. (b) A phylogeny of the same species, where the branch length represents the extent of homoeologous expression divergence among 1383 genes.
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The evolutionary framework provided by the five natural Gossypium allotetraploids offers an excellent opportunity to study replicated evolutionary trajectories following the combination of diversified genomes. In addition to their compelling natural history, two allotetraploid cottons, G. hirsutum and G. barbadense, are primary contributors of natural fiber for use in the textile and apparel industries, making it agriculturally and economically important to understand their evolutionary history. The study of these allopolyploids has benefited from considerable genomic resources, including a sizable expressed sequence tag (EST) collection (Udall et al., 2006a), with ESTs from both model diploid parents (A genome: G. arboreum; D genome: G. raimondii), which are not the exact progenitors of the natural allotetraploid cottons, but are the closest modern representatives, as well as the allotetraploid G. hirsutum (Table 1). This genomic resource has been used to create a novel microarray platform, which can be used to explore global gene expression levels among c. 42 000 genes using probes targeted at conserved genic regions of the A and D cotton genomes, and homoeologous (genes duplicated by polyploidy) expression levels for c. 1400 genes using pairs of probes differentiated by a genome-specific single nucleotide polymorphism (Udall et al., 2006b; Flagel et al., 2008).
Table 1. Gossypium taxa used in this study
|Species’ name||Genome designation||Accession||Ploidy level||Geographic origin of species||Petal harvest dates1|
|G. arboreum||A2||cv. AKA-8410||Diploid||Africa||May 2–June 5|
|G. raimondii||D5||Accession unnamed||Diploid||South America||Mar 9–Apr 6|
|G. hirsutum||AD1||cv. Maxxa||Allotetraploid||Mexico/Central America||May 9–May 29|
|G. barbadense||AD2||cv. Pima S7||Allotetraploid||South America||May 8–May 31|
|G. tomentosum||AD3||WT936||Allotetraploid||Hawaii||Apr 4–Apr 19|
|G. mustelinum||AD4||15C||Allotetraploid||NE Brazil||Jan 24–Feb 24|
|G. darwinii||AD5||PW45||Allotetraploid||Galapagos Islands||Jan 24–Feb 11|
|F1 hybrid||A2♀ × D5♂||Accession unnamed||Diploid||Synthetic hybrid||Jan 25–Mar 3|
Using this microarray platform, several key findings have been made regarding polyploidy in Gossypium. Most relevant to the present study, we have shown previously that both genomic merger and allopolyploid evolution play important roles in homoeolog expression evolution (Flagel et al., 2008), and that homoeolog expression is biased in favor of the D genome in G. hirsutum in both petal and fiber tissues (Flagel et al., 2008; Hovav et al., 2008). Following these initial findings regarding homoeologous expression, continued work with this microarray platform has highlighted a form of genomic expression dominance, whereby the allotetraploid assumes an expression state of the D genome parent significantly more often than it does the A genome parent, regardless of whether this state is up- or down-regulation (Rapp et al., 2009). Beyond these studies in Gossypium, work in allopolyploid wheat (Bottley et al., 2006; Bottley & Koebner, 2008; Pumphrey et al., 2009) and Tragopogon (Tate et al., 2006) has further demonstrated a considerable frequency of biases in the genomic contribution among homoeologs, and work in hybrids between Arabidopsis autotetraploids has shown global down-regulation of the A. thaliana genome in favor of the A. arenosa genome (Wang et al., 2006), which could be considered as another form of genomic dominance. Together, these observations are beginning to confirm the notion that the genomic disruptions associated with allopolyploidy may contribute considerably to gene expression evolution within established and nascent polyploids (Osborn et al., 2003; Chen, 2007; Paun et al., 2007; Doyle et al., 2008).
Here, we extend the scope of earlier findings by demonstrating significant levels of expression evolution among a diversified collection of natural allopolyploid species, further refining our temporal perspective on expression evolution and revealing extraordinary variation in the rate of expression evolution among a diversifying lineage. We also show aspects of expression evolution that are shared among the five natural allotetraploid cotton species and that are different from those exhibited in recently formed synthetic intergenomic hybrids.