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One of the unsolved mysteries of plant evolutionary biology is the functional significance of the two thousand-fold variation in the genome size of individual species, particularly among the angiosperms. Genome size ranges from around 108 Mb for Fragaria viridis (Bennett & Leitch, 2005) to over 120,000 Mb in some Liliaceae members (Leitch, Beaulieu, Cheung, Hanson, Lysak, & Fay, 2007). This variation is largely attributable to different proportions of non-coding repetitive DNA, such as the TEs, satellite DNA, introns, and psuedogenes (Leitch, Soltis, Soltis, & Bennett, 2005; DuÅ¡ková et al., 2010). The relationship between genome size and introns is of particular interest, because it reflects the evolution of specific types of DNA sequences that may be subjected to different constraints in selection. Genome size might be correlated with intron size across broad phylogenies, due to more rapid evolution of such unconstrained regions compared to coding regions (McLysaght, Enright, Skrabanek, & Wolfe, 2000). In general, increases in genome size are the result of deleterious mutations which fix via drift in small populations (Vinogradov, 1999). Results of previous studies indicated that intron size is subject to natural selection. For example, intron size was asymmetrically distributed in a number of organisms, which had numerous "short introns" with a minimal range of lengths, and "long introns" with a broader range of lengths, from hundreds to thousands nucleotides (Yu, Yang, Kibukawa, Paddock, Passey, & Wong, 2002; Parsch, 2003). Other studies reported that differences in intron length were consistent with variation in genome size, and that accumulation of different types of TEs was responsible for genome variation in Drosophila (Moriyama, Petrov, & Hartl, 1998) and smooth puffer fish (McLysaght et al., 2000; Guo, 2010). In contrast, Wendel, Cronn, Alvarez, Liu, Small, and Senchina (2002) reported that intron size remained remarkably static in plants, even though they are confronted with mechanisms that effect large changes in other genomic components. Despite these previous studies, the correlation between introns and genome size in plants is not well understood, especially in the Asteraceae.
Polyploidy, a key factor in the evolution of new higher plant species, has some unexpected consequences with respect to genomic characteristics. Hybridization and polyploidy can induce rapid genomic changes, including loss or gain of DNA, and such changes in nuclear DNA content are largely attributable to differences in intron size, particularly in diploid plants. Synthetic and newly formed polyploids generally have larger C-values (the amount of DNA in the haploid genome of an organism, such as in a gamete) than their progenitors, with C-value increasing in direct proportion to ploidy (Pires et al., 2004). However, many angiosperm species show no corresponding increase in C-value with ploidy, due to DNA loss succeeding polyploidy formation or to genome downsizing (Leitch & Bennet, 2004). For example, about half of all duplicated genes have been lost in the 11 million years since the polyploidy event that gave rise to the progenitor of maize (Lai et al., 2004). During the million years following the polyploidization of the ancestor of Arabidopsis thaliana, waves of chromosomal rearrangement have modified the chromosomal architecture, but the segmental architecture of the genome has been largely conserved (Ziolkowski, Kaczmarek, Babula, & Sadowski, 2006).
Nuclear genomes of plants are extremely dynamic and vary considerably in structure and size (Stebbins, 1971). Differential gene loss following polyploidy - i.e., loss of some duplicates, but not others - is responsible for much of the diversity in genome size among closely related plants (Paterson, Bowers, Peterson, Estill, & Chapman, 2003). Genome size is a good predictor of evolutionary relationships and genome constitution in species that are influenced by frequent inter- and intra-specific hybridization and polyploidization (Suda, Krahulcová, Trávnícek, Rosenbaumová, Peckert, & Krahulec, 2007). In Hieracium subgenus Pilosella, the genome size of hybrids is not subject to post-hybridization changes, and accurately reflects the nuclear DNA values of the parental taxa. In such cases, genome size can be useful in the interpretation of species relationships and provide insight into microevolutionary processes. However, unknown or unstudied co-variables could confound the relationship between genome size and intron size, if the divergence time between related species is great. Closely related taxa that share recent evolutionary history and life-history features, such as plants in the Asteraceae family, might provide more valuable information about the relationship between genome size and intron size.
Comparison of lettuce and sunflower led to three hypotheses that might explain why genome size does not correspond more closely to ploidy changes within the Asteraceae. Lettuce (2n = 18) is believed to be diploid, and sunflower (2n = 34) is thought to be an ancient tetraploid (Solbrig, 1977), yet the genome sizes of these species are similar (1C = 2.65 and 3.65 pg, respectively). The first hypothesis is that the lettuce genome has expanded via "junk" DNA; therefore, inter- and intragenic sequences (introns) might be larger in lettuce than in sunflower, leading to "genomic upsizing" in lettuce. Junk DNA has an equal chance of being added to introns or to spaces between the genes, so if lettuce has more junk DNA than sunflower, the difference should be evident as differences in intron length. The second hypothesis is that sunflower lost most of its duplicated DNA sequences following polyploidy formation, while the genome size for lettuce has remained relatively constant. In this case, intron size would have decreased in size in sunflower, but not in lettuce. In the process of diploidization, old polyploids, such as sunflower, show a tendency towards diploidy through accumulation of DNA sequence mutations between the chromosomes, and the diploidy is eventually fixed by genetic drift (Soltis, Soltis, & Tate, 2003). Leitch and Bennett (2004) compared diploids and polyploids using the Plant DNA C-values Database (http://www.rbgkew.org.uk/cval/homepage.html), and also found that genome size tended to decrease with increasing ploidy level. The third hypothesis is that lettuce and sunflower have the same ploidy, and that different chromosome numbers reflect chromosome breaks, fusions, and rearrangements, or invasion of TEs. Colinearity between highly divergent species is low, and 70% or more of angiosperms have, at least once, undergone polyploidization associated with chromosomal rearrangements, gene loss, and functional diversity (Leitch & Bennet, 1997).
The average genome size of a genus is negatively correlated with the number of species in that genus, suggesting that evolution of new species is constrained by the size of the genome (Vinogradov, 2003). Some researchers have hypothesized that large genomes are maladaptive at the species level, leading to a reduction in abundance of species (Bennett & Leitch, 2005). Vingradov (2003) found that species listed as rare or endangered have larger genomes than more common, invasive species, possibly because increases in genome size result from deleterious mutations that become fixed in small populations via drift initiated by non-adaptive processes (Lynch & Conery, 2003). Using the Plant DNA C-values Database (Bennett, Cox, & Leitch, 2001), Knight, Molinari, and Petrov (2005) found that genera with small average genome sizes did not necessarily diversify at faster rates than lineages with large genomes. However, when the analysis was restricted to lineages with relatively large genome sizes, the genomic constraint on diversification became more pronounced, and the relationship between genome size and species number was more evident. The constraint of large genomes on evolution must be due to phenotypic variation, directly or indirectly caused by changes in DNA content. Environmental stress may also influence the relationship between genome size and speciation rate by reducing the population size of species with large genomes and, therefore, increasing the probability of extinction (Lynch, Bürger, Butcher, & Gabriel, 1993).
Differences between annuals and perennials may cause a generation time effect on rates of molecular evolution and, ultimately, rates of species divergence in plants (Andreasen & Baldwin, 2001). Annual species generally have shorter life cycles, shorter minimum generation times, shorter mean cell cycle times, and shorter mean meiotic duration than perennial species (Bennett, 1972). Genome size is positively correlated with the durations of both mitosis and meiosis (Van't Hof & Sparrow, 1963; Bennett, 1971). Therefore, annuals might have smaller mean genome and intron sizes than perennial species.
The goals of the research presented in this chapter was to test the hypotheses that intron size is varies with 1) intraspecific differences in genome size and/or ploidy; 2) population size, i.e., between rare vs. widespread species; 3) generation time, i.e., between annual and perennial species; and 4) phylogenetic relationship, i.e., among subfamilies. The hypotheses were tested by using members of the Asteraceae.