Mechanisms of recent genome size variation in flowering plants

BACKGROUND AND AIMS: Plant nuclear genomes vary tremendously in DNA content, mostly due to differences in ancestral ploidy and variation in the degree of transposon amplification. These processes can increase genome size, but little is known about mechanisms of genome shrinkage and the degree to which these can attenuate or reverse genome expansion. This research focuses on characterizing DNA removal from the rice and Arabidopsis genomes, and discusses whether loss of DNA has effectively competed with amplification in these species. METHODS: Retrotransposons were analyzed for sequence variation within several element families in rice and Arabidopsis. Nucleotide sequence changes in the two termini of individual retrotransposons were used to date their time of insertion. KEY RESULTS: An accumulation of small deletions was found in both species, caused by unequal homologous recombination and illegitimate recombination. The relative contribution of unequal homologous recombination compared to illegitimate recombination was higher in rice than in Arabidopsis. However, retrotransposons are rapidly removed in both species, as evidenced by the similar apparent ages of intact elements (most less than 3 million years old) in these two plants and all other investigated plant species. CONCLUSIONS: Differences in the activity of mechanisms for retrotransposon regulation or deletion generation between species could explain current genome size variation without any requirement for natural selection to act on this trait, although the results do not preclude selection as a contributing factor. The simplest model suggests that significant genome size variation is generated by lineage-specific differences in the molecular mechanisms of DNA amplification and removal, creating major variation in nuclear DNA content that can then serve as the substrate for fitness-based selection.     

Mechanisms and rates of genome expansion and contraction in flowering plants

Plant genomes are exceptional for their great variation in genome size, an outcome derived primarily from their frequent polyploid origins and from the amplification of retrotransposons. Although most studies of plant genome size variation have focused on developmental or physiological effects of nuclear DNA content that might influence plant fitness, more recent studies have begun to investigate possible mechanisms for plant genome expansion and contraction. Analyses of relatively neutral genome components, like transposable elements, have been particularly fruitful, largely due to the enormous growth in genomic sequence information from many different plant species. Current data suggest that unequal recombination can slow the growth in genome size caused by retrotransposon amplification, but that illegitimate recombination and other deletion processes may be primarily responsible for the removal of non-essential DNA from small genome plants.     

The bat genome: GC-biased small chromosomes associated with reduction in genome size

Bats are distinct from other mammals in their small genome size as well as their high metabolic rate, possibly related to flight ability. Although the genome sequence has been published in two species, the data lack cytogenetic information. In this study, the size and GC content of each chromosome are measured from the flow karyotype of the mouse-eared bat, Myotis myotis (MMY). The smaller chromosomes are GC-rich compared to the larger chromosomes, and the relative proportions of homologous segments between MMY and human differ among the MMY chromosomes. The MMY genome size calculated from the sum of the chromosome sizes is 2.25 Gb, and the total GC content is 42.3 %, compared to human and dog with 41.0 and 41.2 %, respectively. The GC-rich small MMY genome is characterised by GC-biased smaller chromosomes resulting from preferential loss of AT-rich sequences. Although the association between GC-rich small chromosomes and small genome size has been reported only in birds so far, we show in this paper, for the first time, that the same phenomenon is observed in at least one group of mammals, implying that this may be a mechanism common to genome evolution in general.     

Sex determination in flowering plants.

In many ways, plants offer unique systems through which to study sex determination. Because the production of unisexual flowers has evolved independently in many plant species, different and novel mechanisms may be operational. Hence, there is probably not one unifying mechanism that explains sex determination in plants. Advances in our understanding of sex determination will come from the analysis of the genetics, molecular biology, and biochemistry of genes controlling sexual determination in plants. Several excellent model systems for bisexual floral development (Arabidopsis and Antirrhinum), monoecy (maize), and dioecy (Silene, asparagus, and mercury) are available for such analyses. The important questions that remain concern the mechanism of action of sex determination genes and their interrelationship, if any, with homeotic genes that determine the sexual identity of floral organ primordia. At the physiological level, the connection between hormone signaling and sexuality is not well understood, although significant correlations have been discovered. Finally, once the genes that regulate these processes are identified, cloned, and studied, new strategies for the manipulation of sexuality in plants should be forthcoming.     

Self-incompatibility in flowering plants

Self-pollination in some groups of plants is prevented by a sophisticated biochemical signalling system. The molecule active in the female emerges as a highly charged glycoprotein, but the identity of the male determinant remains unknown. Studies of both the molecular biology and the physiology of the interaction suggest that the female polypeptide belongs to a family of glycoproteins which may play an additional, and more general, role in pollination. Pollen compatibility is controlled by one of two genetic systems and new information indicates a mechanism by which they may have arisen, together with the different stigma types with which they are correlated.     

Apomixis and amphimixis in flowering plants

The objective of the present article is to compare apomictic and sexual reproduction (amphimixis) in flowering plants. Light-optical and ultrastructural aspects of the cytoembryological processes in apomicts, beginning with the early stages of development of the ovule and concluding with the newly formed seed, are considered. In the overwhelming majority of apomicts, an inability to develop an autonomous endosperm or to form viable seeds without the involvement of the process of fertilization of the nuclei of the central cell of the embryo sac is observed. Characteristic features of the ultrastructural differentiation of the megasporocytes in diplospory, of aposporous initial cells in apospory, of embryocytes in adventive embryony, and of ovicells in parthenogenesis and synergids in apogamety are identified and are compared to the generative structures of amphimicts. The hypothesis is made that the mechanisms of genetic regulation in the formation and development of the generative structures in apomixis and amphimixis are similar at the cellular level. The present study is not a survey of apomixis in general. Previously published original results that have been obtained by the present author as a result of many years of research in the area of apomixis have served as a basis for the preparation of the study.     

Polyploidy and self-fertilization in flowering plants

Mating systems directly control the transmission of genes across generations, and understanding the diversity and distribution of mating systems is central to understanding the evolution of any group of organisms. This basic idea has been the motivation for many studies that have explored the relationships between plant mating systems and other biological and/or ecological phenomena, including a variety of floral and environmental characteristics, conspecific and pollinator densities, growth form, parity, and genetic architecture. In addition to these examples, a potentially important but poorly understood association is the relationship between plant mating systems and genome duplication, i.e., polyploidy. It is widely held that polyploid plants self-fertilize more than their diploid relatives, yet a formal analysis of this pattern does not exist. Data from 235 species of flowering plants were used to analyze the association between self-fertilization and ploidy. Phylogenetically independent contrasts and cross-species analyses both lend support to the hypothesis that polyploids self-fertilize more than diploids. Because polyploidy and self-fertilization are so common among angiosperms, these results contribute not only to our understanding of the relationship between mating systems and polyploidy in particular, but more generally, to our understanding of the evolution of flowering plants.     

The relationship between genome size and synaptonemal complex length in higher plants

There appears to be only a weak correlation between genome size and the corresponding total length of a complete set of synaptonemal complexes (SCs) based on published evidence for several fungal, plant, and animal species. This result is unexpected, considering the strong positive correlations between genome size (DNA amount) and total chromosome length and volume and between relative lengths of chromosomes and SCs. Because the observed weak correlation was based on limited data, we systematically investigated the relationship between genome size and SC length, using ten higher plant species. Two-dimensional spreads of SCs from primary microsporocytes at pachytene were prepared using a hypotonic bursting technique. The SC spreads were examined either by light or electron microscopy, and the lengths of at least ten complete sets of SCs were measured for each of the ten species. Additionally, the genome size of each species was determined from pollen tetrad protoplasts using flow cytometry. A strong correlation (r = 0.97) between total SC length and genome size was observed for higher plants, indicating a constant amount of DNA is associated with a given length of SC, at least when averaged over the whole genome.     

Cryptic dioecy in flowering plants

In some dioecious plant species, mates and/or females have large and presumably costly opposite-sex structures that are sterile. This is termed 'cryptic dioecy'. Several new cases of cryptic dioecy have recently been studied. They may give information about the minimal requirements for the evolution of separate sexes from hermaphroditism, because the most important differences contributing to the initial advantage of the breeding system have not been obscured by further developments. Reviewed in this light, cryptic dioecy can provide evidence on the role of reallocation of reproductive resources in the evolution of dioecy.     

Statistical analysis of nuclear genome size of plants with flow cytometer data.

BACKGROUND: There is a mismatch between the sophistication of the cytometer and the resulting data, made possible by the computing power of today, and the traditional statistical methods based on the computing power of the early 1930s. The purpose here is to apply modern statistical techniques that similarly take advantage of this computer power. METHODS: Likelihood functions and their graphs are introduced as direct measures of plausibility of the parameters of interest. These methods are valid for samples of any size. They are exemplified on an experimental plant flow cytometer data set with n = 2 replications. RESULTS: The likelihood functions revealed important features of the data that would have been missed by the traditional methods, and in fact would invalidate them. CONCLUSIONS: The likelihood function produced highly informative graphs that allow quantitative comparisons of different aspects of 2C DNA nuclear contents among different groups or varieties of plants.     

Egg activation in flowering plants

Compared to animals and algae, egg activation in flowering plants is still poorly understood because of the inaccessibility and complexity of the fertilization process which is double and internal. However, the development of in vitro fertilization (IVF) systems in maize and a few other plants, despite some limitations, offers new possibilities for the study of early post- fusional events and signals leading to egg activation under defined conditions. This review reports recent data on calcium events induced by gamete fusion during maize IVF and presents perspectives on the role of calcium in egg activation and in early development. Received: 2 December 2000 / Accepted: 7 June 2001     

Infraspecific categories in flowering plants

Infraspecific categories imply infraspecific classification, but there are few species whose internal diversity has been sufficiently studied to permit this in any detail. Important variation may be physiological, continuous and unassociated with convenient morphological markers. Conspicuous variation may be biologically trivial and the use of names for these variants gives a misleading view of the species-structure. If we are to classify we must know the relation between the internal and external characters. The suitability of a hierarchical system cannot be assumed. Informal classifications are likely to be of more use than those provided by the Code of Nomenclature. Nevertheless variation undesignated may easily become variation overlooked.     

Infraspecific categories in flowering plants

Infraspecific categories imply infraspecific classification, but there are few species whose internal diversity has been sufficiently studied to permit this in any detail. Important variation may be physiological, continuous and unassociated with convenient morphological markers. Conspicuous variation may be biologically trivial and the use of names for these variants gives a misleading view of the species-structure. If we are to classify we must know the relation between the internal and external characters. The suitability of a hierarchical system cannot be assumed. Informal classifications are likely to be of more use than those provided by the Code of Nomenclature. Nevertheless variation undesignated may easily become variation overlooked.     

Nuclear genome size in Selaginella.

Estimates of nuclear genome size for 9 Selaginella species were obtained using flow cytometry, and measurements for 7 of these species are reported for the first time. Estimates range from 0.086 to 0.112 pg per holoploid genome (84-110 Mb). The data presented here agree with the previously published flow cytometric results for S. moellendorffii. Within the 9 species sampled here, chromosome number varies from 2n = 16 to 2n = 27. Nuclear genome size appears to be strongly correlated with chromosome number (Spearman's rank correlation; p = 0.00003725). Cultivated S. moellendorffii lacks sexual reproduction--manifest by the production of abortive megasporangia. Flow cytometric data generated from a herbarium specimen of a fertile wild-collected S. moellendorffii are virtually indistinguishable from the data generated from fresh material (0.088 vs. 0.089 pg/1C). Therefore, the limited fertility observed in cultivated plants is probably not the result of abnormal chromosome number (e.g., induced by interspecific hybridization).     

LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model

Long Terminal Repeat (LTR) retrotransposons are ubiquitous components of plant genomes. Because of their copy-and-paste mode of transposition, these elements tend to increase their copy number while they are active. In addition, it is now well established that the differences in genome size observed in the plant kingdom are accompanied by variations in LTR retrotransposon content, suggesting that LTR retrotransposons might be important players in the evolution of plant genome size, along with polyploidy. The recent availability of large genomic sequences for many crop species has made it possible to examine in detail how LTR retrotransposons actually drive genomic changes in plants. In the present paper, we provide a review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective. These studies have shown that plant genomes undergo genome size increases through bursts of retrotransposition, while there is a counteracting process that tends to eliminate the transposed copies from the genomes. This process involves recombination mechanisms that occur either between the LTRs of the elements, leading to the formation of solo-LTRs, or between direct repeats anywhere in the sequence of the element, leading to internal deletions. All these studies have led to the emergence of a new model for plant genome evolution that takes into account both genome size increases (through retrotransposition) and decreases (through solo-LTR and deletion formation). In the conclusion, we discuss this new model and present the future prospects in the study of plant genome evolution in relation to the activity of transposable elements.