Genome evolution: sex and the transposable element

Using a meiosis detection toolkit to investigate ancient asexual "scandals" and the evolution of sex

Sexual reproduction is the dominant reproductive mode in eukaryotes but, in many taxa, it has never been observed. Molecular methods that detect evidence of sex are largely based on the genetic consequences of sexual reproduction. Here we describe a powerful new approach to directly search genomes for genes that function in meiosis. We describe a "meiosis detection toolkit", a set of meiotic genes that represent the best markers for the presence of meiosis. These genes are widely present in eukaryotes, function only in meiosis and can be isolated by degenerate PCR. The presence of most, or all, of these genes in a genome would suggest they have been maintained for meiosis and, implicitly, sexual reproduction. In contrast, their absence would be consistent with the loss of meiosis and asexuality. This approach will help to understand both meiotic gene evolution and the capacity for meiosis and sex in putative obligate asexuals.

Active miniature transposons from a plant genome and its nonrecombining Y chromosome

Mechanisms involved in eroding fitness of evolving Y chromosomes have been the focus of much theoretical and empirical work. Evolving Y chromosomes are expected to accumulate transposable elements (TEs), but it is not known whether such accumulation contributes to their genetic degeneration. Among TEs, miniature inverted-repeat transposable elements are nonautonomous DNA transposons, often inserted in introns and untranslated regions of genes. Thus, if they invade Y-linked genes and selection against their insertion is ineffective, they could contribute to genetic degeneration of evolving Y chromosomes. Here, we examine the population dynamics of active MITEs in the young Y chromosomes of the plant Silene latifolia and compare their distribution with those in recombining genomic regions. To isolate active MITEs, we developed a straightforward approach on the basis of the assumption that recent transposon insertions or excisions create singleton or low-frequency size polymorphisms that can be detected in alleles from natural populations. Transposon display was then used to infer the distribution of MITE insertion frequencies. The overall frequency spectrum showed an excess of singleton and low-frequency insertions, which suggests that these elements are readily removed from recombining chromosomes. In contrast, insertions on the Y chromosomes were present at high frequencies. Their potential contribution to Y degeneration is discussed.

The mode and tempo of genome size evolution in eukaryotes

Eukaryotic genome size varies over five orders of magnitude; however, the distribution is strongly skewed toward small values. Genome size is highly correlated to a number of phenotypic traits, suggesting that the relative lack of large genomes in eukaryotes is due to selective removal. Using phylogenetic contrasts, we show that the rate of genome size evolution is proportional to genome size, with the fastest rates occurring in the largest genomes. This trend is evident across the 20 major eukaryotic clades analyzed, indicating that over long time scales, proportional change is the dominant and universal mode of genome-size evolution in eukaryotes. Our results reveal that the evolution of eukaryotic genome size can be described by a simple proportional model of evolution. This model explains the skewed distribution of eukaryotic genome sizes without invoking strong selection against large genomes.

The fate of transposable elements in asexual populations

Sexual reproduction and recombination are important for maintaining a stable copy number of transposable elements (TEs). In sexual populations, elements can be contained by purifying selection against host carriers with higher element copy numbers; however, in the absence of sex and recombination, asexual populations could be driven to extinction by an unchecked proliferation of TEs. Here we provide a theoretical framework for analyzing TE dynamics under asexual reproduction. Analytic results show that, in an infinite asexual population, an equilibrium in copy number is achieved if no element excision is possible, but that all TEs are eliminated if there is some excision. In a finite population, computer simulations demonstrate that small populations are driven to extinction by a Muller's ratchet-like process of element accumulation, but that large populations can be cured of vertically transmitted TEs, even with excision rates well below transposition rates. These results may have important consequences for newly arisen asexual lineages and may account for the lack of deleterious retrotransposons in the putatively ancient asexual bdelloid rotifers.

Retrotransposon Sequence Variation in Four Asexual Plant Species

Transposable elements (TEs) can be viewed as genetic parasites that persist in populations due to their capacity for increase in copy number and the inefficacy of selection against them. A corollary of this hypothesis is that TEs are more likely to spread within sexual populations and be eliminated or inactivated within asexual populations. While previous work with animals has shown that asexual taxa may contain less TE diversity than sexual taxa, comparable work with plants has been lacking. Here we report the results of a study of Ty1/copia, Ty3/gypsy, and LINE-like retroelement diversity in four asexual plant species. Retroelement-like sequences, with a high degree of conservation both within and between species, were isolated from all four species. The sequences correspond to several previously annotated retroelement subfamilies. They also exhibit a pattern of nucleotide substitution characterized by an excess of synonymous substitutions, suggestive of a history of purifying selection. These findings were compared with retroelement sequence evolution in sexual plant taxa. One likely explanation for the discovery of conserved TE sequences in the genomes of these asexual taxa is simply that asexuality within these taxa evolved relatively recently, such that the loss and breakdown of TEs is not yet detectable through analysis of sequence diversity. This explanation is examined by conducting stochastic simulation of TE evolution and by using published information to infer rough estimates of the ages of asexual taxa.

Genetic variability and adaptive evolution in parthenogenetic root-knot nematodes

Root-knot nematodes (RKN) of the genus Meloidogyne are biotrophic plant parasites of major agricultural importance, which exhibit very variable modes of reproduction, from classical amphimixis to mitotic parthenogenesis. This review focuses on those RKN species that reproduce exclusively by mitotic parthenogenesis (apomixis), in contrast to those that have meiotic/amphimitic events in their life cycle. Although populations of clonal organisms are often represented as being ecologically isolated and evolutionary inert, a considerable volume of literature provides evidence that asexual RKN are neither: they are widely distributed, extremely polyphagous, and amenable to selection and adaptive variation. The ancestors of the genus are unknown, but it is assumed that the parthenogenetic RKN have evolved from amphimictic species through hybridization and subsequent aneuploidization and polyploidization events. Molecular studies have indeed confirmed that the phylogenetic divergence between meiotic and mitotic RKN lineages occurred early, and have revealed an unexpected level of clonal diversity among populations within apomictic species. Laboratory experiments have shown that asexual RKN can rapidly adapt to new environmental constraints (eg host resistance), although with some fitness costs. Lastly, the molecular and chromosomal mechanisms that could contribute to genome plasticity leading to persistent genetic variation and adaptive evolution in apomictic RKN are discussed. It is concluded that RKN provide an excellent model system in which to study the dynamic nature and adaptive potential of clonal genomes.

Molecular typing of aspergilli: Recent developments and outcomes

Aspergillus spp. have been the subject of numerous epidemiological studies. The most useful typing techniques are DNA based methods including the random amplified polymorphic DNA technique, microsatellite length polymorphisms, restriction fragment length polymorphism (RFLP) analysis using retrotransposon-like sequences as probes, and multilocus sequence typing. The results of typing clinical isolates indicate that most of the invasive aspergillosis (IA) patients were infected by a single strain. Genetic analysis could not discriminate between clinical and environmental isolates of Aspergillus. fumigatus, indicating that every strain present in the environment is a potential pathogen if it encounters the appropriate host. The source of infection can also be monitored by typing. Typing studies led to the discovery of a new pathogenic species, A. lentulus, and to the identification of several species not known previously to be pathogenic. Typing studies revealed the existence of two genetically isolated groups within a global A. fumigatus population. Aspergillus fumigatus was found to be the first example of a true cosmopolitan fungus. Additionally, the results obtained in several studies support the premise that recombination played an important role in A. fumigatus populations. The discovery of functional mating type genes in A. fumigatus indicates that past or recent sexual processes could be responsible for the observed recombining population structure.

Mobile genetic elements and sexual reproduction

Transposable elements (TE) are prominent components of most eukaryotic genomes. In addition to their possible participation in the origin of sexual reproduction in eukaryotes, they may be also involved in its maintenance as important contributors to the deleterious mutation load. Comparative analyses of transposon content in the genomes of sexually reproducing and anciently asexual species may help to understand the contribution of different TE classes to the deleterious load. The apparent absence of deleterious retrotransposons from the genomes of ancient asexuals is in agreement with the hypothesis that they may play a special role in the maintenance of sexual reproduction and in early extinction for which most species are destined upon the abandonment of sex.

Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus

Aspergillus fumigatus is a medically important opportunistic pathogen and a major cause of respiratory allergy. The species has long been considered an asexual organism. However, genome analysis has revealed the presence of genes associated with sexual reproduction, including a MAT-2 high-mobility group mating-type gene and genes for pheromone production and detection (Galagan et al., personal communication; Nierman et al., personal communication). We now demonstrate that A. fumigatus has other key characteristics of a sexual species. We reveal the existence of isolates containing a complementary MAT-1 alpha box mating-type gene and show that the MAT locus has an idiomorph structure characteristic of heterothallic (obligate sexual outbreeding) fungi. Analysis of 290 worldwide clinical and environmental isolates with a multiplex-PCR assay revealed the presence of MAT1-1 and MAT1-2 genotypes in similar proportions (43% and 57%, respectively). Further population genetic analyses provided evidence of recombination across a global sampling and within North American and European subpopulations. We also show that mating-type, pheromone-precursor, and pheromone-receptor genes are expressed during mycelial growth. These results indicate that A. fumigatus has a recent evolutionary history of sexual recombination and might have the potential for sexual reproduction. The possible presence of a sexual cycle is highly significant for the population biology and disease management of the species.

Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres

The recent release of sequences of several unexplored yeast species that cover an evolutionary range comparable to the entire phylum of chordates offers us a unique opportunity to investigate how genes involved in adaptation have been shaped by evolution. We have examined how three different sets of genes, all related to adaptative processes at the genomic level, have evolved in hemiascomycetes: (1) the mating-type genes that govern sexuality, (2) the silencing genes that are connected to regulation of mating-type cassettes and to telomere position effect, and (3) the gene families found repeated in subtelomeric regions. We report new combinations of mating-type genes and cassettes in hemiascomycetous species; we show that silencing proteins diverge rapidly. We have also found that in all species studied, subtelomeric gene families exist and are specific to each species.

Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana

Transposable elements (TEs) comprise a major component of eukaryotic genomes, and exhibit striking deviations from random distribution across the genomes studied, including humans, flies, nematodes, and plants. Although considerable progress has been made in documenting these patterns, the causes are subject to debate. Here, we use the genome sequence of Arabidopsis thaliana to test for the importance of competing models of natural selection against TE insertions. We show that, despite TE accumulation near the centromeres, recombination does not generally correlate with TE abundance, suggesting that selection against ectopic recombination does not influence TE distribution in A. thaliana. In contrast, a consistent negative correlation between gene density and TE abundance, and a strong under-representation of TE insertions in introns suggest that selection against TE disruption of gene expression is playing a more important role in A. thaliana. High rates of self-fertilization may reduce the importance of recombination rate in genome structuring in inbreeding organisms such as A. thaliana and Caenorhabditis elegans.

Symbiotic and genetic diversity of Rhizobium galegae isolates collected from the Galega orientalis gene center in the Caucasus

This paper explores the relationship between the genetic diversity of rhizobia and the morphological diversity of their plant hosts. Rhizobium galegae strains were isolated from nodules of wild Galega orientalis and Galega officinalis in the Caucasus, the center of origin for G. orientalis. All 101 isolates were characterized by genomic amplified fragment length polymorphism fingerprinting and by PCR-restriction fragment length polymorphism (RFLP) of the rRNA intergenic spacer and of five parts of the symbiotic region adjacent to nod box sequences. By all criteria, the R. galegae bv. officinalis and R. galegae bv. orientalis strains form distinct clusters. The nod box regions are highly conserved among strains belonging to each of the two biovars but differ structurally to various degrees between the biovars. The findings suggest varying evolutionary pressures in different parts of the symbiotic genome of closely related R. galegae biovars. Sixteen R. galegae bv. orientalis strains harbored copies of the same insertion sequence element; all were isolated from a particular site and belonged to a limited range of chromosomal genotypes. In all analyses, the Caucasian R. galegae bv. orientalis strains were more diverse than R. galegae bv. officinalis strains, in accordance with the gene center theory.

Experimental tests of the adaptive significance of sexual recombination

Numerous theories have been proposed to explain the advantages of sexual recombination the exchange of hereditary material between different genomes or homologous chromosomes. Many of these candidate benefits have been evaluated in controlled laboratory experiments, which, collectively, strongly indicate that sexual recombination provides important long-term advantages.

Evolution of sex: The costs and benefits of sex: new insights from old asexual lineages

Discussions that are aimed at understanding the maintenance of sexual reproduction are in a bit of a quagmire owing to the many competing theories that have been proposed. Also, one of the central observations that asexual lineages are typically short lived still needs to be properly quantified. Exciting new results on ancient asexual organisms show that lineages can persist for many millions of generations without recombination. Understanding how they do so might well provide crucial new insights into the problem of sex.

Breeding systems and genome evolution

The profound effects of inbreeding and other non-recombining breeding systems on genetic variability and molecular evolution are now beginning to be understood. Theoretical models predict how such populations are expected to differ from outcrossed populations, and DNA sequence data are being collected and used to test the predictions.