Meiosis-driven genome variation in plants

Meiosis includes two successive divisions of the nucleus with one round of DNA replication and leads to the formation of gametes with half of the chromosomes of the mother cell during sexual reproduction. It provides a cytological basis for gametogenesis and nheritance in eukaryotes. Meiotic cell division is a complex and dynamic process that involves a number of molecular and cellular events, such as DNA and chromosome replication, chromosome pairing, synapsis and recombination, chromosome segregation, and cytokinesis. Meiosis maintains genome stability and integrity over sexual life cycles. On the other hand, meiosis generates genome variations in several ways. Variant meiotic recombination resulting from specific genome structures induces deletions, duplications, and other rearrangements within the genic and non-genic genomic regions and has been considered a major driving force for gene and genome evolution in nature. Meiotic abnormalities in chromosome segregation lead to chromosomally imbalanced gametes and aneuploidy. Meiotic restitution due to failure of the first or second meiotic division gives rise to unreduced gametes, which triggers polyploidization and genome expansion. This paper reviews research regarding meiosis-driven genome variation, including deletion and duplication of genomic regions, aneuploidy, and polyploidization, and discusses the effect of related meiotic events on genome variation and evolution in plants. Knowledge of various meiosis-driven genome variations provides insight into genome evolution and genetic variability in plants and facilitates plant genome research.     

抑制植物减数分裂重组的分子机理

减数分裂重组不仅保证了真核生物有性生殖过程中染色体数量的稳定,还通过父母亲本间遗传物质的互换在后代中产生遗传变异。因此,减数分裂重组是遗传多样性形成的重要途径,也是生物多样性和物种进化的主要动力。在绝大多数真核生物中,不管染色体数目的多少或基因组的大小,减数分裂重组的形成都受到严格的调控,但抑制减数分裂重组的分子机理目前仍不清楚。近年来,通过正向遗传学筛选鉴定出多个减数分裂重组抑制基因,揭示了抑制基因的功能和调控途径。本文基于拟南芥中减数分裂重组抑制基因的研究现状,综述了植物减数分裂重组抑制基因研究取得的突破性进展,并结合基因功能与其调控网络阐述了抑制植物减数分裂重组的分子机理。     

Sex and speciation: The paradox that non-recombining DNA promotes recombination

The benefits of sexual reproduction that outweigh its costs have long puzzled biologists. Increased genetic diversity generated by new allelic combinations, as enhanced by recombination during meiosis, is considered a primary benefit of sex. Sex-determining systems have evolved independently on numerous occasions. One of the most familiar is the use of sex chromosomes in vertebrates. Other eukaryotic groups also use sex chromosomes or smaller sex-determining regions within their chromosomes, such as the mating type loci in the fungi. In these organisms, sexual reproduction and its associated meiotic recombination are controlled by regions of the genome that are themselves blocked in recombination. Non-recombining DNA that is essential for recombination presents a paradox. One hypothesis is that sex-determination requires or leads to highly diverse alleles, establishing this block in recombination. A second hypothesis to account for the common occurrence of these types of sex-determining systems is that they combine mechanisms for recombination suppression and reproductive isolation, thereby promoting the evolution of new species. The fungal kingdom represents the ideal eukaryotic lineage to elucidate the functions of non-recombining regions in sex-determination and speciation.     

Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism,Allowing Mapping of a Mating Identity Locus

Horizontal gene transfer (HGT) in bacteria generates variation and drives evolution, and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species. We previously described a novel form of chromosomal conjugation in mycobacteria that does not conform to classic oriT-based conjugation models, and whose potential evolutionary significance has not been evaluated. Here, we determined the genome sequences of 22 F1-generation transconjugants, providing the first genome-wide view of conjugal HGT in bacteria at the nucleotide level. Remarkably, mycobacterial recipients acquired multiple, large, unlinked segments of donor DNA, far exceeding expectations for any bacterial HGT event. Consequently, conjugal DNA transfer created extensive genome-wide mosaicism within individual transconjugants, which generated large-scale sibling diversity approaching that seen in meiotic recombination. We exploited these attributes to perform genome-wide mapping and introgression analyses to map a locus that determines conjugal mating identity in M. smegmatis. Distributive conjugal transfer offers a plausible mechanism for the predicted HGT events that created the genome mosaicism observed among extant Mycobacterium tuberculosis and Mycobacterium canettii species. Mycobacterial distributive conjugal transfer permits innovative genetic approaches to map phenotypic traits and confers the evolutionary benefits of sexual reproduction in an asexual organism.     

Levels of polymorphism on the sex‐limited chromosome: a clue to Y from W?

Nucleotide diversity of the human Y chromosome is much lower than that in the rest of the genome. A new hypothesis postulates that this invariance may result from mutations in maternally inherited mitochondrial DNA (mtDNA), leading to impaired reproduction among males and lowered male effective population size. If correct, we should expect to see low levels of polymorphism in the male-specific Y chromosome of many organisms but not necessarily in the female-specific W chromosome in organisms with female heterogamety. However, recent observations from birds suggest that the avian W chromosome is very low in nucleotide diversity. This indicates that mtDNA mutations cannot broadly explain the evolution of the sex-limited chromosome. Other work has suggested that sexual selection at loci involved in sex determination or secondary sexual characteristics might reduce levels of genetic variability on Y through hitch-hiking effects. Although the W chromosome does not seen to play a dominant role for sex determination in birds, it cannot be excluded that selective sweeps arising from natural or sexual selection contribute to the low levels of genetic variability seen on this chromosome.     

The resolution of sexual antagonism by gene duplication

Disruptive selection between males and females can generate sexual antagonism, where alleles improving fitness in one sex reduce fitness in the other. This type of genetic conflict arises because males and females carry nearly identical sets of genes: opposing selection, followed by genetic mixing during reproduction, generates a population genetic "tug-of-war" that constrains adaptation in either sex. Recent verbal models suggest that gene duplication and sex-specific cooption of paralogs might resolve sexual antagonism and facilitate evolutionary divergence between the sexes. However, this intuitive proximal solution for sexual dimorphism potentially belies a complex interaction between mutation, genetic drift, and positive selection during duplicate fixation and sex-specific paralog differentiation. The interaction of these processes--within the explicit context of duplication and sexual antagonism--has yet to be formally described by population genetics theory. Here, we develop and analyze models of gene duplication and sex-specific differentiation between paralogs. We show that sexual antagonism can favor the fixation and maintenance of gene duplicates, eventually leading to the evolution of sexually dimorphic genetic architectures for male and female traits. The timescale for these evolutionary transitions is sensitive to a suite of genetic and demographic variables, including allelic dominance, recombination, sex linkage, and population size. Interestingly, we find that female-beneficial duplicates preferentially accumulate on the X chromosome, whereas male-beneficial duplicates are biased toward autosomes, independent of the dominance parameters of sexually antagonistic alleles. Although this result differs from previous models of sexual antagonism, it is consistent with several findings from the empirical genomics literature.     

Origin of sex

The competitive advantage of sex consists in being able to use redundancy to recover lost genetic information while minimizing the cost of redundancy. We show that the major selective forces acting early in evolution lead to RNA protocells in which each protocell contains one genome, since this maximizes the growth rate. However, damages to the RNA which block replication and failure of segregation make it advantageous to fuse periodically with another protocell to restore reproductive ability. This early, simple form of genetic recovery is similar to that occurring in extant segmented single stranded RNA viruses. As duplex DNA became the predominant form of the genetic material, the mechanism of genetic recovery evolved into the more complex process of recombinational repair, found today in a range of species. We thus conclude that sexual reproduction arose early in the evolution of life and has had a continuous evolutionary history. We cite reasons to reject arguments for gaps in the evolutionary sequence of sexual reproduction based on the presumed absence of sex in the cyanobacteria. Concerning the maintenance of the sexual cycle among current organisms, we take care to distinguish between the recombinational and outbreeding aspects of the sexual cycle. We argue that recombination, whether it be in outbreeding organisms, self-fertilizing organisms or automictic parthenogens, is maintained by the advantages of recombinational repair. We also discuss the role of DNA repair in maintaining the outbreeding aspects of the sexual cycle.     

FROM CLONAL TO SEXUAL HYBRIDS: GENETIC RECOMBINATION VIA TRIPLOIDS IN ALL-HYBRID POPULATIONS OF WATER FROGS

Speciation via interspecific hybrids is very rare in animals, as compared to plants. Whereas most plants overcome the problem of meiosis between different chromosome sets by tetraploidization, animal hybrids often escape hybrid sterility by clonal reproduction. This comes at the expense of genetic diversity and the ability to purge deleterious mutations. However, here we show that all-hybrid populations of diploid (LR) and triploid (LLR and LRR) water frogs ( Pelophylax esculentus ) have secondarily acquired sexual reproduction. First, in a crossing experiment analyzed with microsatellite markers, triploid hybrids of both sexes and genotypes (LLR and LRR) recombined their homospecific genomes. Second, the great majority of natural populations investigated had low multilocus linkage disequilibrium, indicating a high recombination rate. As predicted from mating system models, the L genome had constant, low levels of linkage disequilibrium, whereas linkage disequilibrium in the R genome showed a significant reduction with increasing proportion of recombining triploids. This direct evidence of sexual reproduction in P. esculentus calls for a change of the conventional view of hybridogens as clonally reproducing diploids. Rather, hybridogens can be independent sexually reproducing units with an evolutionary potential.     

Evolving Concepts of Bacterial Species

The same evolutionary forces that cause diversification in sexual eukaryotes are expected to cause diversification in bacteria. However, in bacteria, the wider variety of mechanisms for gene exchange (or lack thereof) increases the range of expected diversity patterns compared to those of sexual organisms. Two parallel concepts for bacterial speciation have developed, based on ecological divergence or barriers to recombination in turn. Recent evidence from DNA sequence data shows that both processes can generate independently evolving groups that are equivalent to sexual species and that represent separate arenas within which recombination (when it occurs), selection and drift occur. It remains unclear, however, how often different processes act in concert to generate simple units of diversity, or whether a more complex model of diversity is required, specifying hierarchical levels at which different cohesive processes operate. We advocate an integrative approach that evaluates the effects of multiple evolutionary forces on diversity patterns. There is also great potential for laboratory studies of bacterial evolution that test evolutionary mechanisms inferred from population genetic analyses of multi-locus and genome sequence data.     

Unisexual and Heterosexual Meiotic Reproduction Generate Aneuploidy and Phenotypic Diversity De Novo in the Yeast Cryptococcus neoformans

Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down''s syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug resistance and enables rapid adaptive evolution. We report here that sexual reproduction generates phenotypic and genotypic diversity in the human pathogenic yeast Cryptococcus neoformans, which is globally distributed and commonly infects individuals with compromised immunity, such as HIV/AIDS patients, causing life-threatening meningoencephalitis. C. neoformans has a defined a-α opposite sexual cycle; however, >99% of isolates are of the α mating type. Interestingly, α cells can undergo α-α unisexual reproduction, even involving genotypically identical cells. A central question is: Why would cells mate with themselves given that sex is costly and typically serves to admix preexisting genetic diversity from genetically divergent parents? In this study, we demonstrate that α-α unisexual reproduction frequently generates phenotypic diversity, and the majority of these variant progeny are aneuploid. Aneuploidy is responsible for the observed phenotypic changes, as chromosome loss restoring euploidy results in a wild-type phenotype. Other genetic changes, including diploidization, chromosome length polymorphisms, SNPs, and indels, were also generated. Phenotypic/genotypic changes were not observed following asexual mitotic reproduction. Aneuploidy was also detected in progeny from a-α opposite-sex congenic mating; thus, both homothallic and heterothallic sexual reproduction can generate phenotypic diversity de novo. Our study suggests that the ability to undergo unisexual reproduction may be an evolutionary strategy for eukaryotic microbial pathogens, enabling de novo genotypic and phenotypic plasticity and facilitating rapid adaptation to novel environments.     

Synergy from reproductive division of labor and genetic complexity drive the evolution of sex

Computer experiments that mirror the evolutionary dynamics of sexual and asexual organisms as they occur in nature were used to test features proposed to explain the evolution of sexual recombination. Results show that this evolution is better described as a network of interactions between possible sexual forms, including diploidy, thelytoky, facultative sex, assortation, bisexuality, and division of labor between the sexes, rather than a simple transition from parthenogenesis to sexual recombination. Diploidy was shown to be fundamental for the evolution of sex; bisexual reproduction emerged only among anisogamic diploids with a synergistic division of reproductive labor; and facultative sex was more likely to evolve among haploids practicing assortative mating. Looking at the evolution of sex as a complex system through individual-based simulations explains better the diversity of sexual strategies known to exist in nature, compared to classical analytical models.     

The origin and evolution of sexual reproduction up to the evolution of the male-female phenomenon

Summary Sexual reproduction is a composite, not a singular, phenomenon and as such can be subdivided into a number of componentsi.e. fusion, recombination, fission, and the male-female phenomenon. These components can evolve independently, though any evolutionary change in one component is likely to influence the future evolution of the other components. The ambiguity that surrounds the term sex due to a failure to recognise the composite nature of sexual reproduction has led to considerable confusion in past discussions of the evolution of the phenomenon. This paper considers the possible chronological interaction of the components of sexual reproduction both with each other and with the sequence of selective pressures that seem likely to have acted. This chronological approach is used to consider: the origin of sexual reproduction; the evolution of sexual reproduction in the common ancestor of the procaryotes and eucaryotes; the modification of the ancestral system in the procaryote line following the procaryote-eucaryote dichotomy; and the modification of the ancestral system in the eucaryote line up to the origin of the male-female phenomenon.It is suggested that the fusion and recombination of the first living organisms were chronological continuations of the fusion and recombination of complex organic molecules that led up to the origin of life. The evolution of the third major component of sexual reproductioni.e. fission (replication), by definition coincided with the origin of life. Initial selection on the components of sexual reproduction are likely to have been related to the optimum manifestations of size, complexity, diversity, multiplication, and distribution. Resultant early evolutionary trends are likely to have been: selective fusion between more-similar organisms; increase in number of fissions per fusion; and less recombination.The procaryote-eucaryote dichotomy is argued to have evolved in response to the increasing cellular problems of packing and replicating an increasing amount of hereditary material. The evolution of a single circular hereditary organelle in the procaryote line is argued to have led to the loss of total fusion and the specialisation of individuals into either donors or recipients. The donor-recipient phenomenon of procaryotes is directly analogous to the male-female phenomenon of eucaryotes and leads to parallel evolution due to sexual selection in both groups. In the eucaryote line the ancestral mechanism of sexual reproduction is argued to have persisted through, but to have been greatly modified by, the evolution of complex machinery (mitotic/meiotic) for the handling of multiple hereditary organelles at cell division and reduction division. The evolutionary modification of the ancestral system of sexual reproduction is suggested to have led in eucaryotes to the evolution of: the species phenomenon; allelic recombination; and the male-female phenomenon.     

Evolutionary genetics: the evils of abstinence from sex

The evolutionary significance of sexual reproduction and genetic recombination is a long-standing puzzle. Some recent experiments on Drosophila show that a lack of recombination can impede adaptive evolution.     

Anisogamy,sexual selection,and the evolution and maintenance of sex

Summary In the present paper we distinguish between two aspects of sexual reproduction. Genetic recombination is a universal features of the sexual process. It is a primitive condition found in simple, single-celled organisms, as well as in higher plants and animals. Its function is primarily to repair genetic damage and eliminate deleterious mutations. Recombination also produces new variation, however, and this can provide the basis for adaptive evolutionary change in spatially and temporally variable environments.The other feature usually associated with sexual reproduction, differentiated male and female roles, is a derived condition, largely restricted to complex, diploid, multicellular organisms. The evolution of anisogamous gametes (small, mobile male gametes containing only genetic material, and large, relatively immobile female gametes containing both genetic material and resources for the developing offspring) not only established the fundamental basis for maleness and femaleness, it also led to an asymmetry between the sexes in the allocation of resources to mating and offspring. Whereas females allocate their resources primarily to offspring, the existence of many male gametes for each female one results in sexual selection on males to allocate their resources to traits that enhance success in competition for fertilizations. A consequence of this reproductive competition, higher variance in male than female reproductive success, results in more intense selection on males.The greater response of males to both stabilizing and directional selection constitutes an evolutionary advantage of males that partially compensates for the cost of producing them. The increased fitness contributed by sexual selection on males will complement the advantages of genetic recombination for DNA repair and elimination of deleterious mutations in any outcrossing breeding system in which males contribute only genetic material to their offspring. Higher plants and animals tend to maintain sexual reproduction in part because of the enhanced fitness of offspring resulting from sexual selection at the level of individual organisms, and in part because of the superiority of sexual populations in competition with asexual clones.     

Similarity in recombination rate estimates highly correlates with genetic differentiation in humans

Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans.     

Interplay between modifications of chromatin and meiotic recombination hotspots

Meiotic recombination lies at the heart of sexual reproduction. It is essential for producing viable gametes with a normal haploid genomic content and its dysfunctions can be at the source of aneuploidies, such as the Down syndrome, or many genetic disorders. Meiotic recombination also generates genetic diversity that is transmitted to progeny by shuffling maternal and paternal alleles along chromosomes. Recombination takes place at non-random chromosomal sites called 'hotspots'. Recent evidence has shown that their location is influenced by properties of chromatin. In addition, many studies in somatic cells have highlighted the need for changes in chromatin dynamics to allow the process of recombination. In this review, we discuss how changes in the chromatin landscape may influence the recombination map, and reciprocally, how recombination events may lead to epigenetic modifications at sites of recombination, which could be transmitted to progeny.     

Selfish DNA: A Sexually-Transmitted Nuclear Parasite

A quantitative population genetics model for the evolution of transposable genetic elements is developed. This model shows that "selfish" DNA sequences do not have to be selectively neutral at the organismic level; indeed, such DNA can produce major deleterious effects in the host organism and still spread through the population. The model can be used to explain the evolution of introns within eukaryotic genes; this explanation does not invoke a long-term evolutionary advantage for introns, nor does it depend on the hypothesis that eukaryotic gene structure may be an evolutionary relic. Transposable genes that carried information specifying sexual reproduction in the host organism would favor their own spread. Consequently, it is tempting to speculate that some of the genes controlling sex were originally selected as transposable elements.     

Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

Background  

The existence of "ancient asexuals", taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of the asexual organism but also for its genome. Several genetic signatures are predicted from long-term asexual (apomictic) reproduction including (i) large "allelic" sequence divergence (ii) lack of phylogenetic clustering of "alleles" within morphological species and (iii) decay and loss of genes specific to meiosis and sexual reproduction. These genetic signatures can be hard to assess since it is difficult to demonstrate the allelic nature of very divergent sequences, divergence levels may be complicated by processes such as inter-specific hybridization, and genes may have secondary roles unrelated to sexual reproduction. Apomictic species of Meloidogyne root knot nematodes have been suggested previously to be ancient asexuals. Their relatives reproduce by meiotic parthenogenesis or facultative sexuality, which in combination with the abundance of nematode genomic sequence data, makes them a powerful system in which to study the consequences of reproductive mode on genomic divergence.     

The uncertainty of "fitness:" what prevents understanding of the role of genetic exchange

The evolutionary development of highly organized species is attained through an increase in average survival of individuals, whereas the evolution of primitive species involves only an increase in fecundity (Zavadsky, 1958, 1961). However, in population genetics, survival (or ecological resistance) and fecundity are regarded as components of a single character, fitness. Employment of the notion of fitness, which lacks a strict definition, hinders understanding of the mechanism of progressive evolution as the process that enhances ecological resistance of organisms. The notion of fitness also exacerbates understanding the role of genetic exchange, since the primary advantage of genetic recombination and sexual reproduction apparently is producing of progeny with high ecological resistance rather than with high genetic diversity as such. Thus, the regular genetic exchange ensures restoration of the level of ecological resistance characteristic for the species, and on the macroevolutionary scale leads to the formation of new genomes and new species with high ecological resistance.