Mating is rare within as well as between clades of the human pathogen Candida albicans

Candida albicans is a diploid yeast that can undergo mating and a parasexual cycle, but is apparently unable to undergo meiosis. Characterization of the population structure of C. albicans has shown that reproduction is largely clonal and that mating, if it occurs, is rare or limited to genetically related isolates. Because molecular typing has delineated distinct clades in C. albicans, we have tested whether recombination was common within clades, but rare between clades. Two hundred and three C. albicans isolates have been subjected to multilocus sequence typing (MLST) and the haplotypes at heterozygous MLST genotypes characterized. The C. albicans isolates were distributed among nine clades, of which five corresponded to those previously identified by Ca3 fingerprinting. In each of these clades with more than 10 isolates, polymorphic nucleotide positions located on between 3 and 4 of the six loci were in Hardy-Weinberg disequilibrium. Moreover, each of these polymorphic sites contained excess heterozygotes. This was confirmed by an expanded analysis performed on a recently published MLST dataset for 1044 isolates. On average, 66% of polymorphic positions in the individual clades were in significant excess of heterozygotes over the five clades. These data indicate that mating within clades as well as self-fertilization are both limited and that C. albicans clades do not represent a collection of cryptic species. The study of haplotypes at heterozygous loci performed on our dataset indicates that loss of heterozygosity events due to mitotic recombination is moderately common in natural populations of C. albicans. The maintenance of substantial heterozygosity despite relatively frequent loss of heterozygosity could result from a selective advantage conferred by heterozygosity.     

Mating is rare within as well as between clades of the human pathogen Candida albicans.

Candida albicans is a diploid yeast that can undergo mating and a parasexual cycle, but is apparently unable to undergo meiosis. Characterization of the population structure of C. albicans has shown that reproduction is largely clonal and that mating, if it occurs, is rare or limited to genetically related isolates. Because molecular typing has delineated distinct clades in C. albicans, we have tested whether recombination was common within clades, but rare between clades. Two hundred and three C. albicans isolates have been subjected to multilocus sequence typing (MLST) and the haplotypes at heterozygous MLST genotypes characterized. The C. albicans isolates were distributed among nine clades, of which five corresponded to those previously identified by Ca3 fingerprinting. In each of these clades with more than 10 isolates, polymorphic nucleotide positions located on between 3 and 4 of the six loci were in Hardy-Weinberg disequilibrium. Moreover, each of these polymorphic sites contained excess heterozygotes. This was confirmed by an expanded analysis performed on a recently published MLST dataset for 1044 isolates. On average, 66% of polymorphic positions in the individual clades were in significant excess of heterozygotes over the five clades. These data indicate that mating within clades as well as self-fertilization are both limited and that C. albicans clades do not represent a collection of cryptic species. The study of haplotypes at heterozygous loci performed on our dataset indicates that loss of heterozygosity events due to mitotic recombination is moderately common in natural populations of C. albicans. The maintenance of substantial heterozygosity despite relatively frequent loss of heterozygosity could result from a selective advantage conferred by heterozygosity.     

Demonstration of loss of heterozygosity by single-nucleotide polymorphism microarray analysis and alterations in strain morphology in Candida albicans strains during infection

Candida albicans is a diploid yeast with a predominantly clonal mode of reproduction, and no complete sexual cycle is known. As a commensal organism, it inhabits a variety of niches in humans. It becomes an opportunistic pathogen in immunocompromised patients and can cause both superficial and disseminated infections. It has been demonstrated that genome rearrangement and genetic variation in isolates of C. albicans are quite common. One possible mechanism for generating genome-level variation among individuals of this primarily clonal fungus is mutation and mitotic recombination leading to loss of heterozygosity (LOH). Taking advantage of a recently published genome-wide single-nucleotide polymorphism (SNP) map (A. Forche, P. T. Magee, B. B. Magee, and G. May, Eukaryot. Cell 3:705-714, 2004), an SNP microarray was developed for 23 SNP loci residing on chromosomes 5, 6, and 7. It was used to examine 21 strains previously shown to have undergone mitotic recombination at the GAL1 locus on chromosome 1 during infection in mice. In addition, karyotypes and morphological properties of these strains were evaluated. Our results show that during in vivo passaging, LOH events occur at observable frequencies, that such mitotic recombination events occur independently in different loci across the genome, and that changes in karyotypes and alterations of phenotypic characteristics can be observed alone, in combination, or together with LOH.     

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.     

Conservation of genetic linkage in nonisogenic isolates of Candida albicans

A number of laboratories are now engaged in the genetic analysis of Candida albicans. This diploid yeast, the major fungal pathogen of humans, is imperfect. Parasexual techniques have been devised for complementation and recombination analysis in this organism. This paper attempts to address the question of the extent to which nonisogenic strains of C. albicans have conserved a common genetic map. This analysis is a prerequisite for the integration of work done in different laboratories and may also provide useful information on the taxonomy of the genus Candida. The paper also reports the analysis of an interspecific hybrid between C. albicans and Candida stellatoidea. The method employed in these studies was the analysis of the mitotic recombination relationships of a group of linked genes and their centromere. Strains carrying linked auxotrophic mutations were fused with isogenic and nonisogenic complementary strains to form tetraploids. The mitotic recombination analyses of these tetraploids suggest that in the isolates studied the genetic map is conserved. A comparison of tetraploid and diploid mitotic recombination analyses is also presented.     

Allele intersection analysis: a novel tool for multi locus sequence assignment in multiply infected hosts

Wolbachia are wide-spread, endogenous α-Proteobacteria of arthropods and filarial nematodes. 15-75% of all insect species are infected with these endosymbionts that alter their host's reproduction to facilitate their spread. In recent years, many insect species infected with multiple Wolbachia strains have been identified. As the endosymbionts are not cultivable outside living cells, strain typing relies on molecular methods. A Multi Locus Sequence Typing (MLST) system was established for standardizing Wolbachia strain identification. However, MLST requires hosts to harbour individual and not multiple strains of supergroups without recombination. This study revisits the applicability of the current MLST protocols and introduces Allele Intersection Analysis (AIA) as a novel approach. AIA utilizes natural variations in infection patterns and allows correct strain assignment of MLST alleles in multiply infected host species without the need of artificial strain segregation. AIA identifies pairs of multiply infected individuals that share Wolbachia and differ in only one strain. In such pairs, the shared MLST sequences can be used to assign alleles to distinct strains. Furthermore, AIA is a powerful tool to detect recombination events. The underlying principle of AIA may easily be adopted for MLST approaches in other uncultivable bacterial genera that occur as multiple strain infections and the concept may find application in metagenomic high-throughput parallel sequencing projects.     

The red queen coupled with directional selection favours the evolution of sex

Why sexual reproduction has evolved to be such a widespread mode of reproduction remains a major question in evolutionary biology. Although previous studies have shown that increased sex and recombination can evolve in the presence of host-parasite interactions (the 'Red Queen hypothesis' for sex), many of these studies have assumed that multiple loci mediate infection vs. resistance. Data suggest, however, that a major locus is typically involved in antigen presentation and recognition. Here, we explore a model where only one locus mediates host-parasite interactions, but a second locus is subject to directional selection. Even though the effects of these genes on fitness are independent, we show that increased rates of sex and recombination are favoured at a modifier gene that alters the rate of genetic mixing. This result occurs because of selective interference in finite populations (the 'Hill-Robertson effect'), which also favours sex. These results suggest that the Red Queen hypothesis may help to explain the evolution of sex by contributing a form of persistent selection, which interferes with directional selection at other loci and thereby favours sex and recombination.     

Thelytokous Parthenogenesis in the Fungus-Gardening Ant Mycocepurus smithii (Hymenoptera: Formicidae)

The general prevalence of sexual reproduction over asexual reproduction among organisms testifies to the evolutionary benefits of recombination, such as accelerated adaptation to changing environments and elimination of deleterious mutations. Documented instances of asexual reproduction in groups otherwise dominated by sexual reproduction challenge evolutionary biologists to understand the special circumstances that might confer an advantage to asexual reproductive strategies. Here we report one such instance of asexual reproduction in the ants. We present evidence for obligate thelytoky in the asexual fungus-gardening ant, Mycocepurus smithii, in which queens produce female offspring from unfertilized eggs, workers are sterile, and males appear to be completely absent. Obligate thelytoky is implicated by reproductive physiology of queens, lack of males, absence of mating behavior, and natural history observations. An obligate thelytoky hypothesis is further supported by the absence of evidence indicating sexual reproduction or genetic recombination across the species'' extensive distribution range (Mexico-Argentina). Potential conflicting evidence for sexual reproduction in this species derives from three Mycocepurus males reported in the literature, previously regarded as possible males of M. smithii. However, we show here that these specimens represent males of the congeneric species M. obsoletus, and not males of M. smithii. Mycocepurus smithii is unique among ants and among eusocial Hymenoptera, in that males seem to be completely absent and only queens (and not workers) produce diploid offspring via thelytoky. Because colonies consisting only of females can be propagated consecutively in the laboratory, M. smithii could be an adequate study organism a) to test hypotheses of the population-genetic advantages and disadvantages of asexual reproduction in a social organism and b) inform kin conflict theory.For a Portuguese translation of the abstract, please see Abstract S1.     

Deleterious effects of recombination and possible nonrecombinatorial advantages of sex in a fungal model

Why sexual reproduction is so prevalent in nature remains a major question in evolutionary biology. Most of the proposed advantages of sex rely on the benefits obtained from recombination. However, it is still unclear whether the conditions under which these recombinatorial benefits would be sufficient to maintain sex in the short term are met in nature. Our study addresses a largely overlooked hypothesis, proposing that sex could be maintained in the short term by advantages due to functions linked with sex, but not related to recombination. These advantages would be so essential that sex could not be lost in the short term. Here, we used the fungus Aspergillus nidulans to experimentally test predictions of this hypothesis. Specifically, we were interested in (i) the short‐term deleterious effects of recombination, (ii) possible nonrecombinatorial advantages of sex particularly through the elimination of mutations and (iii) the outcrossing rate under choice conditions in a haploid fungus able to reproduce by both outcrossing and haploid selfing. Our results were consistent with our hypotheses: we found that (i) recombination can be strongly deleterious in the short term, (ii) sexual reproduction between individuals derived from the same clonal lineage provided nonrecombinatorial advantages, likely through a selection arena mechanism, and (iii) under choice conditions, outcrossing occurs in a homothallic species, although at low rates.     

Cryptic sex in fungi

It is generally accepted that genetic recombination in eukaryotes is mostly driven by meiotic divisions as part of the sexual cycle. The maintenance of the sexual cycle that combines beneficial genes in sexual offspring from two parents provides an advantage for a species in novel or changing environments. Sex thus preserves beneficial and removes deleterious mutations. However, some eukaryotes, including many fungi lack sex entirely, and thus, it was assumed that recombination occurring during mitotic (somatic) divisions is the main force to shape the genome of these asexually propagating microbes. However, several recent reports of a sexual cycle in asexually propagating fungi put this concept in question. Here, we summarize the accumulating evidence for the general occurrence of cryptic sex in filamentous fungi in which sexual reproduction has not been previously reported.     

Sexual healing: mating induces a protective immune response in bumblebees

The prevalence of sexual, as opposed to clonal, reproduction given the many costs associated with sexual recombination has been an enduring question in evolutionary biology. In addition to these often discussed costs, there are further costs associated with mating, including the induction of a costly immune response, which leaves individuals prone to infection. Here, we test whether mating results in immune activation and susceptibility to a common, ecologically important, parasite of bumblebees. We find that mating does result in immune activation as measured by gene expression of known immune genes, but that this activation improves resistance to this parasite. We conclude that although mating can corrupt immunity in some systems, it can also enhance immunity in others.     

Sex and recombination in the Hötzel aging model

Why sex evolved and it prevails in nature remain one of thegreat puzzles of evolution. Most biologists would explain that it promotes genetic variability, however this explanation suffers from several difficulties. What advantages might sex confer? The present communication aims at certain investigations related to this question, in this way we introduce sexual recombination on the Hötzel model (with males and females) and wecompare these results with those from asexual reproduction without recombination.     

Constraints on the evolution of asexual reproduction

Sexual reproduction is almost ubiquitous among multicellular organisms even though it entails severe fitness costs. To resolve this apparent paradox, an extensive body of research has been devoted to identifying the selective advantages of recombination that counteract these costs. Yet, how easy is it to make the transition to asexual reproduction once sexual reproduction has been established for a long time? The present review approaches this question by considering factors that impede the evolution of parthenogenesis in animals. Most importantly, eggs need a diploid chromosome set in most species in order to develop normally. Next, eggs may need to be activated by sperm, and sperm may also contribute centrioles and other paternal factors to the zygote. Depending on how diploidy is achieved mechanistically, further problems may arise in offspring that stem from 'inbreeding depression' or inappropriate sex determination systems. Finally, genomic imprinting is another well-known barrier to the evolution of asexuality in mammals. Studies on species with occasional, deficient parthenogenesis indicate that the relative importance of these constraints may vary widely. The intimate evolutionary relations between haplodiploidy and parthenogenesis as well as implications for the clade selection hypothesis of the maintenance of sexual reproduction are also discussed.     

A system for studying genetic changes in Candida albicans during infection

Candida albicans is a diploid yeast with a dimorphic life history. It exists commensally in many healthy humans but becomes a potent pathogen in immunocompromised hosts. The underlying genetic mechanisms by which C. albicans switches from a commensal to a pathogenic form in the host are not well understood. To study the evolution of virulence in mammalian hosts, we used GAL1 as selectable marker system that allows for both positive and negative selection in selective media. We show that the deletion of one or both copies of GAL1 in the C. albicans genome does not change virulence in a systemic mouse model. We obtained estimates for the frequency of mitotic recombination at the GAL1 locus during systemic infection. Our observations suggest that genetic changes such as mitotic recombination and gene conversion occur at a high enough frequency to be important in the transition of C. albicans from a commensal to a pathogenic organism.     

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.     

白念珠菌生物被膜形成的遗传调控机制

白念珠菌是人体重要的条件性致病真菌。形态的多样性和可塑性是白念珠菌典型的生物学特征,这与它的致病性、宿主适应能力以及有性生殖过程密切相关。白念珠菌生物被膜(Biofilm)是由不同形态细胞(包括酵母型、菌丝和假菌丝)以及胞外基质组成的致密结构,也是毒性和耐药性形成的重要因子。生物被膜对抗真菌药物、宿主免疫系统和环境胁迫因子等都表现出较强的抵抗力和耐受性,是临床上病原真菌感染防治的重大挑战。随着基因表达谱和遗传操作技术的发展,白念珠菌生物被膜的形成及其耐药性的获得所依赖的遗传调控通路和分子调控机制越来越清楚。主要包括MAPK和cAMP介导的信号途径以及Bcr1和Tec1等因子介导的转录调控。此外,白念珠菌生物被膜的形成与形态转换和有性生殖之间存在密切的联系。文中综述了白念珠菌生物被膜形成的遗传调控机制,重点介绍了细胞壁相关蛋白、转录因子和交配型对该过程的调控以及生物被膜的耐药机制。     

Sex and recombination purge the genome of deleterious alleles: An Individual Based Modeling Approach

The prevalence of sexual reproduction in most animal species despite its considerable costs such as useless males, energy spent on mating, the cost of meiosis and genome dilution remains a puzzle in evolutionary theory. One prominent single factor attempt to solve this persistent puzzle is the claim that sexual reproduction is instrumental in eliminating deleterious alleles from the species genome by the mechanism of recombination. There are three major versions of the deleterious allele hypothesis: First, the mutational deterministic hypothesis (MDH), which rests on the assumption of negative epistasis, predicts that recombination will help to purge the species genome of deleterious alleles by breaking apart linkages between these alleles. The assumption is that the joint negative effects of linked deleterious alleles is sometimes greater than the effects of the alleles considered separately. Second, there is the hypothesis that sexual reproduction speeds up purifying (negative) selection, which purges the genome of deleterious alleles. Alleles that are less deleterious than the wild type are naturally selected. These alleles, attained via recombination, are sometimes ‘leaky’ mutations giving rise to reduced functionality of attendant proteins. This hypothesis does not necessarily rest on the assumption of negative epistasis, which some argue is relatively rare in nature (Kouyos, Silander and Bonhoeffer (2012)) and which arguably could be seen as a virtue of the purifying selection hypothesis vs. the MDH. Third, Muller's ratchet hypothesis predicts that recombination will help to prevent the buildup of deleterious mutations by the mechanism of recombination. In this study, we focus primarily on testing the purifying selection hypothesis. We performed an individual-based model computer simulation using the program EcoSim to test this hypothesis. The experimental runs for sexual reproduction, asexual reproduction and facultative reproduction involved introducing a deleterious allele into the genome, which exacts an intermediate-level energy penalty on individuals. It was found that whereas on average, deleteriousness consistently declined over 18,000 time-steps due to recombination in sexual reproduction, deleteriousness did not decline for asexual and facultative runs. These results corroborate the hypothesis that recombination due to sexual reproduction helps to eliminate deleterious alleles from the genome through the selection of reduced function mutations.     

Multilocus sequence typing confirms synonymy but highlights differences between Candida albicans and Candida stellatoidea

We used multi-locus sequence typing (MLST) to investigate 35 yeast isolates representing the two genome-sequenced strains plus the type strain of Candida albicans, four isolates originally identified as Candida stellatoidea type I and 28 representing type strains of other species now regarded as synonymous with C. albicans. DNA from all 32 C. albicans synonyms readily formed PCR products with the C. albicans MLST primer sets. Their sequences placed all of them within the existing C. albicans clade structure, represented by 1516 isolates. One isolate, originally received as Mycotorula sinensis, was resistant to flucytosine, but no other unusual susceptibilities were found to polyene, azole or echinocandin antifungal agents. The four isolates of C. stellatoidea type I coclustered with two other sucrose-negative isolates, originally identified as examples of Candida africana, in a group of strains highly distinct from the majority of C. albicans. Our results not only confirm the synonymity of all the isolates with C. albicans but also confirm an obvious genotypic difference in the case of C. stellatoidea type I.     

Food quality triggers the reproductive mode in the cyclical parthenogen <Emphasis Type="Italic">Daphnia</Emphasis> (Cladocera)

Cyclic parthenogenesis (heterogony) is a widespread reproductive mode found in diverse taxa such as digenean trematodes, gall wasps, gall midges, aphids, cladocerans and rotifers. It is of particular interest as it combines the advantages of asexual reproduction (rapid population growth) and sexual reproduction (recombination). Usually sexual reproduction is initiated when, or slightly before, environmental conditions deteriorate, and often results in the production of resting stages. The optimal timing of diapause induction must thus be under strong natural selection. Using the cladoceran Daphnia as a model system, we show here for the first time that the switch from parthenogenetic to sexual reproduction in a cyclical parthenogenetic organism can be influenced by the chemical composition of food. Under crowding conditions Daphnia reproduced parthenogenetically with subitaneous eggs when fed the algal species Cryptomonas sp., but started the production of resting eggs when fed with the green algal species Scenedesmus obliquus. Supplementation experiments with lipids and especially proteins showed that the induction of resting egg production in two clones of different Daphnia species was due to a dietary deficiency in the green alga. Hence, the low food quality induced a switch in the reproductive mode that may contribute to optimal timing of the sexual reproduction of Daphnia in nature. Furthermore, our results have two other major implications: first, they suggest that protein compounds should be added to the list of diet constituents potentially limiting or influencing Daphnia reproduction. Second, we show that the role of food quality goes far beyond the up to now documented effects of food quality on somatic growth and trophic transfer efficiency of herbivores: due to its effects on sexual reproduction and the production of resting eggs, food quality might influence genetic diversity and long-term persistence of Daphnia in lakes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Population genetics provides evidence for recombination in Giardia

Giardia lamblia (syn. Giardia intestinalis, Giardia duodenalis) is an enteric protozoan parasite with two nuclei, and it might be one of the earliest branching eukaryotes. However, the discovery of at least rudimentary forms of certain features, such as Golgi and mitochondria, has refuted the proposal that its emergence from the eukaryotic lineage predated the development of certain eukaryotic features. The recent recognition of many of the genes known to be required for meiosis in the genome has also cast doubt on the idea that Giardia is primitively asexual, but so far there has been no direct evidence of sexual reproduction in Giardia, and population data have suggested clonal reproduction. We did a multilocus sequence evaluation of the genotype A2 reference strain, JH, and five genotype A2 isolates from a highly endemic area in Peru. Loci from different chromosomes yielded significantly different phylogenetic trees, indicating that they do not share the same evolutionary history; within individual loci, tests for recombination yielded significant statistical support for meiotic recombination. These observations provide genetic data supportive of sexual reproduction in Giardia.