Stability of large segmental duplications in the yeast genome

Local Genomic Instability of the SpTransformer Gene Family in the Purple Sea Urchin Inferred from BAC Insert Deletions

The SpTransformer (SpTrf) gene family in the purple sea urchin, Strongylocentrotus purpuratus, encodes immune response proteins. The genes are clustered, surrounded by short tandem repeats, and some are present in genomic segmental duplications. The genes share regions of sequence and include repeats in the coding exon. This complex structure is consistent with putative local genomic instability. Instability of the SpTrf gene cluster was tested by 10 days of growth of Escherichia coli harboring bacterial artificial chromosome (BAC) clones of sea urchin genomic DNA with inserts containing SpTrf genes. After the growth period, the BAC DNA inserts were analyzed for size and SpTrf gene content. Clones with multiple SpTrf genes showed a variety of deletions, including loss of one, most, or all genes from the cluster. Alternatively, a BAC insert with a single SpTrf gene was stable. BAC insert instability is consistent with variations in the gene family composition among sea urchins, the types of SpTrf genes in the family, and a reduction in the gene copy number in single coelomocytes. Based on the sequence variability among SpTrf genes within and among sea urchins, local genomic instability of the family may be important for driving sequence diversity in this gene family that would be of benefit to sea urchins in their arms race with marine microbes.

Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey

Aureobasidium melanogenum TN3-1 strain and A. melanogenum P16 strain were isolated from the natural honey and the mangrove ecosystem, respectively. The former can produce much higher pullulan from high concentration of glucose than the latter. In order to know what happened to their genomes, the PacBio sequencing and Hi-C technologies were used to create the first high-quality chromosome-level reference genome assembly of A. melanogenum TN3-1 (51.61 Mb) and A. melanogenum P16 (25.82 Mb) with the contig N50 of 2.19 Mb and 2.26 Mb, respectively. Based on the Hi-C results, a total of 93.33% contigs in the TN3-1 strain and 92.31% contigs in the P16 strain were anchored onto 24 and 12 haploid chromosomes, respectively. The genomes of the TN3-1 strain had two subgenomes A and B. Synteny analysis showed that the genomic contents of the two subgenomes were asymmetric with many structural variations. Intriguingly, the TN3-1 strain was revealed as a recent hybrid/fusion between the ancestor of A. melanogenum CBS105.22/CBS110374 and the ancestor of another unidentified strain of A. melanogenum similar to P16 strain. We estimated that the two ancient progenitors diverged around 18.38 Mya and merged around 10.66-9.98 Mya. It was found that in the TN3-1 strain, telomeres of each chromosome contained high level of long interspersed nuclear elements (LINEs), but had low level of the telomerase encoding gene. Meanwhile, there were high level of transposable elements (TEs) inserted in the chromosomes of the TN3-1 strain. In addition, the positively selected genes of the TN3-1 strain were mainly enriched in the metabolic processes related to harsh environmental adaptability. Most of the stress-related genes were found to be related to the adjacent LTRs, and the glucose derepression was caused by the mutation of the Glc7-2 in the Snf-Mig1 system. All of these could contribute to its genetic instability, genome evolution, high stress resistance, and high pullulan production from glucose.

A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains

The early development of aneuploidy from an accidental chromosome missegregation shows contrasting effects. On the one hand, it is associated with significant cellular stress and decreased fitness. On the other hand, it often carries a beneficial effect and provides a quick (but typically transient) solution to external stress. These apparently controversial trends emerge in several experimental contexts, particularly in the presence of duplicated chromosomes. However, we lack a mathematical evolutionary modeling framework that comprehensively captures these trends from the mutational dynamics and the trade-offs involved in the early stages of aneuploidy. Here, focusing on chromosome gains, we address this point by introducing a fitness model where a fitness cost of chromosome duplications is contrasted by a fitness advantage from the dosage of specific genes. The model successfully captures the experimentally measured probability of emergence of extra chromosomes in a laboratory evolution setup. Additionally, using phenotypic data collected in rich media, we explored the fitness landscape, finding evidence supporting the existence of a per-gene cost of extra chromosomes. Finally, we show that the substitution dynamics of our model, evaluated in the empirical fitness landscape, explains the relative abundance of duplicated chromosomes observed in yeast population genomics data. These findings lay a firm framework for the understanding of the establishment of newly duplicated chromosomes, providing testable quantitative predictions for future observations.

Chromosomal polymorphism of the Ceratocystis fimbriata species complex in Brazil

Ceratocystis fimbriata is an important pathogen that causes wilt in several plant species. Despite the importance of this pathogen, knowledge about its karyotypic polymorphism and genomic architecture is limited. The main objective of this study was to investigate the karyotype of isolates of the C. fimbriata species complex from different host plants and geographical origins in Brazil. First, the identity of the isolates was confirmed conducting multilocus sequence analysis (MLSA) phylogeny using β-tubulin (TUBB), translation elongation factor 1α (TEF-1α) and mating-type (MAT1 and MAT2) gene sequences. To investigate the chromosomal polymorphism, two conditions of pulsed-field gel electrophoresis (PFGE) were used and the karyotypes of the isolates obtained. The retrotransposon-microsatellite amplified polymorphism (REMAP) molecular marker was utilized to assess the genetic variability among isolates. In the MLSA utilizing the concatenated gene sequences, Ceratocystis cacaofunesta and C. fimbriata formed separate clades, but considerable variation among C. fimbriata isolates was observed. Polymorphism in chromosome number and size was found, indicating the existence of genomic differences among isolates and occurrence of chromosomal rearrangements in the species complex. The number of chromosomes varied from seven to nine and the estimated minimum chromosome sizes were estimated to be between 2.7 to 6.0 Mbp. Small polymorphic chromosomes ranging from 1.2 to 1.8 Mbp were observed in all isolates, raising the hypothesis that they could be supernumerary chromosomes. REMAP analysis revealed a high genetic variability and that isolates from the same host tend to group together in a same cluster. Our results bring new insights into the chromosomal diversity and genome organization of the C. fimbriata complex.

The MyLO CRISPR-Cas9 toolkit: a markerless yeast localization and overexpression CRISPR-Cas9 toolkit

The genetic tractability of the yeast Saccharomyces cerevisiae has made it a key model organism for basic research and a target for metabolic engineering. To streamline the introduction of tagged genes and compartmental markers with powerful Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) - CRISPR-associated protein 9 (Cas9)-based genome editing tools, we constructed a Markerless Yeast Localization and Overexpression (MyLO) CRISPR-Cas9 toolkit with 3 components: (1) a set of optimized Streptococcus pyogenes Cas9-guide RNA expression vectors with 5 selectable markers and the option to either preclone or cotransform the gRNAs; (2) vectors for the one-step construction of integration cassettes expressing an untagged or green fluorescent protein/red fluorescent protein/hemagglutinin-tagged gene of interest at one of 3 levels, supporting localization and overexpression studies; and (3) integration cassettes containing moderately expressed green fluorescent protein- or red fluorescent protein-tagged compartmental markers for colocalization experiments. These components allow rapid, high-efficiency genomic integrations and modifications with only transient selection for the Cas9 vector, resulting in markerless transformations. To demonstrate the ease of use, we applied our complete set of compartmental markers to colabel all target subcellular compartments with green fluorescent protein and red fluorescent protein. Thus, the MyLO toolkit packages CRISPR-Cas9 technology into a flexible, optimized bundle that allows the stable genomic integration of DNA with the ease of use approaching that of transforming plasmids.

Evolutionary engineering to improve Wickerhamomyces subpelliculosus and Kazachstania gamospora for baking

The conventional baker's yeast, Saccharomyces cerevisiae, is the indispensable baking yeast of all times. Its monopoly coupled to its major drawbacks, such as streamlined carbon substrate utilisation base and a poor ability to withstand a number of baking associated stresses, prompt the need to search for alternative yeasts to leaven bread in the era of increasingly complex consumer lifestyles. Our previous work identified the inefficient baking attributes of Wickerhamomyces subpelliculosus and Kazachstania gamospora as well as preliminarily observations of improving the fermentative capacity of these potential alternative baker's yeasts using evolutionary engineering. Here we report on the characterisation and improvement in baking traits in five out of six independently evolved lines incubated for longer time and passaged for at least 60 passages relative to their parental strains as well as the conventional baker's yeast. In addition, the evolved clones produced bread with a higher loaf volume when compared to bread baked with either the ancestral strain or the control conventional baker's yeast. Remarkably, our approach improved the yeasts' ability to withstand baking associated stresses, a key baking trait exhibited poorly in both the conventional baker's yeast and their ancestral strains. W. subpelliculosus evolved the best characteristics attractive for alternative baker's yeasts as compared to the evolved K. gamospora strains. These results demonstrate the robustness of evolutionary engineering in development of alternative baker's yeasts.

Cohesin regulates homology search during recombinational DNA repair

Homologous recombination repairs DNA double-strand breaks (DSB) using an intact dsDNA molecule as a template. It entails a homology search step, carried out along a conserved RecA/Rad51-ssDNA filament assembled on each DSB end. Whether, how and to what extent a DSB impacts chromatin folding, and how this (re)organization in turns influences the homology search process, remain ill-defined. Here we characterize two layers of spatial chromatin reorganization following DSB formation in Saccharomyces cerevisiae. Although cohesin folds chromosomes into cohesive arrays of ~20-kb-long chromatin loops as cells arrest in G2/M, the DSB-flanking regions interact locally in a resection- and 9-1-1 clamp-dependent manner, independently of cohesin, Mec1ATR, Rad52 and Rad51. This local structure blocks cohesin progression, constraining the DSB region at the base of a loop. Functionally, cohesin promotes DSB-dsDNA interactions and donor identification in cis, while inhibiting them in trans. This study identifies multiple direct and indirect ways by which cohesin regulates homology search during recombinational DNA repair.

Thermo-adaptive evolution to generate improved Saccharomyces cerevisiae strains for cocoa pulp fermentations

Cocoa pulp fermentation is a consequence of the succession of indigenous yeasts, lactic acid bacteria and acetic acid bacteria that not only produce a diversity of metabolites, but also cause the production of flavour precursors. However, as such spontaneous fermentations are less reproducible and contribute to produce variability, interest in a microbial starter culture is growing that could be used to inoculate cocoa pulp fermentations. This study aimed to generate robust S. cerevisiae strains by thermo-adaptive evolution that could be used in cocoa fermentation. We evolved a cocoa strain in a sugary defined medium at high temperature to improve both fermentation and growth capacity. Moreover, adaptive evolution at high temperature (40 °C) also enabled us to unveil the molecular basis underlying the improved phenotype by analysing the whole genome sequence of the evolved strain. Adaptation to high-temperature conditions occurred at different genomic levels, and promoted aneuploidies, segmental duplication, and SNVs in the evolved strain. The lipid profile analysis of the evolved strain also evidenced changes in the membrane composition that contribute to maintain an appropriate cell membrane state at high temperature. Our work demonstrates that experimental evolution is an effective approach to generate better-adapted yeast strains at high temperature for industrial processes.

An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences. Indeed, these bioinformatic approaches differ according to the underlying duplication mechanism. Hence, understanding the specificity of the duplicated genes of interest is a great asset for tool selection and should be taken into account when exploring a biological question.

Genomic Multiplication and Drug Efflux Influence Ketoconazole Resistance in Malassezia restricta

Malassezia restricta is an opportunistic fungal pathogen on human skin; it is associated with various skin diseases, including seborrheic dermatitis and dandruff, which are usually treated using ketoconazole. In this study, we clinically isolated ketoconazole-resistant M. restricta strains (KCTC 27529 and KCTC 27550) from patients with dandruff. To understand the mechanisms of ketoconazole resistance in the isolates, their genomes were sequenced and compared with the susceptible reference strain M. restricta KCTC 27527. Using comparative genome analysis, we identified tandem multiplications of the genomic loci containing ATM1 and ERG11 homologs in M. restricta KCTC 27529 and KCTC 27550, respectively. Additionally, we found that the copy number increase of ATM1 and ERG11 is reflected in the increased expression of these genes; moreover, we observed that overexpression of these homologs caused ketoconazole resistance in a genetically tractable fungal pathogen, Cryptococcus neoformans. In addition to tandem multiplications of the genomic region containing the ATM1 homolog, the PDR5 homolog, which encodes the drug efflux pump protein was upregulated in M. restricta KCTC 27529 compared to the reference strain. Biochemical analysis confirmed that drug efflux was highly activated in M. restricta KCTC 27529, implying that upregulation of the PDR5 homolog may also contribute to ketoconazole resistance in the strain. Overall, our results suggest that multiplication of the genomic loci encoding genes involved in ergosterol synthesis, mitochondrial iron metabolism, and oxidative stress response and overexpression of the drug efflux pumps are the mechanisms underlying ketoconazole resistance in M. restricta.

Improvement of thermotolerance in Lachancea thermotolerans using a bacterial selection pressure

The use of thermotolerant yeast strains is an important attribute for a cost-effective high temperature biofermentation processes. However, the availability of thermotolerant yeast strains remains a major challenge. Isolation of temperature resistant strains from extreme environments or the improvements of current strains are two major strategies known to date. We hypothesised that bacteria are potential “hurdles” in the life cycle of yeasts, which could influence the evolution of extreme phenotypes, such as thermotolerance. We subjected a wild-type yeast, Lachancea thermotolerans to six species of bacteria sequentially for several generations. After coevolution, we observed that three replicate lines of yeasts grown in the presence of bacteria grew up to 37 °C whereas the controls run in parallel without bacteria could only grow poorly at 35 °C retaining the ancestral mesophilic trait. In addition to improvement of thermotolerance, our results show that the fermentative ability was also elevated, making the strains more ideal for the alcoholic fermentation process because the overall productivity and ethanol titers per unit volume of substrate consumed during the fermentation process was increased. Our unique method is attractive for the development of thermotolerant strains or to augment the available strain development approaches for high temperature industrial biofermentation.

Yeast-bacteria competition induced new metabolic traits through large-scale genomic rearrangements in Lachancea kluyveri

Large-scale chromosomal rearrangements are an important source of evolutionary novelty that may have reshaped the genomes of existing yeast species. They dramatically alter genome organization and gene expression fueling a phenotypic leap in response to environmental constraints. Although the emergence of such signatures of genetic diversity is thought to be associated with human exploitation of yeasts, less is known about the driving forces operating in natural habitats. Here we hypothesize that an ecological battlefield characteristic of every autumn when fruits ripen accounts for the genomic innovations in natural populations. We described a long-term cross-kingdom competition experiment between Lachancea kluyveri and five species of bacteria. Now, we report how we further subjected the same yeast to a sixth species of bacteria, Pseudomonas fluorescens, resulting in the appearance of a fixed and stably inherited large-scale genomic rearrangement in two out of three parallel evolution lines. The 'extra-banded' karyotype, characterized by a higher fitness and an elevated fermentative capacity, conferred the emergence of new metabolic traits in most carbon sources and osmolytes. We tracked down the event to a duplication and translocation event involving a 261-kb segment. Such an experimental setup described here is an attractive method for developing industrial strains without genetic engineering strategies.

Sources of Fungal Genetic Variation and Associating It with Phenotypic Diversity

The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability. Variation in wild populations is a rich resource for associating genetic variation with phenotypic variation, whether through quantitative trait locus mapping, genome-wide association studies, or reverse ecology. Subjects of studies associating genetic and phenotypic variation include model fungi, e.g., Saccharomyces and Neurospora, but pioneering studies have also been made with fungi pathogenic to plants, e.g., Pyricularia (= Magnaporthe), Zymoseptoria, and Fusarium, and to humans, e.g., Coccidioides, Cryptococcus, and Candida.

Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection

The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.

Draft Genome of the Wheat Rust Pathogen (Puccinia triticina) Unravels Genome-Wide Structural Variations during Evolution

Leaf rust is one of the most important diseases of wheat and is caused by Puccinia triticina, a highly variable rust pathogen prevalent worldwide. Decoding the genome of this pathogen will help in unraveling the molecular basis of its evolution and in the identification of genes responsible for its various biological functions. We generated high quality draft genome sequences (approximately 100- 106 Mb) of two races of P. triticina; the variable and virulent Race77 and the old, avirulent Race106. The genomes of races 77 and 106 had 33X and 27X coverage, respectively. We predicted 27678 and 26384 genes, with average lengths of 1,129 and 1,086 bases in races 77 and 106, respectively and found that the genomes consisted of 37.49% and 39.99% repetitive sequences. Genome wide comparative analysis revealed that Race77 differs substantially from Race106 with regard to segmental duplication (SD), repeat element, and SNP/InDel characteristics. Comparative analyses showed that Race 77 is a recent, highly variable and adapted Race compared with Race106. Further sequence analyses of 13 additional pathotypes of Race77 clearly differentiated the recent, active and virulent, from the older pathotypes. Average densities of 2.4 SNPs and 0.32 InDels per kb were obtained for all P. triticina pathotypes. Secretome analysis demonstrated that Race77 has more virulence factors than Race 106, which may be responsible for the greater degree of adaptation of this pathogen. We also found that genes under greater selection pressure were conserved in the genomes of both races, and may affect functions crucial for the higher levels of virulence factors in Race77. This study provides insights into the genome structure, genome organization, molecular basis of variation, and pathogenicity of P. triticina The genome sequence data generated in this study have been submitted to public domain databases and will be an important resource for comparative genomics studies of the more than 4000 existing Puccinia species.

Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast

Gene amplification has been observed in different organisms in response to environmental constraints, such as limited nutrients or exposure to a variety of toxic compounds, conferring them with specific phenotypic adaptations via increased expression levels. However, the presence of multiple gene copies in natural genomes has generally not been found in the absence of specific functional selection. Here, we show that the massive amplification of a chromosomal locus (up to 880 copies per cell) occurs in the absence of any direct selection, and is associated with low-order amplifications of flanking segments in complex chromosomal alterations. These results were obtained from mutants with restored phenotypes that spontaneously appeared from genetically engineered strains of the yeast Saccharomyces cerevisiae suffering from severe fitness reduction. Grossly extended chromosomes (macrotene) were formed, with complex structural alterations but sufficient stability to propagate unchanged over successive generations. Their detailed molecular analysis, including complete genome sequencing, identification of sequence breakpoints, and comparisons between mutants, revealed novel mechanisms causing their formation, whose combined action underlies the astonishing dynamics of eukaryotic chromosomes and their consequences.

From one to many: expanding the Saccharomyces cerevisiae reference genome panel

In recent years, thousands of Saccharomyces cerevisiae genomes have been sequenced to varying degrees of completion. The Saccharomyces Genome Database (SGD) has long been the keeper of the original eukaryotic reference genome sequence, which was derived primarily from S. cerevisiae strain S288C. Because new technologies are pushing S. cerevisiae annotation past the limits of any system based exclusively on a single reference sequence, SGD is actively working to expand the original S. cerevisiae systematic reference sequence from a single genome to a multi-genome reference panel. We first commissioned the sequencing of additional genomes and their automated analysis using the AGAPE pipeline. Here we describe our curation strategy to produce manually reviewed high-quality genome annotations in order to elevate 11 of these additional genomes to Reference status.

Database URL: http://www.yeastgenome.org/

Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes

Copy number variation of chromosomal segments is now recognized as a major source of genetic polymorphism within natural populations of eukaryotes, as well as a possible cause of genetic diseases in humans, including cancer, but its molecular bases remain incompletely understood. In the baker's yeast Saccharomyces cerevisiae, a variety of low-order amplifications (segmental duplications) were observed after adaptation to limiting environmental conditions or recovery from gene dosage imbalance, and interpreted in terms of replication-based mechanisms associated or not with homologous recombination. Here we show the emergence of novel high-order amplification structures, with corresponding overexpression of embedded genes, during evolution under favourable growth conditions of severely unfit yeast cells bearing genetically disabled genomes. Such events form massively extended chromosomes, which we propose to call macrotene, whose characteristics suggest the products of intrachromosomal rolling-circle type of replication structures, probably initiated by increased accidental template switches under important cellular stress conditions.

Targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae

We describe here the first successful construction of a targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had a 5'-deleted pyrG upstream of the region targeted for tandem chromosomal duplication and a 3'-deleted pyrG downstream of the target region. Consequently,strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks(DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under nonselective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method.

The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite

Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI) involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.

Dynamic large-scale chromosomal rearrangements fuel rapid adaptation in yeast populations

Large-scale genome rearrangements have been observed in cells adapting to various selective conditions during laboratory evolution experiments. However, it remains unclear whether these types of mutations can be stably maintained in populations and how they impact the evolutionary trajectories. Here we show that chromosomal rearrangements contribute to extremely high copper tolerance in a set of natural yeast strains isolated from Evolution Canyon (EC), Israel. The chromosomal rearrangements in EC strains result in segmental duplications in chromosomes 7 and 8, which increase the copy number of genes involved in copper regulation, including the crucial transcriptional activator CUP2 and the metallothionein CUP1. The copy number of CUP2 is correlated with the level of copper tolerance, indicating that increasing dosages of a single transcriptional activator by chromosomal rearrangements has a profound effect on a regulatory pathway. By gene expression analysis and functional assays, we identified three previously unknown downstream targets of CUP2: PHO84, SCM4, and CIN2, all of which contributed to copper tolerance in EC strains. Finally, we conducted an evolution experiment to examine how cells maintained these changes in a fluctuating environment. Interestingly, the rearranged chromosomes were reverted back to the wild-type configuration at a high frequency and the recovered chromosome became fixed in less selective conditions. Our results suggest that transposon-mediated chromosomal rearrangements can be highly dynamic and can serve as a reversible mechanism during early stages of adaptive evolution.

Genome hyperevolution and the success of a parasite

The strategy of antigenic variation is to present a constantly changing population phenotype that enhances parasite transmission, through evasion of immunity arising within, or existing between, host animals. Trypanosome antigenic variation occurs through spontaneous switching among members of a silent archive of many hundreds of variant surface glycoprotein (VSG) antigen genes. As with such contingency systems in other pathogens, switching appears to be triggered through inherently unstable DNA sequences. The archive occupies subtelomeres, a genome partition that promotes hypermutagenesis and, through telomere position effects, singular expression of VSG. Trypanosome antigenic variation is augmented greatly by the formation of mosaic genes from segments of pseudo-VSG, an example of implicit genetic information. Hypermutation occurs apparently evenly across the whole archive, without direct selection on individual VSG, demonstrating second-order selection of the underlying mechanisms. Coordination of antigenic variation, and thereby transmission, occurs through networking of trypanosome traits expressed at different scales from molecules to host populations.

Comparative genomics reveals birth and death of fragile regions in mammalian evolution

Background

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals raised some doubts about their existence.

Results

Here we demonstrate that fragile regions are subject to a birth and death process, implying that fragility has a limited evolutionary lifespan.

Conclusions

This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions as a phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome.

Identity and divergence of protein domain architectures after the yeast whole-genome duplication event

Gene duplication is a key mechanism in evolution for generating new functionality, and it is known to have produced a large proportion of genes. Duplication mechanisms include small-scale, or "local", events such as unequal crossing over and retroposition, together with global events, such as chromosomal or whole genome duplication (WGD). In particular, different studies confirmed that the yeast S. cerevisiae arose from a 100-150 million-year old whole-genome duplication. Detection and study of duplications are usually based on sequence alignment, synteny and phylogenetic techniques, but protein domains are also useful in assessing protein homology. We develop a simple and computationally efficient protein domain architecture comparison method based on the domain assignments available from public databases. We test the accuracy and the reliability of this method in detecting instances of gene duplication in the yeast S. cerevisiae. In particular, we analyze the evolution of WGD and non-WGD paralogs from the domain viewpoint, in comparison with a more standard functional analysis of the genes. A large number of domains is shared by genes that underwent local and global duplications, indicating the existence of a common set of "duplicable" domains. On the other hand, WGD and non-WGD paralogs tend to have different functions. We find evidence that this comes from functional migration within similar domain superfamilies, but also from the existence of small sets of WGD and non-WGD specific domain superfamilies with largely different functions. This observation gives a novel perspective on the finding that WGD paralogs tend to be functionally different from small-scale paralogs. WGD and non-WGD superfamilies carry distinct functions. Finally, the Gene Ontology similarity of paralogs tends to decrease with duplication age, while this tendency is weaker or not observable by the comparison of the domain architectures of paralogs. This suggests that the set of domains composing a protein tends to be maintained, while its function, cellular process or localization diversifies. Overall, the gathered evidence gives a different viewpoint on the biological specificity of the WGD and at the same time points out the validity of domain architecture comparison as a tool for detecting homology.

Genetic and epigenetic mechanisms underlying cell-surface variability in protozoa and fungi

Eukaryotic microorganisms have evolved ingenious mechanisms to generate variability at their cell surface, permitting differential adherence, rapid adaptation to changing environments, and evasion of immune surveillance. Fungi such as Saccharomyces cerevisiae and the pathogen Candida albicans carry a family of mucin and adhesin genes that allow adhesion to various surfaces and tissues. Trypanosoma cruzi, T. brucei, and Plasmodium falciparum likewise contain large arsenals of different cell surface adhesion genes. In both yeasts and protozoa, silencing and differential expression of the gene family results in surface variability. Here, we discuss unexpected similarities in the structure and genomic location of the cell surface genes, the role of repeated DNA sequences, and the genetic and epigenetic mechanisms-all of which contribute to the remarkable cell surface variability in these highly divergent microbes.

Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans

Differences between yeast and worm duplicates result from differences in mechanisms of duplication and effective population size.

Background

The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication can be generalized across diverse lineages or are species-specific. Here we present results from an analysis comprising 68 duplication events in the Saccharomyces cerevisiae genome. We partition the yeast duplicates into ohnologs (generated by a whole-genome duplication) and non-ohnologs (from small-scale duplication events) to determine whether their disparate origins commit them to divergent evolutionary trajectories and genomic attributes.

Results

We conclude that, for the most part, ohnologs tend to appear remarkably similar to non-ohnologs in their structural attributes (specifically the relative composition frequencies of complete, partial and chimeric duplicates), the discernible length of the duplicated region (duplication span) as well as genomic location. Furthermore, we find notable differences in the features of S. cerevisiae gene duplicates relative to those of another eukaryote, Caenorhabditis elegans, with respect to chromosomal location, extent of duplication and the relative frequencies of complete, partial and chimeric duplications.

Conclusions

We conclude that the variation between yeast and worm duplicates can be attributed to differing mechanisms of duplication in conjunction with the varying efficacy of natural selection in these two genomes as dictated by their disparate effective population sizes.

Meiosis drives extraordinary genome plasticity in the haploid fungal plant pathogen Mycosphaerella graminicola

Meiosis in the haploid plant-pathogenic fungus Mycosphaerella graminicola results in eight ascospores due to a mitotic division following the two meiotic divisions. The transient diploid phase allows for recombination among homologous chromosomes. However, some chromosomes of M. graminicola lack homologs and do not pair during meiosis. Because these chromosomes are not present universally in the genome of the organism they can be considered to be dispensable. To analyze the meiotic transmission of unequal chromosome numbers, two segregating populations were generated by crossing genetically unrelated parent isolates originating from Algeria and The Netherlands that had pathogenicity towards durum or bread wheat, respectively. Detailed genetic analyses of these progenies using high-density mapping (1793 DArT, 258 AFLP and 25 SSR markers) and graphical genotyping revealed that M. graminicola has up to eight dispensable chromosomes, the highest number reported in filamentous fungi. These chromosomes vary from 0.39 to 0.77 Mb in size, and represent up to 38% of the chromosomal complement. Chromosome numbers among progeny isolates varied widely, with some progeny missing up to three chromosomes, while other strains were disomic for one or more chromosomes. Between 15–20% of the progeny isolates lacked one or more chromosomes that were present in both parents. The two high-density maps showed no recombination of dispensable chromosomes and hence, their meiotic processing may require distributive disjunction, a phenomenon that is rarely observed in fungi. The maps also enabled the identification of individual twin isolates from a single ascus that shared the same missing or doubled chromosomes indicating that the chromosomal polymorphisms were mitotically stable and originated from nondisjunction during the second division and, less frequently, during the first division of fungal meiosis. High genome plasticity could be among the strategies enabling this versatile pathogen to quickly overcome adverse biotic and abiotic conditions in wheat fields.

Comparative genomics and molecular dynamics of DNA repeats in eukaryotes

Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms

The propensity of segmental duplications (SDs) to promote genomic instability is of increasing interest since their involvement in numerous human genomic diseases and cancers was revealed. However, the mechanism(s) responsible for their appearance remain mostly speculative. Here, we show that in budding yeast, replication accidents, which are most likely transformed into broken forks, play a causal role in the formation of SDs. The Pol32 subunit of the major replicative polymerase Polδ is required for all SD formation, demonstrating that SDs result from untimely DNA synthesis rather than from unequal crossing-over. Although Pol32 is known to be required for classical (Rad52-dependant) break-induced replication, only half of the SDs can be attributed to this mechanism. The remaining SDs are generated through a Rad52-independent mechanism of template switching between microsatellites or microhomologous sequences. This new mechanism, named microhomology/microsatellite-induced replication (MMIR), differs from all known DNA double-strand break repair pathways, as MMIR-mediated duplications still occur in the combined absence of homologous recombination, microhomology-mediated, and nonhomologous end joining machineries. The interplay between these two replication-based pathways explains important features of higher eukaryotic genomes, such as the strong, but not strict, association between SDs and transposable elements, as well as the frequent formation of oncogenic fusion genes generating protein innovations at SD junctions.

Duplications of long segments of chromosomes are frequently observed in multicellular organisms (∼5% of our genome, for instance). They appear as a fundamental trait of the recent genome evolution in great apes and are often associated with chromosomal instability, capable of increasing genetic polymorphism among individuals, but also having dramatic consequences as a source of diseases and cancer. Despite their importance, the molecular mechanisms of formation of segmental duplications remain unclear. Using a specifically designed experimental system in the baker's yeast Saccharomyces cerevisiae, hundreds of naturally occurring segmental duplications encompassing dozens of genes were selected. With the help of modern molecular methods coupled to detailed genetic analysis, we show that such duplication events are frequent and result from untimely DNA synthesis accidents produced by two distinct molecular mechanisms: the well-known break-induced replication and a novel mechanism of template switching between low-complexity or microhomologous sequences. These two mechanisms, rather than unequal recombination events, contribute in comparable proportions to duplication formation, the latter being prone to create novel gene fusions at chromosomal junctions. The mechanisms identified in yeast could explain the origin of a variety of genetic diseases in human, such as hemophilia A, Pelizaeus-Merzbacher disease, or some neurological disorders.

Gene duplication and transfer events in plant mitochondria genome

Gene or genome duplication events increase the amount of genetic material available to increase the genomic, and thereby phenotypic, complexity of organisms during evolution. Gene duplication and transfer events have been important to molecular evolution in all three domains of life, and may be the first step in the emergence of new gene functions. Gene transfer events have been proposed as another accelerator of evolution. The duplicated gene or genome, mainly nuclear, has been the subject of several recent reviews. In addition to the nuclear genome, organisms have organelle genomes, including mitochondrial genome. In this review, we briefly summarize gene duplication and transfer events in the plant mitochondrial genome.

Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution

Mobile genetic elements have impacted biological evolution across all studied organisms, but evidence for a role in evolutionary emergence of an entire phylogenetic clade has not been forthcoming. We suggest that mobile element predation played a formative role in emergence of the phytoplasma clade. Phytoplasmas are cell wall-less bacteria that cause numerous diseases in plants. Phylogenetic analyses indicate that these transkingdom parasites descended from Gram-positive walled bacteria, but events giving rise to the first phytoplasma have remained unknown. Previously we discovered a unique feature of phytoplasmal genome architecture, genes clustered in sequence-variable mosaics (SVMs), and suggested that such structures formed through recurrent, targeted attacks by mobile elements. In the present study, we discovered that cryptic prophage remnants, originating from phages in the order Caudovirales, formed SVMs and comprised exceptionally large percentages of the chromosomes of 'Candidatus Phytoplasma asteris'-related strains OYM and AYWB, occupying nearly all major nonsyntenic sections, and accounting for most of the size difference between the two genomes. The clustered phage remnants formed genomic islands exhibiting distinct DNA physical signatures, such as dinucleotide relative abundance and codon position GC values. Phytoplasma strain-specific genes identified as phage morons were located in hypervariable regions within individual SVMs, indicating that prophage remnants played important roles in generating phytoplasma genetic diversity. Because no SVM-like structures could be identified in genomes of ancestral relatives including Acholeplasma spp., we hypothesize that ancient phage attacks leading to SVM formation occurred after divergence of phytoplasmas from acholeplasmas, triggering evolution of the phytoplasma clade.

Human subtelomeric WASH genes encode a new subclass of the WASP family

Subtelomeres are duplication-rich, structurally variable regions of the human genome situated just proximal of telomeres. We report here that the most terminally located human subtelomeric genes encode a previously unrecognized third subclass of the Wiskott-Aldrich Syndrome Protein family, whose known members reorganize the actin cytoskeleton in response to extracellular stimuli. This new subclass, which we call WASH, is evolutionarily conserved in species as diverged as Entamoeba. We demonstrate that WASH is essential in Drosophila. WASH is widely expressed in human tissues, and human WASH protein colocalizes with actin in filopodia and lamellipodia. The VCA domain of human WASH promotes actin polymerization by the Arp2/3 complex in vitro. WASH duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires vary. Thus, human subtelomeres are not genetic junkyards, and WASH's location in these dynamic regions could have advantageous as well as pathologic consequences.

Human subtelomeres are rearrangement-prone regions near chromosome ends. They are concentrations of large, recent interchromosomal duplications. Over half of subtelomeric sequences changed copy number or location since humans and chimpanzee diverged, and subtelomeric content varies greatly among humans. Despite this dynamic activity, subtelomeres contain genes. We report the discovery of genes defining a previously unrecognized third subclass of the Wiskott-Aldrich Syndrome protein (WASP) family within human subtelomeres. The known WASP family members reorganize actin structures in cells in response to various signals, thereby causing cells to change shape and/or move. Representatives of this newly identified subclass, called WASH, exist in many other species, even in Entamoeba and slime mold. Like other WASP family members, WASH colocalizes with actin at the cell periphery and promotes actin polymerization in vitro. Flies lacking WASH die before becoming adults, demonstrating that WASH is critical for survival, and its function is distinct from that of the two other WASP subclasses, Wasp and Scar. Identification of the WASH subclass opens the way for future elucidation of WASH's role in the life cycles of diverse organisms, the implications of human variation in WASH copy number, and the consequences of WASH's location in dynamic telomere-adjacent regions.

A naturally occurring gene amplification leading to sulfonamide and trimethoprim resistance in Streptococcus agalactiae

Gene amplifications have been detected as a transitory phenomenon in bacterial cultures. They are predicted to contribute to rapid adaptation by simultaneously increasing the expression of genes clustered on the chromosome. However, genome amplifications have rarely been described in natural isolates. Through DNA array analysis, we have identified two Streptococcus agalactiae strains carrying tandem genome amplifications: a fourfold amplification of 13.5 kb and a duplication of 92 kb. Both amplifications were located close to the terminus of replication and originated independently from any long repeated sequence. They probably arose in the human host and showed different stabilities, the 13.5-kb amplification being lost at a frequency of 0.003 per generation and the 92-kb tandem duplication at a frequency of 0.035 per generation. The 13.5-kb tandem amplification carried the five genes required for dihydrofolate biosynthesis and led to both trimethoprim (TMP) and sulfonamide (SU) resistance. Resistance to SU probably resulted from the increased synthesis of dihydropteroate synthase, the target of this antibiotic, whereas the amplification of the whole pathway was responsible for TMP resistance. This revealed a new mechanism of resistance to TMP involving an increased dihydrofolate biosynthesis. This is, to our knowledge, the first reported case of naturally occurring antibiotic resistance resulting from genome amplification in bacteria. The low stability of DNA segment amplifications suggests that their role in antibiotic resistance might have been underestimated.

Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?

Background

Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Saccharomyces cerevisiae. We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization.

Results

We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae, (2) reconstruction of gene arrangements ancestral to A. gossypii, S. cerevisiae, and K. waltii, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets. The existence of syntenic patterns between ancestral gene sets and A. gossypii, S. cerevisiae, and K. waltii, and other evidence, suggests that gene-interleaving relationships are the natural consequence of topological rearrangements in chromosomes and that a more gradual scenario of genome evolution involving segmental duplication and recombination constitutes a more parsimonious explanation. Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii. This is clearly incompatible with an ancient genome duplication event in S. cerevisiae.

Conclusion

Because the presence of syntenic patterns appears to be a condition that is necessary, but not sufficient, to support the existence of the whole-genome duplication event, our results prompt careful re-evaluation of paleopolyploidization in the yeast lineage and the evolutionary meaning of syntenic patterns.

Reviewers

This article was reviewed by Kenneth H. Wolfe (nominated by Nicolas Galtier), Austin L. Hughes (nominated by Eugene Koonin), Mikhail S. Gelfand, and Mark Gerstein.

Analysis of the VSG gene silent archive in Trypanosoma brucei reveals that mosaic gene expression is prominent in antigenic variation and is favored by archive substructure

Trypanosoma brucei evades host acquired immunity through differential activation of its large archive of silent variant surface glycoprotein (VSG) genes, most of which are pseudogenes in subtelomeric arrays. We have analyzed 940 VSGs, representing one half to two thirds of the arrays. Sequence types A and B of the VSG N-terminal domains were confirmed, while type C was found to be a constituent of type A. Two new C-terminal domain types were found. Nearly all combinations of domain types occurred, with some bias to particular combinations. One-third of encoded N-terminal domains, but only 13% of C-terminal domains, are intact, indicating a particular need for silent VSGs to gain a functional C-terminal domain to be expressed. About 60% of VSGs are unique, the rest occurring in subfamilies of two to four close homologs (>50%-52% peptide identity). We found a subset of VSG-related genes, differing from VSGs in genomic environment and expression patterns, and predict they have distinct function. Almost all (92%) full-length array VSGs have the partially conserved flanks associated with the duplication mechanism that activates silent genes, and these sequences have also contributed to archive evolution, mediating most of the conversions of segments, containing >/=1 VSG, within and between arrays. During infection, intact array genes became activated by duplication after two weeks, and mosaic VSGs assembled from pseudogenes became expressed by week three and predominated by week four. The small subfamily structure of the archive appears to be fundamental in providing the interacting donors for mosaic formation.