Gabriela Aguileta

Centre for Genomic Regulation | CRG · Comparative Genomics

About 100,000 species of fungi have been described so far, of which a high percentage obtain nutrients by living in close association with other organisms, mainly plants. Many fungi are pathogenic and can have important impact on human health or lead to severe economic losses due to infected crops or to animal diseases. In this chapter, we describe...

Significance Sex chromosomes can display divergent evolution, as seen in humans, in which the Y chromosome underlying maleness is smaller and contains much less information than the X chromosome. The differentiation between sex chromosomes can occur stepwise along their length, which is thought to result from the successive beneficial linkage of ge...

Identifying the genes underlying adaptation, their distribution in genomes, and the evolutionary forces shaping genomic diversity, are key challenges in evolutionary biology. Very few studies have investigated the abundance and distribution of selective sweeps in species with high-quality reference genomes, outside of a handful of model species. Pa...

Nuclear disasters at Chernobyl and Fukushima provide examples of effects of acute ionizing radiation on mutations that can affect the fitness and distribution of species. Here, we investigated the prevalence of Microbotryum lychnidis-dioicae, a pollinator-transmitted fungal pathogen of plants causing anther-smut disease in Chernobyl, its viability,...

Sex chromosomes in plants and animals and fungal mating-type chromosomes often show exceptional genome features, with extensive suppression of homologous recombination and cytological differentiation between members of the diploid chromosome pair. Despite strong interest in the genetics of these chromosomes, their large regions of suppressed recomb...

The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. We determined the haploid genome sequence for M. lychni...

Horizontal gene transfers (HGT), i.e., the transmission of genetic material between species not directly attributable to meiotic gene exchange, have long been acknowledged as a major driver of prokaryotic evolution and is increasingly recognized as an important source of adaptation in eukaryotes. In fungi in particular, many convincing examples of...

Dimorphic mating-type chromosomes in fungi are excellent models for understanding the genomic consequences of recombination suppression. Their suppressed recombination and reduced effective population size are expected to limit the efficacy of natural selection, leading to genomic degeneration. Our aim was to identify the sequences of the mating-ty...

Horizontal gene transfers (HGT), i.e., the transmission of genetic material between species not directly at- tributable to meiotic gene exchange, have long been acknowledged as a major driver of prokaryotic evolu- tion and is increasingly recognized as an important source of adaptation in eukaryotes. In fungi in particu- lar, many convincing exampl...

From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial genomes (mtDNA) but fungi provide new opportunities to study highl...

Fungi are ideal model organisms for dissecting the genomic bases of adaptive divergence in eukaryotes. They have simple morphologies and small genomes, occupy contrasting, well identified ecological niches, tend to have short generation times and many are amenable to experimental approaches. Fungi also display diverse lifestyles, from saprotrophs t...

Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens...

Tests of selective neutrality based on comparative and population genetic data target different time scales of selection. Investigating both time scales on the same genes has rarely been done and yet can provide insights into histories of selection. In pathogens, such a comparison can elucidate whether the same genes experience recurrent positive s...

Parallels have been drawn between the evolution of nonrecombining regions in fungal mating-type chromosomes and animal and plant sex chromosomes, particularly regarding the stages of recombination cessation forming evolutionary strata of allelic divergence. Currently, evidence and explanations for recombination cessation in fungi are sparse, and th...

The rapid evolution of particular genes is essential for the adaptation of pathogens to new hosts and new environments. Powerful methods have been developed for detecting targets of selection in the genome. Here we used divergence data to compare genes among four closely related fungal pathogens adapted to different hosts to elucidate the functions...

This chapter focuses on the application of codon models to study the evolution of fungi. The use of codon models to analyse fungal genomes has served many purposes: from establishing the selective forces behind the evolution of gene families, sexual chromosomes, regulatory networks, or host-pathogen interactions, to predicting ecologically relevant...

Full genome data sets are currently being explored on a regular basis to infer phylogenetic trees, but there are often discordances among the trees produced by different genes. An important goal in phylogenomics is to identify which individual gene and species produce the same phylogenetic tree and are thus likely to share the same evolutionary his...

This chapter discusses the main pathogenic fungi parasitizing humans, animals, and plants, and having important consequences on human health or human activities. It discusses the modern molecular tools used for epidemiology and population genetics of fungal pathogens. The two major groups, Ascomycota and Basidiomycota, are the most common causes of...

Phylogenies are fundamental to comparative biology as they help to identify independent events on which statistical tests rely. Two groups of phylogenetic comparative methods (PCMs) can be distinguished: those that take phylogenies into account by introducing explicit models of evolution and those that only consider phylogenies as a statistical con...

We studied the mode of reproduction and its evolution in the fungal subgenus Penicillium Biverticillium using phylogenetic and experimental approaches. We sequenced mating type (MAT) genes and nuclear DNA fragments in sexual and putatively asexual species. Examination of the concordance between individual trees supported the recognition of the morp...

Several cases of speciation by hybridization have been reported in fungi, mostly involving recent hybridization between closely related species. In the basidiomycete genus Microbotryum by contrast some species were suspected to have arisen by hybridization between moderately distant species. In particular two species, M. lagerheimii and M. silenes-...

We report the development of 17 microsatellite markers in the cheese fungi Penicillium camemberti and P. roqueforti, using an enrichment protocol. Polymorphism and cross-amplification were explored using 23 isolates of P. camemberti, 26 isolates of P. roqueforti, and 2 isolates of each of the P. chrysogenum and P. nalgiovense species, used to produ...

Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to d...

AbstractApproximately 100,000 species of fungi have been described so far, of which, a high percentage obtain nutrients by living in close association with other organisms (mainly plants), being pathogens or symbionts (i.e. commensalists or mutualists). At the genomic level, an association between broad-scale genetic changes and the emergences of t...

The ongoing coevolutionary struggle between hosts and pathogens, with hosts evolving to escape pathogen infection and pathogens evolving to escape host defences, can generate an 'arms race', i.e., the occurrence of recurrent selective sweeps that each favours a novel resistance or virulence allele that goes to fixation. Host-pathogen coevolution ca...

... Rapidly evolving genes in pathogens : Methods for detecting positive selection and examples among fungi ... with hosts evolving to escape pathogen infection and pathogens evolving to escape ... Genes under positive selection in pathogens have mostly been sought among viruses ...

In the majority of sexual organisms, reproduction occurs almost exclusively through the combination of distinct and alternate forms, called sexes or mating types. In some fungi, there can be dozens to hundreds of alternate alleles that determine compatible mating types. Such extensive polymorphism is expected to be maintained by balancing selection...

The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable an...

Phylogenies involving nonmodel species are based on a few genes, mostly chosen following historical or practical criteria. Because gene trees are sometimes incongruent with species trees, the resulting phylogenies may not accurately reflect the evolutionary relationships among species. The increase in availability of genome sequences now provides l...

The globin family of genes and proteins has been a recurrent object of study for many decades. This interest has generated a vast amount of knowledge. However it has also created an inconsistent and confusing nomenclature, due to the lack of a systematic approach to naming genes and failure to reflect the phylogenetic relationships among genes of t...

The globin family of genes and proteins has been a recurrent object of study for many decades. This interest has generated a vast amount of knowledge. How-ever it has also created an inconsistent and confusing nomenclature, due to the lack of a systematic approach to naming genes and to failure to reflect the phylo-genetic relationships among genes...

A comprehensive dataset of 62 beta globin gene sequences from various vertebrates was compiled to test the molecular clock and to estimate dates of gene duplications. We found that evolution of the beta globin family of genes is not clock-like, a result that is at odds with the common use of this family as an example of a constant rate of evolution...

Different models of gene family evolution have been proposed to explain the mechanism whereby gene copies created by gene duplications are maintained and diverge in function. Ohta proposed a model which predicts a burst of nonsynonymous substitutions following gene duplication and the preservation of duplicates through positive selection. An altern...