A5064295564- Plant Pathogens and Fungal Diseases
- Genomics and Phylogenetic Studies
- Antifungal resistance and susceptibility
- Fungal and yeast genetics research
- Genetic diversity and population structure
- Yeasts and Rust Fungi Studies
- Protist diversity and phylogeny
- Microbial Natural Products and Biosynthesis
- Mycorrhizal Fungi and Plant Interactions
- Chromosomal and Genetic Variations
- Insect symbiosis and bacterial influences
- Mycotoxins in Agriculture and Food
- Plant-Microbe Interactions and Immunity
- Fungal Infections and Studies
- Insect-Plant Interactions and Control
- Insect Resistance and Genetics
- Plant Disease Resistance and Genetics
- Microbial Community Ecology and Physiology
- Fermentation and Sensory Analysis
- Edible Oils Quality and Analysis
- Entomopathogenic Microorganisms in Pest Control
- Plant Virus Research Studies
- Ichthyology and Marine Biology
- Bioinformatics and Genomic Networks
- Plant and animal studies
Institute for Research in Biomedicine
2019-2024
Barcelona Supercomputing Center
2019-2024
Universitat Politècnica de Catalunya
2019-2024
Institute of Science and Technology
2024
Instituto de Salud Carlos III
2024
Centro de Investigación Biomédica en Red
2024
Barcelona Institute for Science and Technology
2018-2022
Institució Catalana de Recerca i Estudis Avançats
2013-2021
Centre for Genomic Regulation
2011-2020
Pompeu Fabra University
2011-2020
A major bottleneck in our understanding of the molecular underpinnings life is assignment function to proteins. While experiments provide most reliable annotation proteins, their relatively low throughput and restricted purview have led an increasing role for computational prediction. However, assessing methods protein prediction tracking progress field remain challenging.We conducted second critical assessment functional (CAFA), a timed challenge assess that automatically assign function....
Whole-genome duplications have shaped the genomes of several vertebrate, plant, and fungal lineages. Earlier studies focused on establishing when these events occurred elucidating their functional evolutionary consequences, but we still lack sufficient understanding how genome first originated. We used phylogenomics to study ancient duplication in yeast Saccharomyces cerevisiae lineage found compelling evidence for existence a contemporaneous interspecies hybridization. propose that doubling...
Significance In eusocial insect societies, such as ants and some bees wasps, phenotypes are highly plastic, generating alternative (queens workers) from the same genome. The greatest plasticity is found in simple which individuals can switch between adults. genomic, transcriptional, epigenetic underpinnings of largely unknown. contrast to complex societies honeybee, we find that lack distinct transcriptional differentiation coherently patterned DNA methylomes. Instead, defined by subtle...
Phylogenetic trees representing the evolutionary relationships of homologous genes are entry point for many analyses. For instance, use a phylogenetic tree can aid in inference orthology and paralogy relationships, detection relevant events such as gene family expansions contractions, horizontal transfer, recombination or incomplete lineage sorting. Similarly, given plurality histories among encoded genome, there is need combined analysis genome-wide collections (phylomes). Here, we...
Abstract Background Penicillium digitatum is a fungal necrotroph causing common citrus postharvest disease known as green mold. In order to gain insight into the genetic bases of its virulence mechanisms and high degree host-specificity, genomes two P. strains that differ in their antifungal resistance traits have been sequenced compared with those 28 other Pezizomycotina. Results The are highly similar, but important differences between them include presence unique gene cluster resistant...
Abstract Background Microsporidia is one of the taxa that have experienced most dramatic taxonomic reclassifications. Once thought to be among earliest diverging eukaryotes, fungal nature this group intracellular pathogens now widely accepted. However, specific position microsporidia within tree life still debated. Due presence accelerated evolutionary rates, phylogenetic analyses involving are prone methodological artifacts, such as long-branch attraction, especially when taxon sampling...
The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into phylogeny of this species, much still unknown about how evolutionary processes related to anthropogenic niches have shaped genomes phenotypes S. cerevisiae. To address question, we performed population-level sequencing 82 strains from wine, flor, rum, dairy products, bakeries, natural environment (oak trees). These genomic data enabled us...
BackgroundThe Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently major agricultural importance in region as source oil. The molecular bases underlying phenotypic differences among cultivars, or between their wild relatives, remain poorly understood. Both cultivated have 46 chromosomes (2n).
Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns genomic erosion that might limit viability, offer tools for effective conservation. The Iberian lynx (Lynx pardinus) is the most felid a unique example on brink extinction.
The relationship between secondary metabolism and infection in pathogenic fungi has remained largely elusive. genus Penicillium comprises a group of plant pathogens with varying host specificities the ability to produce wide array metabolites. genomes three expansum strains, main postharvest pathogen pome fruit, one Pencillium italicum strain, citrus were sequenced compared 24 other fungal species. A genomic analysis gene clusters responsible for production metabolites was performed....
Bioluminescence is found across the entire tree of life, conferring a spectacular set visually oriented functions from attracting mates to scaring off predators. Half dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which only bacteria. Here, we report identification fungal luciferase and three other key enzymes together form biosynthetic cycle caffeic...
Abstract Elucidating population structure and levels of genetic diversity recombination is necessary to understand the evolution adaptation species. Candida albicans second most frequent agent human fungal infections worldwide, causing high-mortality rates. Here we present genomic sequences 182 C . isolates collected including commensal isolates, as well ones responsible for superficial invasive infections, constituting largest dataset date this major pathogen. Although, shows a...
Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate origin phenotypic innovation by developing little skate Leucoraja erinacea as a genomically enabled model. Analysis high-quality chromosome-scale genome sequence for shows that it preserves many ancestral jawed vertebrate compared with other sequenced genomes,...
Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, being part Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although was thought be only new pathogens have recently been described within this group: nivariensis and bracarensis. To gain insight into genomic changes underlying emergence virulence, we sequenced genomes these two, three other non-pathogenic compared...
The opportunistic fungal pathogen Candida glabrata is a frequent cause of candidiasis, causing infections ranging from superficial to life-threatening disseminated disease. inherent tolerance C. azole drugs makes this serious clinical threat. To identify novel genes implicated in antifungal drug tolerance, we have constructed large-scale deletion library consisting 619 unique, individually bar-coded mutant strains, each lacking one specific gene, all together representing almost 12% the...
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of genome, represents milestone for both boosting breeding programmes ascertaining origin diversification flatfish. We compare genome model fish genomes to investigate teleost chromosome evolution. observe conserved macrosyntenic pattern within Percomorpha identify large syntenic blocks related...
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including reconstruction large collections phylogenetic trees. Here, we present third version PhylomeDB (http://phylomeDB.org), a public database for genome-wide gene phylogenies (phylomes). Currently, is largest repository and hosts 17 phylomes, comprising 416,093 trees 165,840 alignments. It also major source phylogeny-based orthology paralogy...
Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into molecular basis pathogenicity-associated traits basal Mucorales, we report full genome sequence L. corymbifera and compared it to Rhizopus oryzae, common worldwide. The assembly encompasses 33.6 MB 12,379 protein-coding genes. This study reveals four major differences R. oryzae: (i) presence an highly elevated number gene duplications which unlike oryzae not due whole...
Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage filamentous ascomycetes, there is so far only one genome available, namely that black truffle, Tuber melanosporum, mycorrhizal species with unusual subterranean fruiting bodies. To help close sequence gap among basal to allow...