Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes.

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes

Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes):a fish adapted to demersal life

12 páginas, 5 figuras.-- Antonio Figueras ... et al.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly citedThe 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 the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbotThis work was funded by the Spanish Government: projects Consolider Ingenio: Aquagenomics (CSD2007-00002) and Metagenoma de la Península Ibérica (CSD2007-00005), Ministerio de Economía y Competitividad and European Regional Development Funds (AGL2012-35904), and Ministerio de Economía y Competitividad (AGL2014-51773 and AGL2014-57065-R); and Local Government Xunta de Galicia (GRC2014/010). P.P. and D.R. gratefully acknowledge the Spanish Ministerio de Educación for their FPU fellowships (AP2010-2408, AP2012-0254). Funding to pay the Open Access publication charges for this article was provided by the Ministerio de Economía y Competitividad (AGL2014-51773) and Xunta de Galicia (GRC2014/010)Peer reviewe

Population genomics of the emerging yeast pathogen Candida glabrata

Infections caused by pathogenic fungi are becoming an increasingly serious threat for human health. Pathogenic fungi such as Candida glabrata or Candida albicans, belong to phylogenetically distinct clades and have non-pathogenic close relatives, indicating that the ability to infect humans has evolved several times independently. Despite the many recent advances in biomedicine, we are still lacking an understanding of how virulence evolves across organisms and which mechanisms are involved in the emergence of pathogenesis. Elucidating how human pathogens evolve is of central relevance to understand the bases of virulence and spread of infectious agents. In this context, population genomics provides a powerful tool to uncover recent selection pressures that can shed light on how pathogens adapt to humans. We here evaluated genomic and phenotypic variation across 57 C. glabrata strains. Firstly, we focused on 33 globally-distributed isolates. We catalogued extensive copy number variation, which we found to particularly affect genes encoding cell-wall associated proteins, including adhesins. This variation is structured into seven deeply divergent clades, which show recent geographical dispersion and large within-clade genomic and phenotypic differences. We show compelling evidence of recent admixture between differentiated lineages, and of purifying selection on mating genes, which provide first evidence for the existence of an active sexual (or parasexual) cycle in this yeast. Altogether, our results point to a recent global spread of previously genetically isolated populations and suggest that humans are only a secondary niche for this yeast. Secondly, we analyzed the genomic variability of C. glabrata in pairs of serial isolates, each from the same patient. We detected that patients can host clonal and non-clonal isolates. We observed an active standing genetic diversity with recurrent recombination leading to significant differences in terms of oxidative stress resistance biofilm formation. These results suggested that standing genetic variation and withinhost recombination between divergent strains may play an important role in disease progression and treatment outcome.Infeccions causades per fongs patògens estan esdevenint un greu problema per la salut en humans. La candidiasis, una de les infeccions fungiques més comunes, està provocada principalment per patògens com Candida glabrata o Candida albicans. Aquestes dos especies són filogeneticament distants i tenen altres fongs no patògens al seu voltant, indicant que l’habilitat d’infectar humans ha evolucionat independentment durant els ultims anys. Malgrat els avanços en biomedicina, encara estem lluny d’entendre com la virulencia ha evolucionat en diferents organismes i quins mecanismes principals han actuat en l’emergència d’aquesta patogenicitat. Entendre com actuen els patogens és de principal importància per entendre les bases de la virulencia i expansió d’agents infecciosos. En aquest context, la genòmica de poblacions ens dóna una eina molt valuosa per investigar com la selecció ha actuat en aquests organismes i entendre com els patogens s’han adaptat als humans. Durant aquest projecte de Tesi, s’ha avaluat genomicament i fenotípicament 57 soques de C. glabrata. Primer, ens hem centrat en l’estudi de la variació genòmica de la població de C. glabrata utilitzant 33 soques distribuïdes arreu del mon. S’ha catalogat un gran nombre de delecions, duplicacions i aneuploïdies, les quals estan particularment enriquides en proteïnes de membrana o adhesines. Aquesta variació està estructurada en set clades diferents, els quals mostren una recent dispersió geogràfica i una elevada diferència genòmica i fenotípica dins dels clades. L’evidencia d’una recent barreja genètica entre diferents clades, i la presencia de selecció purificadora en gens relacionats en l’aparellament sexual, proporciona la primera evidencia de l’existencia d’un cicle sexual actiu en C. glabrata. També, s’ha analitzat els canvis genetics de C. glabrata en una serie de mostres aïllades en diferents dies d’un mateix pacient amb candidiasis. S’ha detectat que els pacients poden tenir soques clonals i soques no clonals. S’ha observat una variació genética existent i una recombinació recurrent que condueix a diferencies significatives en la formació de biofilms. Aquests resultats suggereixen que la variacio genética i la recombimnció dins de l’hoste provoca un paper important durant el progrés de la infecció i en el seu futur tractament

Population genomics of the emerging yeast pathogen Candida glabrata

Infections caused by pathogenic fungi are becoming an increasingly serious threat for human health. Pathogenic fungi such as Candida glabrata or Candida albicans, belong to phylogenetically distinct clades and have non-pathogenic close relatives, indicating that the ability to infect humans has evolved several times independently. Despite the many recent advances in biomedicine, we are still lacking an understanding of how virulence evolves across organisms and which mechanisms are involved in the emergence of pathogenesis. Elucidating how human pathogens evolve is of central relevance to understand the bases of virulence and spread of infectious agents. In this context, population genomics provides a powerful tool to uncover recent selection pressures that can shed light on how pathogens adapt to humans. We here evaluated genomic and phenotypic variation across 57 C. glabrata strains. Firstly, we focused on 33 globally-distributed isolates. We catalogued extensive copy number variation, which we found to particularly affect genes encoding cell-wall associated proteins, including adhesins. This variation is structured into seven deeply divergent clades, which show recent geographical dispersion and large within-clade genomic and phenotypic differences. We show compelling evidence of recent admixture between differentiated lineages, and of purifying selection on mating genes, which provide first evidence for the existence of an active sexual (or parasexual) cycle in this yeast. Altogether, our results point to a recent global spread of previously genetically isolated populations and suggest that humans are only a secondary niche for this yeast. Secondly, we analyzed the genomic variability of C. glabrata in pairs of serial isolates, each from the same patient. We detected that patients can host clonal and non-clonal isolates. We observed an active standing genetic diversity with recurrent recombination leading to significant differences in terms of oxidative stress resistance biofilm formation. These results suggested that standing genetic variation and withinhost recombination between divergent strains may play an important role in disease progression and treatment outcome.Infeccions causades per fongs patògens estan esdevenint un greu problema per la salut en humans. La candidiasis, una de les infeccions fungiques més comunes, està provocada principalment per patògens com Candida glabrata o Candida albicans. Aquestes dos especies són filogeneticament distants i tenen altres fongs no patògens al seu voltant, indicant que l’habilitat d’infectar humans ha evolucionat independentment durant els ultims anys. Malgrat els avanços en biomedicina, encara estem lluny d’entendre com la virulencia ha evolucionat en diferents organismes i quins mecanismes principals han actuat en l’emergència d’aquesta patogenicitat. Entendre com actuen els patogens és de principal importància per entendre les bases de la virulencia i expansió d’agents infecciosos. En aquest context, la genòmica de poblacions ens dóna una eina molt valuosa per investigar com la selecció ha actuat en aquests organismes i entendre com els patogens s’han adaptat als humans. Durant aquest projecte de Tesi, s’ha avaluat genomicament i fenotípicament 57 soques de C. glabrata. Primer, ens hem centrat en l’estudi de la variació genòmica de la població de C. glabrata utilitzant 33 soques distribuïdes arreu del mon. S’ha catalogat un gran nombre de delecions, duplicacions i aneuploïdies, les quals estan particularment enriquides en proteïnes de membrana o adhesines. Aquesta variació està estructurada en set clades diferents, els quals mostren una recent dispersió geogràfica i una elevada diferència genòmica i fenotípica dins dels clades. L’evidencia d’una recent barreja genètica entre diferents clades, i la presencia de selecció purificadora en gens relacionats en l’aparellament sexual, proporciona la primera evidencia de l’existencia d’un cicle sexual actiu en C. glabrata. També, s’ha analitzat els canvis genetics de C. glabrata en una serie de mostres aïllades en diferents dies d’un mateix pacient amb candidiasis. S’ha detectat que els pacients poden tenir soques clonals i soques no clonals. S’ha observat una variació genética existent i una recombinació recurrent que condueix a diferencies significatives en la formació de biofilms. Aquests resultats suggereixen que la variacio genética i la recombimnció dins de l’hoste provoca un paper important durant el progrés de la infecció i en el seu futur tractament

The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata

The yeast Candida glabrata is an opportunistic human fungal pathogen whose incidence has increased in the last two decades. Despite its name, this yeast is only distantly related to the model fungal pathogen C. albicans, and more closely related to Saccharomyces cerevisiae and other yeasts that underwent an ancient whole-genome duplication. Understanding what specific traits make C. glabrata a successful opportunistic pathogen within a clade of mostly innocuous yeasts, and how these compare to virulence traits in distant pathogens such as C. albicans is a focus of intense research. From an evolutionary perspective, uncovering how the ability to infect humans has emerged multiple, independent times in different lineages may reveal new disease mechanisms and provide us with the capacity to predict which genomic features in a clade may confer a higher potential to develop virulence against humans.TG group acknowledges support of the Spanish Ministry of Economy and Competitiveness grants, ‘Centro de Excelencia Severo Ochoa 2013–2017’ SEV-2012-0208, and BIO2012-37161 cofounded by European Regional Development Fund (ERDF); from the European Union and ERC Seventh Framework Programme (FP7/2007-2013) under grant agreements FP7-PEOPLE-2013-ITN-606786 and ERC-2012-StG-310325, and grant from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No H2020-MSCA-ITN-2014-642095

The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata

The yeast Candida glabrata is an opportunistic human fungal pathogen whose incidence has increased in the last two decades. Despite its name, this yeast is only distantly related to the model fungal pathogen C. albicans, and more closely related to Saccharomyces cerevisiae and other yeasts that underwent an ancient whole-genome duplication. Understanding what specific traits make C. glabrata a successful opportunistic pathogen within a clade of mostly innocuous yeasts, and how these compare to virulence traits in distant pathogens such as C. albicans is a focus of intense research. From an evolutionary perspective, uncovering how the ability to infect humans has emerged multiple, independent times in different lineages may reveal new disease mechanisms and provide us with the capacity to predict which genomic features in a clade may confer a higher potential to develop virulence against humans.TG group acknowledges support of the Spanish Ministry of Economy and Competitiveness grants, ‘Centro de Excelencia Severo Ochoa 2013–2017’ SEV-2012-0208, and BIO2012-37161 cofounded by European Regional Development Fund (ERDF); from the European Union and ERC Seventh Framework Programme (FP7/2007-2013) under grant agreements FP7-PEOPLE-2013-ITN-606786 and ERC-2012-StG-310325, and grant from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No H2020-MSCA-ITN-2014-642095

Art pop i curtmetratges a una biblioteca penitenciària: tallers de dinamització cultural a la Biblioteca del Centre Penitenciari de Joves de Barcelona

Se describen y analizan dos actividades de extensión cultural realizadas en la Biblioteca del Centre Penitenciari de Joves de Barcelona a partir de una colaboración externa. Se incluye una descripción del Centro, de la Biblioteca y del perfil del usuario al que van destinadas las actividades. Seguidamente, se resumen las diferentes fases de preparación de la actividad, su desarrollo y valoración posterior. Las actividades se presentaron como talleres y estaban centradas en el hecho visual y de la imagen: pintura de estética art pop y cineforum de un cortometraje

Arte pop y cortometrajes en una biblioteca penitenciaria: talleres de dinamización cultural en la Biblioteca del Centre Penitenciari de Joves de Barcelona

Es descriuen i s'analitzen dues activitats d'extensió cultural dutes a terme a la Biblioteca del Centre Penitenciari de Joves de Barcelona a partir d'una col·laboració externa. S'inclou una descripció del Centre, de la Biblioteca i del perfil d'usuari a qui s'han dirigit les activats. Seguidament, es resumeixen els diferents passos duts a terme per a la confecció de les activitats, com s'han desenvolupat i la posterior valoració. Les activitats es van presentar com a tallers i se centraven en el fet visual i de la imatge: pintura d'estètica art pop i cinefòrum d'un curtmetratge.Two activities of cultural extension are described and analysed. These were carried out, with external collaboration, at the library of the Juvenile Penitentiary Centre of Barcelona. The description covers the Centre, the library, and the profile of the users to whom the activities are directed. The article then explains the different steps undertaken to set up the activities, how they developed, and their subsequent evaluation. The activities took the form of workshops centred on visual happenings and images: pop art style painting and a forum on a short-length movie.Se describen y analizan dos actividades de extensión cultural realizadas en la Biblioteca del Centre Penitenciari de Joves de Barcelona a partir de una colaboración externa. Se incluye una descripción del Centro, de la Biblioteca y del perfil del usuario al que van destinadas las actividades. Seguidamente, se resumen las diferentes fases de preparación de la actividad, su desarrollo y valoración posterior. Las actividades se presentaron como talleres y estaban centradas en el hecho visual y de la imagen: pintura de estética art pop y cineforum de un cortometraje

HaploTypo: a variant-calling pipeline for phased genomes

SUMMARY: An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome. AVAILABILITY AND IMPLEMENTATION: HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.This work was supported by the European Union’s Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173 and Marie Sklodowska-Curie grant agreements N° 642095, and 747607; the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and grants ‘Centro de Excelencia Severo Ochoa’ SEV-2012-0208, and BFU2015-67107 co-founded by European Regional Development Fund (ERDF); the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857; and INB Grant (PT17/0009/0023—ISCIII-SGEFI/ERDF)

Art pop i curtmetratges a una biblioteca penitenciària : tallers de dinamització cultural a la Biblioteca del Centre Penitenciari de Joves de Barcelona

Es descriuen i s’analitzen dues activitats d’extensió cultural dutes a terme a la Biblioteca del Centre Penitenciari de Joves de Barcelona a partir d’una col·laboració externa. S’inclou una descripció del Centre, de la Biblioteca i del perfil d’usuari a qui s’han dirigit les activats. Seguidament, es resumeixen els diferents passos duts a terme per a la confecció de les activitats, com s’han desenvolupat i la posterior valoració. Les activitats es van presentar com a tallers i se centraven en el fet visual i de la imatge: pintura d’estètica art pop i cinefòrum d’un curtmetratge.Two activities of cultural extension are described and analysed. These were carried out, with external collaboration, at the library of the Juvenile Penitentiary Centre of Barcelona. The description covers the Centre, the library, and the profile of the users to whom the activities are directed. The article then explains the different steps undertaken to set up the activities, how they developed, and their subsequent evaluation. The activities took the form of workshops centred on visual happenings and images: pop art style painting and a forum on a short-length movie.Se describen y analizan dos actividades de extensión cultural realizadas en la Biblioteca del Centre Penitenciari de Joves de Barcelona a partir de una colaboración externa. Se incluye una descripción del Centro, de la Biblioteca y del perfil del usuario al que van destinadas las actividades. Seguidamente, se resumen las diferentes fases de preparación de la actividad, su desarrollo y valoración posterior. Las actividades se presentaron como talleres y estaban centradas en el hecho visual y de la imagen: pintura de estética art pop y cineforum de un cortometraje