This work was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. H2020-MSCA-ITN-2014-642095. TG group also acknowledges support from 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); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857; and grants from the European Union's Horizon 2020 research and innovation programme under the grant agreements ERC-2016-724173, and MSCA-747607. TG also receives support from an INB Grant (PT17/0009/0023 - ISCIII-SGEFI/ERDF). ; Peer Reviewed ; Postprint (author's final draft)
The question of how phenotypic and genomic complexity are inter‐related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fun ; T.G. acknowledges support from the Spanish Ministry of Science and Innovation for grants 'Centro de Excelencia Severo Ochoa' and PGC2018‐099921‐B‐I00, cofunded by the European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR423, and grants from the European Union's Horizon 2020 research and innovation programme under the grant agreement ERC‐2016‐724173, and the Marie Sklodowska‐Curie grant agreement No H2020‐MSCA‐IF‐2017‐793699. T.G.'s research group also receives support from a INB Grant (PT17/0009/0023 ‐ ISCIII‐SGEFI/ERDF). ; Peer Reviewed ; Postprint (published version)
Nucleariids are a small group of free-living heterotrophic amoebae. Although these organisms present a variety of cell sizes and cell coverings, they are mostly spherical cells with radiating filopodia, sometimes with several nuclei. Nuclearia, the genus that gives the name to the group, contains species that are opportunistic consumers of detritus, bacteria, and algae. The beautiful Pompholyxophrys is covered with endogenous siliceous pearls. Lithocolla covers itself with sand particles, or otherwise diatom frustules. The tiny Parvularia exclusively feeds on bacteria, and Fonticula is adapted to solid substrates and presents aggregative multicellular stages. Nucleariids belong to the Opisthokonta, which comprise animals, fungi, and their protist relatives and, form the earliest branch in the holomycotan clade (fungi and closest relatives). Hence, they are key for understanding the origin and diversification of Opisthokonta, an eukaryotic supergroup that contains organisms with different feeding modes, life-styles, and cell organizations. In this review, the reader will find an introduction to nucleariids, from their discovery in the 19th century until the most recent studies. It summarizes available information on their morphology, life history, cell organisation, ecology, diversity, systematics and evolution. ; The authors acknowledge all researchers who generated the knowledge on filose amoebae that has been introduced in this review, the Biodiversity Heritage Library for providing access to old references, and the reviewers for their thorough and constructive comments. T.G. received funding from the Spanish Ministry of Science and Innovation, cofounded by European Regional Development Fund (ERDF) [grant number PGC2018-099921-B-I00]; from the Catalan Research Agency (AGAUR) [grant number SGR423]; from the European Union's Horizon 2020 research and innovation programme [grant number ERC-2016-724173]; and from the Gordon and Betty Moore Foundation [grant number GBMF9742]. E.V. thanks Steffen Clauß for imaging. ...
Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the functions of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activated by DNA damage (NORAD) is an atypical lncRNA due to its abundant expression and high sequence conservation. NORAD regulates genomic stability by interacting with proteins and microRNAs. Previous sequence-based characterization has identified a modular organization of NORAD composed of several NORAD repeat units (NRUs). These units comprise the protein-binding elements and are separated by regular spacers. Here, we experimentally determine for the first time the secondary structure of NORAD using the nextPARS approach. Our results suggest that the spacer regions provide structural stability to NRUs. Furthermore, we uncover two previously unreported NRUs, and determine the core structural motifs conserved across NRUs. Overall, these findings will help to elucidate the function and evolution of NORAD. ; UC was funded in part through H2020 Marie Skłodowska-Curie Actions (H2020-MSCA-IF-2017-793699) and MICINN (IJC2019-039402-I). TG group acknowledges support from the Spanish Ministry of Science and Innovation for grant PGC2018-099921-B-I00, cofounded by European Regional Development Fund (ERDF); from the Catalan Research Agency (AGAUR) SGR423; from the European Union's Horizon 2020 research and innovation programme (ERC-2016-724173); from the Gordon and Betty Moore Foundation (Grant GBMF9742) and from the Instituto de Salud Carlos III (INB Grant PT17/0009/0023 - ISCIII-SGEFI/ERDF). ; Peer Reviewed ; Postprint (published version)
Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight into the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ∼4% of the genes studied. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ∼9.5% of the heterozygous genes in the hybrids. This effect was larger in the hybrid with more extensive loss of heterozygosity, which may indicate a tendency to avoid loss of heterozygosity in these genes. Consistently, the number of shared genes with allele-specific expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. Some of the imbalanced genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids. ; We thank Verónica Mixão (BSC/IRB, Barcelona, Spain) for her help in performing analysis with the HaploTypo pipeline. This work received funding from the European Union's Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie grant agreement H2020-MSCA-ITN-2014-642095. T.G.'s research group also acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, from grants "Centro de Excelencia Severo Ochoa 2013–2017" SEV-2012-0208, and BFU2015-67107 cofounded by European Regional Development Fund (ERDF), from the CERCA Program/Generalitat de Catalunya, from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 Research and Innovation Program under grant agreement ERC-2016-724173. T.G. also receives support from an INB grant (PT17/0009/0023 – ISCIII-SGEFI/ERDF). ; Peer Reviewed ; Postprint (published version)
Homologous recombination (HR) enables the exchange of genetic material between and within species. Recent studies suggest that this process plays a major role in the microevolution of microbial genomes, contributing to core genome homogenization and to the maintenance of cohesive population structures. However, we still have a very poor understanding of the possible adaptive roles of intraspecific HR and of the factors that determine its differential impact across clades and lifestyles. Here we used a unified methodological framework to assess HR in 338 complete genomes from 54 phylogenetically diverse and representative prokaryotic species, encompassing different lifestyles and a broad phylogenetic distribution. Our results indicate that lifestyle and presence of restriction-modification (RM) machineries are among the main factors shaping HR patterns, with symbionts and intracellular pathogens having the lowest HR levels. Similarly, the size of exchanged genomic fragments correlated with the presence of RM and competence machineries. Finally, genes exchanged by HR showed functional enrichments which could be related to adaptations to different environments and ecological strategies. Taken together, our results clarify the factors underlying HR impact and suggest important adaptive roles of genes exchanged through this mechanism. Our results also revealed that the extent of genetic exchange correlated with lifestyle and some genomic features. Moreover, the genes in exchanged regions were enriched for functions that reflected specific adaptations, supporting identification of HR as one of the main evolutionary mechanisms shaping prokaryotic core genomes. ; The group of J.A. is funded by grant CLG2015_66686-C3-03 from the Spanish Ministry of Economy and Competitiveness (MINECO), which is cofinanced with FEDER support from the European Union. P.G.-T. was an FPI-MINECO fellow associated with project CGL2012-39627-C03-01 (to J.A.). The T.G. group acknowledges support from the Spanish Ministry of Economy and Competitiveness (grants "Centro de Excelencia Severo Ochoa 2013-2017" SEV-2012-0208 and BFU2015-67107; cofounded by European Regional Development Fund [ERDF]); from the CERCA Program/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) (grant SGR857); and from the European Union's Horizon 2020 research and innovation program under grant agreement ERC-2016-724173 (Marie Sklodowska-Curie grant agreement no. H2020-MSCA-ITN-2014-642095).
The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A. fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A. fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A. fumigatus. This review paper comprehensively discusses the current clinical challenges caused by A. fumigatus and provides insights on how to address them. ; AA, RGR, and DSP were supported by NIH AI 109025. MH was supported by NIH UL1TR001442. AC was supported by the Fundação para a Ciência e a Tecnologia (FCT) (CEECIND/03628/2017 and PTDC/MED GEN/28778/2017). Additional support was provided by FCT (UIDB/50026/2020 and UIDP/50026/2020), the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) (NORTE-01-0145-FEDER-000013 and NORTE-01-0145-FEDER-000023), the European Union's Horizon 2020 Research and Innovation programme under grant agreement no. 847507, and the "la Caixa" Foundation (ID 100010434) and FCT under the agreement LCF/PR/HP17/52190003. DJA was supported by CF Trust Strategic Research Centre TrIFIC (SRC015), Wellcome Trust Collaborative Award 219551/Z/19/Z and the NIHR Centre for Antimicrobial Optimisation. ; Peer Reviewed ; "Article signat per 21 autors/es: A.Arastehfar, A.Carvalho, J.Houbraken, L.Lombardi, R.Garcia-Rubio, J.D.Jenks, O.Rivero Menendez, R. Aljohani, I.D.Jacobsen, J.Berman, N.Osherov, M.T.Hedayati, M.Ilkit, D.James-Armstrong, T.Gabaldón, J.Meletiadis, M.Kostrzewa, W.Pan, C.Lass-Flörl, D.S.Perlin, M.Hoenigl" ; Postprint (published version)
Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times in diverse eukaryotic lineages. The causes and consequences of these convergent losses remain poorly understood. Here, we used a comparative genomics approach to reconstruct evolutionary paths leading to complex I loss and infer possible evolutionary scenarios. By mining available mitochondrial and nuclear genomes, we identified eight independent events of mitochondrial complex I loss across eukaryotes, of which six occurred in fungal lineages. We focused on three recent loss events that affect closely related fungal species, and inferred genomic changes convergently associated with complex I loss. Based on these results, we predict novel complex I functional partners and relate the loss of complex I with the presence of increased mitochondrial antioxidants, higher fermentative capabilities, duplications of alternative dehydrogenases, loss of alternative oxidases and adaptation to antifungal compounds. To explain these findings, we hypothesize that a combination of previously acquired compensatory mechanisms and exposure to environmental triggers of oxidative stress (such as hypoxia and/or toxic chemicals) induced complex I loss in fungi. ; This work was supported by grants from the Spanish Ministry of Science and Innovation (grant no. PGC2018-099921-B-I00), cofounded by European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR423; from the European Union's Horizon 2020 research and (grant no. ERC-2016-724173); and from the Instituto de Salud Carlos III—Instituto Nacional de Bioinformatica, (grant no. PT17/0009/0023—ISCIII-SGEFI/ERDF). M.À.S.-T. received a Predoctoral Each Fellowship from 'Caixa' Foundation (grant no. LCF/BQ/DR19/11740023). ; Peer Reviewed ; Postprint (published version)
Yeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats. ; TG acknowledges support from the Spanish Ministry of Science and Innovation for grant PGC2018-099921-B-I00, cofounded by European Regional Development Fund (ERDF); from the Catalan Research Agency (AGAUR) SGR423; from the European Union's Horizon 2020 research and innovation program (ERC-2016–724173); from the Gordon and Betty Moore Foundation (Grant # GBMF9742). JG acknowledges support from the Lendület Program (award no. 96049) of the Hungarian Academy of Sciences and the Eötvös Lóránd Research Network. Q-MW was supported by grants No. 31961133020 and No. 31770018 from the National Natural Science Foundation of China (NSFC). ASA and FEB were supported by grant 9343 from the Gordon and Betty Moore Foundation: https://doi.org/10.37807/GBMF9343. ; "Article signat per 12 autors/es: Teun Boekhout, Anthony S. Amend, Fouad El Baidouri, Toni Gabaldón, József Geml, Moritz Mittelbach, Vincent Robert, Chen Shuhui Tan, Benedetta Turchetti, Duong Vu, Qi-Ming Wang & Andrey Yurkov " ; Postprint (published version)
The number of invasive infections caused by Candida species is increasing worldwide. The incidence of candidiasis cases caused by non-albicans Candida species, such as Candida parapsilosis, is also increasing, and non-albicans Candida species are currently responsible for more invasive infections than C. albicans. Additionally, while the development of azole resistance during invasive disease with C. albicans remains uncommon, azole-resistant C. parapsilosis strains are frequently isolated in the hospital setting. In this study, we applied direct selection to generate azole-adapted and azole-evolved C. parapsilosis strains in order to examine the effect of azole resistance development on fungal viability and pathogenesis progression. Depending on the drug applied, the different evolved strains developed distinct cross-resistance patterns: the fluconazole-evolved (FLUEVO) and voriconazole-evolved (VOREVO) strains gained resistance to fluconazole and voriconazole only, while posaconazole evolution resulted in cross-resistance to all azoles and the posaconazole-evolved (POSEVO) strains showed higher echinocandin MIC values than the FLUEVO and VOREVO strains. Whole-genome sequencing results identified the development of different resistance mechanisms in the evolved strains: the FLUEVO and VOREVO strains harbored amino acid substitutions in Mrr1p (A808T and N394Y, respectively), and the POSEVO strain harbored an amino acid change in Erg3p (D14Y). By revealing increased efflux pump activity in both the FLUEVO and the VOREVO strains, along with the altered sterol composition of the POSEVO strain, we now highlight the impact of the above-mentioned amino acid changes in C. parapsilosis azole resistance development. We further revealed that the virulence of this species was only slightly or partially affected by fluconazole and voriconazole adaptation, while it significantly decreased after posaconazole adaptation. Our results suggest that triazole adaptation can result in azole cross-resistance and that this process may also result in virulence alterations in C. parapsilosis, depending on the applied drug. ; László Bodai was supported by a János Bolyai research scholarship (scholarship BO/00522/19/8) of the Hungarian Academy of Sciences. Attila Gácser was supported by grants 20391 3/2018/FEKUSTRAT, NKFIH K 123952, and GINOP-2.3.2.-15-2016-00035. Attila Gácser was additionally funded by grant LP2018-15/2018. Toni Gabaldón was supported by grants from the Spanish Ministry of Science and Innovation (grant PGC2018-099921-B-I00), cofounded by the European Regional Development Fund (ERDF); from the CERCA Program/Generalitat de Catalunya; from the Catalan Research Agency (grants AGAUR and SGR423); from the European Union's Horizon 2020 Research and Innovation Program (grant ERC-2016-724173); and from the Instituto Carlos III and Instituto Nacional de Bioinformática (grant PT17/0009/0023-ISCIII-SGEFI/ERDF). ; Peer Reviewed ; "Article signat per 12 autors/es: Csaba Papp, Flóra Bohner, Katica Kocsis, Mónika Varga, András Szekeres, László Bodai, Jesse R. Willis, Toni Gabaldón, Renáta Tóth, Joshua D. Nosanchuk, Csaba Vágvölgyi, and Attila Gácser" ; Postprint (published version)
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology—evolutionary relatedness—is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit—from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses. ; We thank the National Institute for Basic Biology, the Japanese Society for Bioinformatics and the Daiko Foundation for supporting the 67th NIBB Conference/The 6th Quest for Orthologs Meeting. We wish to acknowledge the following support for attending the meetings and/or writing this manuscript: EMBO Young Investigator meeting grant (to C.D.). Service and Infrastructure grant from the Swiss Institute of Bioinformatics, Swiss National Science Foundation [183723] (to C.D.); IdEX Unistra in the framework of the Investments for the future program of the French government (to O.L. and Y.N.); NSF (Award No. 1724300), KAKENHI (Grant No. JP18H01325) (to S.E.M.); support by the research funding program Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) of the State of Hessen, Research Center for Translational Biodiversity Genomics (TBG) (to I.E.); funding from the Wellcome Trust (108749/Z/15/Z) and the European Molecular Biology Laboratory (to M.P.); National Human Genome Research Institute, National Institutes of Health NIH (grant no. U41HG002273), National Science Foundation NSF (award no. 1917302) (to P.D.T.); Japan Society for the Promotion of Science (16H06279 and 19F19089) (to W.I. and S.C.). ; Peer Reviewed ; "Article signat per 14 autors/es: Benjamin Linard, Ingo Ebersberger, Shawn E McGlynn, Natasha Glover, Tomohiro Mochizuki, Mateus Patricio, Odile Lecompte, Yannis Nevers, Paul D Thomas, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz, Ikuo Uchiyama, QFO Consortium" "Members of the Quest for Orthologs (QFO) Consortium: Adrian Altenhoff, Aida Ouangraoua, Alex Warwick Vesztrocy, Benjamin Linard, Christophe Dessimoz, Damian Szklarczyk, Dannie Durand, David Emms, David Moi, David Thybert, Erik Sonnhammer, Evgenia Kriventseva, Haiming Tang, Hirokazu Chiba, Ikuo Uchiyama, Ingo Ebersberger, Jaime Huerta-Cepas, Jesualdo Tomas Fernandez-Breis, Judith A. Blake, Leszek Pryszcz, Maria-Jesus Martin, Marina Marcet Houben, Mateus Patricio, Matthieu Muffato, Natasha Glover, Odile Lecompte, Paul D. Thomas, Philipp Schiffer, Salvador Capella-Gutierrez, Salvatore Cosentino, Shawn E McGlynn, Shigehiro Kuraku, Sofia Forslund, Steven Kelly, Suzanna Lewis, Tamsin Jones, Tarcisio Mendes de Farias, Taro Maeda, Toni Gabaldon, Wataru Iwasaki, William Pearson, Yan Wang, Yannis Nevers, Yuichiro Hara. All members acknowledged and gave their approval to the content of this manuscript." ; Postprint (published version)
C The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution 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 cited. ; [EN] Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been identified where a lncRNA acts by sequestering miRNAs. This implies the down-regulation in the interaction of the miRNAs with their mRNA targets, what has been called a sponge effect. Multiple approaches exist for the prediction of miRNA targets in mRNAs. However, few methods exist for the prediction of miRNA response elements (MREs) in lncRNAs acting as ceRNAs (sponges). Here, we present spongeScan (http://spongescan.rc.ufl.edu), a graphical web tool to compute and visualize putative MREs in lncRNAs, along with different measures to assess their likely behavior as ceRNAs. ; FP7 STATegra project [agreement number 36000]; MINECO, co-funded with European Regional Development Funds (ERDF) [BIO2012-40244]; European Molecular Biology Laboratory and the European Union and ERC Seventh Framework Programme (FP7/2007-2013) [ERC-2012-StG-310325]. Funding for open access charge: University of Florida funds. ; Furió-Tarí, P.; Tarazona Campos, S.; Gabaldón, T.; Enright, AJ.; Conesa, A. (2016). spongeScan: A web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Research. 44((W1)):176-180. https://doi.org/10.1093/nar/gkw443 ; S ; 176 ; 180 ; 44 ; (W1) ...
PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org. ; Spanish Ministry of Science and Innovation (MICINN) [PGC2018-099921-B-I00], cofounded by European Regional Development Fund (ERDF); Catalan Research Agency (AGAUR) [SGR423]; European Union's Horizon 2020 research and innovation programme [ERC-2016–724173]; Gordon and Betty Moore Foundation [GBMF9742]; Instituto de Salud Carlos III [INB Grant PT17/0009/0023 – ISCIII-SGEFI/ERDF]; U.C. was funded in part through H2020 Marie Skłodowska-Curie Actions [H2020-MSCA-IF-2017-793699]; MICINN [IJC2019- 039402-I]. Funding for open access charge: ERC. ; Peer Reviewed ; Postprint (published version)
Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, C. subhashii was initially described as the causative agent of a case of peritonitis. Considering the relevance of whole-genome sequencing and analysis for our understanding of genome evolution and pathogenicity, we sequenced, assembled and annotated the genome of C. subhashii type strain. Our results show that C. subhashii presents a highly heterozygous genome and other signatures that point to a hybrid ancestry. The presence of functional pathways for assimilation of hydroxyaromatic compounds goes in line with the affiliation of this yeast with soil microbial communities involved in lignin decomposition. Furthermore, we observed that different clones of this strain may present circular or linear mitochondrial DNA. Re-sequencing and comparison of strains with differential mitochondrial genome topology revealed five candidate genes potentially associated with this conformational change: MSK1, SSZ1, ALG5, MRPL9 and OYE32. ; This work was supported by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement No. H2020-MSCA-ITN-2014-642095. T.G. group also acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and grants 'Centro de Excelencia Severo Ochoa 2013-2017' SEV-2012-0208 and BFU2015-67107 co-founded by European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 Research and Innovation Programme under the grant agreement ERC-2016-724173. T.G. also receives support from an INB Grant (PT17/0009/0023 - ISCIII-SGEFI/ERDF). J.N. group was supported by the Slovak Research and Development Agency (APVV-18-0239) and the Scientific Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic (VEGA 1/0027/19). ; Peer Reviewed ; Postprint (published version)
Comparative genomics, metagenomics, and single-cell technologies have shown that populations of microbial species encompass assemblages of closely related strains. This raises the question of whether individual bacterial lineages respond to the presence of their close relatives by modifying their gene expression or, instead, whether assemblages simply act as the arithmetic addition of their individual components. Here, we took advantage of transcriptome sequencing to address this question. For this, we analyzed the transcriptomes of two closely related strains of the extremely halophilic bacterium Salinibacter ruber grown axenically and in coculture. These organisms dominate bacterial assemblages in hypersaline environments worldwide. The strains used here cooccurred in the natural environment and are 100% identical in their 16S rRNA genes, and each strain harbors an accessory genome representing 10% of its complete genome. Overall, transcriptomic patterns from pure cultures were very similar for both strains. Expression was detected along practically the whole genome albeit with some genes at low levels. A subset of genes was very highly expressed in both strains, including genes coding for the light-driven proton pump xanthorhodopsin, genes involved in the stress response, and genes coding for transcriptional regulators. Expression differences between pure cultures affected mainly genes involved in environmental sensing. When the strains were grown in coculture, there was a modest but significant change in their individual transcription patterns compared to those in pure culture. Each strain sensed the presence of the other and responded in a specific manner, which points to fine intraspecific transcriptomic modulation. ; The group of J.A. is funded by grant CGL2012-39627-C03-01 from the Spanish Ministry of Economy and Competitiveness (MINECO), which is cofinanced with FEDER support from the European Union. P.G.-T. was an FPI-MINECO fellow. Research by the group of T.G. is funded in part by a grant from the ...
