Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes.

Project Information

RETVOLUTION

Grant agreement ID: 724173

DOI 10.3030/724173

Project closed

EC signature date 19 April 2017

Start date 1 January 2018

End date 30 September 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 986 178,00

EU contribution € 1 986 178,00

Coordinated by

BARCELONA SUPERCOMPUTING CENTER CENTRO NACIONAL DE SUPERCOMPUTACION
Spain

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (99)

Genomics of the expanding pine pathogen Lecanosticta acicola reveals patterns of ongoing genetic admixture.

Author(s): Marcet-Houben M, Cruz F, Gómez-Garrido J, Alioto TS, Nunez-Rodriguez JC, Mesanza N, Gut M, Iturritxa E, Gabaldon T.
Published in: msystems, 2024, ISSN 2379-5077
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00928-23

Collateral sensitivity counteracts the evolution of antifungal drug resistance in Candida auris

Author(s): Hans Carolus, Dimitrios Sofras, Giorgio Boccarella, Stef Jacobs, Vladislav Biriukov, Louise Goossens, Alicia Chen, Ina Vantyghem, Tibo Verbeeck, Siebe Pierson, Celia Lobo Romero, Hans Steenackers, Katrien Lagrou, Pieter van den Berg, Judith Berman, Toni Gabaldón, Patrick Van Dijck
Published in: Nature Microbiology, Issue 9, 2024, Page(s) 2954-2969, ISSN 2058-5276
Publisher: Nature research
DOI: 10.1038/s41564-024-01811-w

Quest for Orthologs in the Era of Biodiversity Genomics

Author(s): Felix Langschied, Nicola Bordin, Salvatore Cosentino, Diego Fuentes-Palacios, Natasha Glover, Michael Hiller, Yanhui Hu, Jaime Huerta-Cepas, Luis Pedro Coelho, Wataru Iwasaki, Sina Majidian, Saioa Manzano-Morales, Emma Persson, Thomas A Richards, Toni Gabaldón, Erik Sonnhammer, Paul D Thomas, Christophe Dessimoz, Ingo Ebersberger
Published in: Genome Biology and Evolution, Issue 16, 2024, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evae224

Origin and Early Evolution of the Eukaryotic Cell

Author(s): Gabaldón T.
Published in: Annual Review of Microbiology, 2021, ISSN 0066-4227
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-micro-090817-062213

Probing RNA structural landscapes across Candida yeast genomes

Author(s): Chorostecki, Uciel Saus, Ester Gabaldon, Toni
Published in: Frontiers in Microbiology, 2024, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2024.1362067

Several secondary metabolite gene clusters in the genomes of ten Penicillium spp. raise the risk of multiple mycotoxin occurrence in chestnuts

Author(s): Garello, Marco Piombo, Edoardo Buonsenso, Fabio Prencipe, Simona Valente, Silvia Meloni, Giovanna Roberta Marcet Houben, Marina Gabaldon, Toni Spadaro, Davide
Published in: Food Microbiology, 2024, ISSN 0740-0020
Publisher: Academic Press
DOI: 10.1016/j.fm.2024.104532

Phylogenomics of the Olea europaea complex using 15 whole genomes supports recurrent genetic admixture together with differentiation into seven subspecies

Author(s): Irene Julca; Pablo Vargas; Toni Gabaldón
Published in: BMC Biology, 2023, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-023-01583-5

Microbiome Profiling from Fecal Immunochemical Test Reveals Microbial Signatures with Potential for Colorectal Cancer Screening

Author(s): Olfat Khannous-Lleiffe, Jesse R. Willis, Ester Saus, Victor Moreno, Sergi Castellví-Bel, Toni Gabaldón, null null
Published in: Cancers, Issue 15, 2024, Page(s) 120, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers15010120

MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life

Author(s): Uciel Chorostecki; Manuel Molina; Leszek P. Pryszcz; Toni Gabaldón
Published in: Nucleic Acids Research, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa282

Recent gene selection and drug resistance underscore clinical adaptation across Candida species

Author(s): Recent gene selection and drug resistance underscore clinical adaptation across Candida species
Published in: Nature microbiology, 2024, ISSN 2058-5276
Publisher: Springer Nature
DOI: 10.1038/s41564-023-01547-z

Oral microbiome in down syndrome and its implications on oral health

Author(s): Jesse R. Willis; Susana Iraola-Guzmán; Ester Saus; Ewa Ksiezopolska; Luca Cozzuto; Luis A. Bejarano; Nuria Andreu-Somavilla; Miriam Alloza-Trabado; Anna Puig-Sola; Andrea Blanco; Elisabetta Broglio; Carlo Carolis; Jochen Hecht; Julia Ponomarenko; Toni Gabaldón
Published in: Journal of Oral Microbiology, Issue 1, 2021, ISSN 2000-2297
Publisher: Co-Action Publishing
DOI: 10.1080/20002297.2020.1865690

Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients.

Author(s): Anaïs Hérivaux; Jesse R. Willis; Toine Mercier; Katrien Lagrou; Samuel M. Gonçalves; Relber Aguiar Gonçales; Johan Maertens; Agostinho Carvalho; Toni Gabaldón; Cristina Cunha
Published in: Thorax, 2021, ISSN 0040-6376
Publisher: BMJ Publishing Group
DOI: 10.1136/thoraxjnl-2020-216179

Triazole Evolution of Candida parapsilosis Results in Cross-Resistance to Other Antifungal Drugs, Influences Stress Responses, and Alters Virulence in an Antifungal Drug-Dependent Manner

Author(s): Csaba Papp; Flóra Bohner; Katica Kocsis; Mónika Varga; András Szekeres; László Bodai; Jesse R. Willis; Toni Gabaldón; Renáta Tóth; Joshua D. Nosanchuk; Csaba Vágvölgyi; Attila Gácser
Published in: mSphere, 2020, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/msphere.00821-20

Phenotypic Variability in a Coinfection With Three Independent Candida parapsilosis Lineages

Author(s): Emilia Gómez-Molero, Jesse R. Willis, Anna Dudakova, Laia Carreté, Michael Weig, Uwe Groß, Attila Gácser, Toni Gabaldón, Oliver Bader
Published in: Frontiers in Microbiology, Issue 11, 2020, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2020.01994

Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata

Author(s): Ewa Ksiezopolska; Miquel Àngel Schikora-Tamarit; Reinhard Beyer; Juan Carlos Nunez-Rodriguez; Christoph Schüller; Toni Gabaldón
Published in: Current Biology, 2021, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2021.09.084

Echinocandin-Induced Microevolution of Candida parapsilosis Influences Virulence and Abiotic Stress Tolerance

Author(s): Csaba Papp, Katica Kocsis, Renáta Tóth, László Bodai, Jesse R. Willis, Ewa Ksiezopolska, Nancy E. Lozoya-Pérez, Csaba Vágvölgyi, Hector Mora Montes, Toni Gabaldón, Joshua D. Nosanchuk, Attila Gácser
Published in: mSphere, 2018, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/msphere.00547-18

Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans

Author(s): Shelby J. Priest; Marco A. Coelho; Verónica Mixão; Shelly Applen Clancey; Yitong Xu; Sheng Sun; Toni Gabaldón; Toni Gabaldón; Joseph Heitman
Published in: PLoS Genetics, 2021, ISSN 1553-7390
Publisher: Public Library of Science
DOI: 10.1371/journal.pgen.1008871

Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire

Author(s): Marina Marcet-Houben, Ewa Księżopolska, Toni Gabaldón
Published in: BMC Genomics, Issue 25, 2024, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-024-10979-8

Performance of a Shotgun Prediction Model for Colorectal Cancer When Using 16S rRNA Sequencing Data

Author(s): Ramon E, Obón-Santacana M, Khannous-Lleiffe O, Saus E, Gabaldón T, Guinó E, Bars-Cortina D, Ibáñez-Sanz G, Rodríguez-Alonso L, Mata A, García-Rodríguez A, Moreno V
Published in: International Journal of molecular sciences, 2024, ISSN 1661-6596
Publisher: MDPI AG
DOI: 10.3390/ijms25021181

Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift

Author(s): Toni Gabaldón
Published in: Annals of the New York Academy of Sciences, Issue 14, 2020, ISSN 0077-8923
Publisher: New York Academy of Sciences
DOI: 10.1111/nyas.14471

Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units.

Author(s): Uciel Chorostecki; Ester Saus; Toni Gabaldón
Published in: Computational and Structural Biotechnology Journal, 2021, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2021.05.045

A Mouse Model Suggests That Heart Failure and Its Common Comorbidity Sleep Fragmentation Have No Synergistic Impacts on the Gut Microbiome.

Author(s): Olfat Khannous-Lleiffe; Jesse R. Willis; Ester Saus; Ignacio Cabrera-Aguilera; Ignacio Cabrera-Aguilera; Isaac Almendros; Ramon Farré; David Gozal; Núria Farré; Toni Gabaldón
Published in: Microorganisms, Issue 11, 2021, ISSN 2076-2607
Publisher: MDPI AG
DOI: 10.3390/microorganisms9030641

Hybrids unleashed: exploring the emergence and genomic insights of pathogenic yeast hybrids

Author(s): Olmo, Valentina del Gabaldón, Toni
Published in: Current Opinion in Microbiology, 2024, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2024.102491

Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations

Author(s): Verónica Mixão; Eva Hegedűsová; Ester Saus; Leszek P. Pryszcz; Andrea Cillingová; Jozef Nosek; Toni Gabaldón
Published in: DNA Research, 2021, ISSN 1340-2838
Publisher: Oxford University Press
DOI: 10.1093/dnares/dsab006

Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens

Author(s): Schikora-Tamarit, Miquel Àngel Gabaldon, Toni
Published in: Biochemical Society Transactions, 2020, ISSN 0300-5127
Publisher: Portland Press, Ltd.
DOI: 10.1042/bst20211123

Whole genome analysis of two sympatric human Mansonella: Mansonella perstans and Mansonella sp “DEUX”

Author(s): Miriam Rodi, Caspar Gross, Thaisa Lucas Sandri, Lilith Berner, Marina Marcet-Houben, Ersoy Kocak, Michaela Pogoda, Nicolas Casadei, Carsten Köhler, Andrea Kreidenweiss, Selidji Todagbe Agnandji, Toni Gabaldón, Stephan Ossowski and Jana Held
Published in: Frontiers in Cellular and Infection Microbiology, 2023, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2023.1159814

The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems.

Author(s): Jesse R. Willis; Toni Gabaldón
Published in: Microorganisms, 2020, ISSN 2076-2607
Publisher: MDPI AG
DOI: 10.3390/microorganisms8020308

Long-term stability of acquired drug resistance and resistance associated mutations in the fungal pathogen Nakaseomyces glabratus (Candida glabrata)

Author(s): Ewa Ksiezopolska, Miquel Àngel Schikora-Tamarit, Juan Carlos Nunez-Rodriguez, Toni Gabaldón
Published in: Frontiers in Cellular and Infection Microbiology, Issue 14, 2024, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2024.1416509

Transient Mitochondria Dysfunction Confers Fungal Cross-Resistance against Phagocytic Killing and Fluconazole

Author(s): Sofía Siscar-Lewin; Toni Gabaldón; Alexander M. Aldejohann; Oliver Kurzai; Bernhard Hube; Sascha Brunke
Published in: mBio, Vol 12, Iss 3 (2021), Issue 1, 2021, ISSN 2161-2129
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.01128-21

JLOH: Inferring loss of heterozygosity blocks from sequencing data

Author(s): Schiavinato M, Del Olmo V, Muya VN, Gabaldón T.
Published in: Computational and Structural Biotechnology Journal, 2023, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2023.11.003

Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources

Author(s): Andrea Cillingová, Renáta Tóth, Anna Mojáková, Igor Zeman, Romana Vrzoňová, Barbara Siváková, Peter Baráth, Martina Neboháčová, Zuzana Klepcová, Filip Brázdovič, Hana Lichancová, Viktória Hodorová, Broňa Brejová, Tomáš Vinař, Sofia Mutalová, Veronika Vozáriková, Giacomo Mutti, Ľubomír Tomáška, Atilla Gácser, Toni Gabaldón, Jozef Nosek
Published in: PLOS Genetics, Issue 18, 2022, Page(s) e1009815, ISSN 1553-7404
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pgen.1009815

OCT1 – a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway

Author(s): Romana Vrzoňová, Renáta Tóth, Barbara Siváková, Anna Moťovská, Katarína Gaplovská-Kyselá, Peter Baráth, Ľubomír Tomáška, Attila Gácser, Toni Gabaldón, Jozef Nosek, Martina Neboháčová
Published in: FEMS Yeast Research, Issue 21, 2021, ISSN 1567-1364
Publisher: Oxford University Press
DOI: 10.1093/femsyr/foab034

Assessing Diagnosis of Candida Infections: A Study on Species Prevalence and Antifungal Resistance in Northern Morocco

Author(s): Ahaik, Islam Nuñez Rodríguez, Juan Carlos Abrini, Jamal Bouhdid, Samira Gabaldon, Toni
Published in: Journal of Fungi, 2024, ISSN 2309-608X
Publisher: MDPI
DOI: 10.3390/jof10060373

The long non-coding RNA landscape of Candida yeast pathogens

Author(s): Hovhannisyan H, Gabaldón T.
Published in: Nature communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27635-4

Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors

Author(s): Jesse R. Willis; Ester Saus; Susana Iraola-Guzmán; Ewa Ksiezopolska; Luca Cozzuto; Luis A. Bejarano; Nuria Andreu-Somavilla; Miriam Alloza-Trabado; Andrea Blanco; Anna Puig-Sola; Elisabetta Broglio; Carlo Carolis; Julia Ponomarenko; Jochen Hecht; Toni Gabaldón
Published in: npj Biofilms and Microbiomes, Issue 4, 2022, ISSN 2055-5008
Publisher: Nature Portfolio
DOI: 10.1038/s41522-022-00279-y

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi.

Author(s): Miguel A. Naranjo-Ortiz; Toni Gabaldón
Published in: Biological Reviews, 2019, ISSN 1464-7931
Publisher: Cambridge University Press
DOI: 10.1111/brv.12550

EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods

Author(s): Marcet-Houben M, Collado-Cala I, Fuentes-Palacios D, Gómez AD, Molina M, Garisoain-Zafra A, Chorostecki U, Gabaldón T.
Published in: Journal of molecular biology, 2023, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2023.168013

Trends in yeast diversity discovery

Author(s): 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
Published in: Fungal Diversity, 2022, ISSN 1560-2745
Publisher: Fungal Diversity Press
DOI: 10.1007/s13225-021-00494-6

Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens

Author(s): Verónica Mixão; Juan Carlos Nunez-Rodriguez; Valentina del Olmo; Ewa Ksiezopolska; Ester Saus; Teun Boekhout; Attila Gacser; Toni Gabaldón
Published in: BMC Biology, Issue 9, 2023, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-023-01608-z

Evolclust: automated inference of evolutionary conserved gene clusters in eukaryotes

Author(s): Marina Marcet-Houben; Toni Gabaldón
Published in: Bioinformatics, 2019, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz706

On the Biology, Diversity and Evolution of Nucleariid Amoebae (Amorphea, Obazoa, Opisthokonta

Author(s): Gabaldón, Toni; Völcker, Eckhard; Torruella, Guifré
Published in: Protist, 2022, ISSN 1434-4610
Publisher: Elsevier BV
DOI: 10.1016/j.protis.2022.125895

Chromosome-level assembly, annotation and phylome of <i>Pelobates cultripes</i>, the western spadefoot toad

Author(s): Hans Christoph Liedtke; Fernando Cruz; Jèssica Gómez-Garrido; Diego Fuentes Palacios; Marina Marcet-Houben; Marta Gut; Tyler Alioto; Toni Gabaldón; Ivan Gomez-Mestre
Published in: DNA Research, 2022, ISSN 1340-2838
Publisher: Oxford University Press
DOI: 10.1093/dnares/dsac013

Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins.

Author(s): Adrian Gabriel Torres; Marta Rodríguez-Escribà; Marina Marcet-Houben; Helaine Graziele Santos Vieira; Noelia Camacho; Helena Catena; Marina Murillo Recio; Àlbert Rafels-Ybern; Oscar Reina; Francisco Miguel Torres; Ana Pardo-Saganta; Toni Gabaldón; Eva Maria Novoa; Lluís Ribas de Pouplana
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab461

Microbiome and colorectal cancer: Roles in carcinogenesis and clinical potential.

Author(s): Ester Saus; Susana Iraola-Guzmán; Jesse R. Willis; Anna Brunet-Vega; Toni Gabaldón
Published in: Molecular aspects of medicine, 2019, ISSN 0098-2997
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.mam.2019.05.001

Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees ( Olea europaea L.)

Author(s): Irene Julca; Irene Julca; Marina Marcet-Houben; Fernando Cruz; Jèssica Gómez-Garrido; Brandon S. Gaut; Concepción M. Díez; Ivo Gut; Tyler Alioto; Pablo Vargas; Toni Gabaldón
Published in: BMC Biology, 2020, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-020-00881-6

Fungal evolution: cellular, genomic and metabolic complexity

Author(s): Miguel A. Naranjo-Ortiz; Toni Gabaldón
Published in: Biological Reviews, 2020, ISSN 1464-7931
Publisher: Cambridge University Press
DOI: 10.1111/brv.12605

Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples.

Author(s): Iraola-Guzmán, Susana; Brunet Vega, Anna; Pegueroles, Cinta; Saus, Ester; Hovhannisyan, Hrant; Casalots, Alex; Pericay, Carles; Gabaldón, Toni; Universitat Autònoma de Barcelona
Published in: Cancers, 2020, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12102844

Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans

Author(s): Verónica Mixão; Ester Saus; Teun Boekhout; Toni Gabaldón; Toni Gabaldón
Published in: Genetics, 2020, ISSN 0016-6731
Publisher: Genetics Society of America
DOI: 10.1093/genetics/iyaa004

Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter

Author(s): Alexandros A. Pittis; Valerie Goh; Alberto Cebrian-Serrano; Jennifer Wettmarhausen; Fabiana Perocchi; Toni Gabaldón
Published in: Nature Communications, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17705-4

Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi.

Author(s): Miquel Àngel Schikora-Tamarit; Marina Marcet-Houben; Jozef Nosek; Toni Gabaldón; Toni Gabaldón
Published in: Open Biology, 2021, ISSN 2046-2441
Publisher: Royal Society Publishing
DOI: 10.1098/rsob.200362

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

Author(s): Cinta Pegueroles, Susana Iraola-Guzmán, Uciel Chorostecki, Ewa Ksiezopolska, Ester Saus, Toni Gabaldón
Published in: RNA Biology, Issue 16/3, 2019, Page(s) 320-329, ISSN 1547-6286
Publisher: Landes Bioscience
DOI: 10.1080/15476286.2019.1572438

Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa

Author(s): Miguel A. Naranjo-Ortíz, Silvia Rodríguez-Píres, Rosario Torres, Antonieta De Cal, Josep Usall, Toni Gabaldón
Published in: Genome Announcements, Issue 6/17, 2018, ISSN 2169-8287
Publisher: ASM
DOI: 10.1128/genomeA.00214-18

Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes

Author(s): Pedro González-Torres, Francisco Rodríguez-Mateos, Josefa Antón, Toni Gabaldón
Published in: mBio, Issue 10/1, 2019, ISSN 2150-7511
Publisher: ASM
DOI: 10.1128/mBio.02494-18

Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal

Author(s): Toni Gabaldón, Cécile Fairhead
Published in: Current Genetics, Issue 65/1, 2019, Page(s) 93-98, ISSN 0172-8083
Publisher: Springer Verlag
DOI: 10.1007/s00294-018-0867-z

Fungal evolution: major ecological adaptations and evolutionary transitions

Author(s): Miguel A. Naranjo‐Ortiz, Toni Gabaldón
Published in: Biological Reviews, 2019, ISSN 1464-7931
Publisher: Cambridge University Press
DOI: 10.1111/brv.12510

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

Author(s): Irene Julca, Marina Marcet-Houben, Pablo Vargas, Toni Gabaldón
Published in: BMC Biology, Issue 16/1, 2018, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-018-0482-y

Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens

Author(s): Ewa Ksiezopolska, Toni Gabaldón
Published in: Genes, Issue 9/9, 2018, Page(s) 461, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes9090461

Evolutionary and functional patterns of shared gene neighbourhood in fungi

Author(s): Marina Marcet-Houben, Toni Gabaldón
Published in: Nature Microbiology, Issue 4/12, 2019, Page(s) 2383-2392, ISSN 2058-5276
Publisher: Springer Nature
DOI: 10.1038/s41564-019-0552-0

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin

Author(s): Verónica Mixão, Antonio Perez Hansen, Ester Saus, Teun Boekhout, Cornelia Lass-Florl, Toni Gabaldón
Published in: Frontiers in Genetics, Issue 10, 2019, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2019.00383

MICU1 Confers Protection from MCU-Dependent Manganese Toxicity

Author(s): Jennifer Wettmarshausen, Valerie Goh, Kai-Ting Huang, Daniela M. Arduino, Utkarsh Tripathi, Anja Leimpek, Yiming Cheng, Alexandros A. Pittis, Toni Gabaldón, Dejana Mokranjac, György Hajnóczky, Fabiana Perocchi
Published in: Cell Reports, Issue 25/6, 2018, Page(s) 1425-1435.e7, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2018.10.037

Genome Comparisons of Candida glabrata Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations

Author(s): Laia Carreté, Ewa Ksiezopolska, Emilia Gómez-Molero, Adela Angoulvant, Oliver Bader, Cécile Fairhead, Toni Gabaldón
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.00112

Genome Variation in the Model Halophilic Bacterium Salinibacter ruber

Author(s): Pedro González-Torres, Toni Gabaldón
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.01499

Relative timing of mitochondrial endosymbiosis and the “pre-mitochondrial symbioses” hypothesis

Author(s): Toni Gabaldón
Published in: IUBMB Life, Issue 70/12, 2018, Page(s) 1188-1196, ISSN 1521-6543
Publisher: Taylor & Francis
DOI: 10.1002/iub.1950

Hybridization and the origin of new yeast lineages

Author(s): Toni Gabaldón
Published in: FEMS Yeast Research, 2020, ISSN 1567-1356
Publisher: Blackwell
DOI: 10.1093/femsyr/foaa040

Gene gain and loss across the metazoan tree of life

Author(s): Rosa Fernández, Toni Gabaldón
Published in: Nature Ecology & Evolution, Issue 4/4, 2020, Page(s) 524-533, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-019-1069-x

Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha

Author(s): Irene Julca, Marina Marcet-Houben, Fernando Cruz, Carlos Vargas-Chavez, John Spencer Johnston, Jèssica Gómez-Garrido, Leonor Frias, André Corvelo, Damian Loska, Francisco Cámara, Marta Gut, Tyler Alioto, Amparo Latorre, Toni Gabaldón
Published in: Molecular Biology and Evolution, Issue 37/3, 2019, Page(s) 730-756, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz261

Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

Author(s): Verónica Mixão, Toni Gabaldón
Published in: BMC Biology, Issue 18/1, 2020, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-020-00776-6

HaploTypo: a variant-calling pipeline for phased genomes

Author(s): Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manu Molina, Toni Gabaldón
Published in: Bioinformatics, Issue 36/8, 2019, Page(s) 2569-2571, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz933

CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies

Author(s): Hrant Hovhannisyan, Ahmed Hafez, Carlos Llorens, Toni Gabaldón
Published in: Bioinformatics, Issue 36/3, 2019, Page(s) 925-927, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz626

Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization

Author(s): Hrant Hovhannisyan, Ester Saus, Ewa Ksiezopolska, Alex J. Hinks Roberts, Edward J. Louis, Toni Gabaldón
Published in: Frontiers in Genetics, Issue 11, 2020, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2020.00404

Multiple Hybridization Events Punctuate the Evolutionary Trajectory of<i>Malassezia furfur</i>

Author(s): Bart Theelen; Verónica Mixão; Giuseppe Ianiri; Joleen Pei Zhen Goh; Jan Dijksterhuis; Joseph Heitman; Thomas L. Dawson; Toni Gabaldón; Teun Boekhout
Published in: mBio, 2022, ISSN 2161-2129
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.03853-21

Genome analysis of five recently described species of the CUG-Ser clade uncovers <i>Candida theae</i> as a new hybrid lineage with pathogenic potential in the <i>Candida parapsilosis</i> species complex

Author(s): Verónica Mixão; Valentina del Olmo; Eva Hegedűsová; Ester Saus; Leszek Pryszcz; Andrea Cillingová; Jozef Nosek; Toni Gabaldón
Published in: DNA Research, 2022, ISSN 1340-2838
Publisher: Oxford University Press
DOI: 10.1093/dnares/dsac010

Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples

Author(s): Hrant Hovhannisyan; Antonio Rodríguez; Ester Saus; Mario Vaneechoutte; Toni Gabaldón
Published in: Frontiers in Cellular and Infection Microbiology, 2023, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2023.1093178

Timing the origin of eukaryotic cellular complexity with ancient duplications

Author(s): Julian Vosseberg; Jolien J. E. van Hooff; Jolien J. E. van Hooff; Marina Marcet-Houben; Anne van Vlimmeren; Anne van Vlimmeren; Leny M. van Wijk; Toni Gabaldón; Berend Snel
Published in: Nature Ecology and Evolution, 2021, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-020-01320-z

Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy

Author(s): A. Arastehfar; M. Marcet-Houben; F. Daneshnia; S.J. Taj-Aldeen; D. Batra; S.R. Lockhart; E. Shor; T. Gabaldón; D.S. Perlin
Published in: Studies in Mycology, 2021, ISSN 0166-0616
Publisher: Centraal Bureau voor Schimmelculturals
DOI: 10.1016/j.simyco.2021.100133

On the impact of incomplete taxon sampling on the relative timing of gene transfer events

Author(s): Bernabeu M, Manzano-Morales S, Gabaldón T.
Published in: PLoS Biology, 2024, ISSN 1544-9173
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.3002460

Origin of fungal hybrids with pathogenic potential from warm seawater environments

Author(s): Valentina del Olmo; Verónica Mixão; Rashmi Fotedar; Ester Saus; Amina Al Malki; Ewa Księżopolska; Juan Carlos Nunez-Rodriguez; Teun Boekhout; Toni Gabaldón
Published in: Origin of fungal hybrids with pathogenic potential from warm seawater environments, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42679-4

Utilization of selenocysteine in early-branching fungal phyla.

Author(s): Mariotti, Marco, Salinas, Gustavo Gabaldón, Toni Gladyshev, Vadim N.
Published in: Nature Microbiology, 2019, ISSN 2058-5276
Publisher: Nature Research
DOI: 10.1038/s41564-018-0354-9

Discovery and Validation of Clinically Relevant Long Non-Coding RNAs in Colorectal Cancer

Author(s): Madison Snyder; Susana Iraola-Guzmán; Ester Saus; Toni Gabaldón
Published in: Cancers, 2022, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14163866

Elevated Vacuolar Uptake of Fluorescently Labeled Antifungal Drug Caspofungin Predicts Echinocandin Resistance in Pathogenic Yeast

Author(s): Qais Z. Jaber, Maayan Bibi, Ewa Ksiezopolska, Toni Gabaldon, Judith Berman, Micha Fridman
Published in: ACS Central Science, Issue 6, 2023, Page(s) 1698-1712, ISSN 2374-7951
Publisher: American Chemical Society
DOI: 10.1021/acscentsci.0c00813

The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis

Author(s): The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis
Published in: mSphere, 2020, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/msphere.00282-20

Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies

Author(s): Naranjo-Ortiz MA, Molina M, Fuentes D, Mixão V, Gabaldón T.
Published in: Gigascience, 2022, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1093/gigascience/giac088

Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species.

Author(s): Jesse R Willis; Ester Saus; Susana Iraola-Guzmán; Elena Cabello-Yeves; Ewa Ksiezopolska; Luca Cozzuto; Luis A. Bejarano; Nuria Andreu-Somavilla; Miriam Alloza-Trabado; Andrea Blanco; Anna Puig-Sola; Elisabetta Broglio; Carlo Carolis; Julia Ponomarenko; Jochen Hecht; Toni Gabaldón
Published in: Journal of Oral Microbiology, 2020, ISSN 2000-2297
Publisher: Co-Action Publishing
DOI: 10.1080/20002297.2021.1897328

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum

Author(s): Rosa Fernández, Marina Marcet-Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, Valentin Wucher, Cinta Pegueroles, Toni Gabaldón, Denis Tagu
Published in: Molecular Biology and Evolution, 2020, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa110

Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes among Monilinia Species.

Author(s): Marina Marcet-Houben; Maria Villarino; Laura Vilanova; Antonieta De Cal; Jan A. L. van Kan; Josep Usall; Toni Gabaldón; Rosario Torres
Published in: Journal of Fungi, 2021, ISSN 2309-608X
Publisher: MDPI AG
DOI: 10.3390/jof7060464

The Quest for Orthologs orthology benchmark service in 2022

Author(s): Yannis Nevers, Tamsin E M Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codo, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Piližota, Cristina Guijarro-Clarke, null null, Adrian Altenhoff, Elspeth A Bruford, Salvatore Cosentino, Christophe Dessimoz, Ingo Ebersberger, David M Emms, To
Published in: Nucleic Acids Research, Issue 50, 2022, Page(s) W623-W632, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac330

Nothing makes sense in drug resistance except in the light of evolution

Author(s): Toni Gabaldón
Published in: Current opinion in microbiology, Issue 1, 2023, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2023.102350

Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap

Author(s): Daneshnia F, de Almeida Júnior JN, Ilkit M, Lombardi L, Perry AM, Gao M, Nobile CJ, Egger M, Perlin DS, Zhai B, Hohl TM, Gabaldón T, Colombo AL, Hoenigl M, Arastehfar A.
Published in: The Lancet Microbe, 2023, ISSN 2666-5247
Publisher: Elsevier
DOI: 10.1016/s2666-5247(23)00067-8

PerSVade: personalized structural variant detection in any species of interest

Author(s): Miquel Àngel Schikora-Tamarit; Toni Gabaldón
Published in: Genome Biology, Issue 3, 2022, ISSN 1465-6906
Publisher: BMC
DOI: 10.1186/s13059-022-02737-4

Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata

Author(s): Marcet-Houben M, Alvarado M, Ksiezopolska E, Saus E, de Groot PWJ, Gabaldón T.
Published in: BMC biology, 2022, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-022-01412-1

Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota

Author(s): David Bars-Cortina, Elies Ramon, Blanca Rius-Sansalvador, Elisabet Guinó, Ainhoa Garcia-Serrano, Núria Mach, Olfat Khannous-Lleiffe, Ester Saus, Toni Gabaldón, Gemma Ibáñez-Sanz, Lorena Rodríguez-Alonso, Alfredo Mata, Ana García-Rodríguez, Mireia Obón-Santacana, Victor Moreno
Published in: BMC Genomics, Issue 25, 2024, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-024-10621-7

Threats from the <i>Candida parapsilosis</i> complex: the surge of multidrug resistance and a hotbed for new emerging pathogens

Author(s): Toni Gabaldón
Published in: Microbiology and Molecular Biology Reviews, Issue 88, 2024, ISSN 1092-2172
Publisher: American Society for Microbiology
DOI: 10.1128/mmbr.00029-23

Genome assemblies of two rare opportunistic yeast pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii)

Author(s): Verónica Mixão; Ester Saus; Antonio Perez Hansen; Cornelia Lass-Flörl; Toni Gabaldón
Published in: G3 Genes Genomes Genetics, 2019, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1534/g3.119.400762

The Quiet and Underappreciated Rise of Drug-Resistant Invasive Fungal Pathogens

Author(s): Amir Arastehfar, Cornelia Lass-Flörl, Rocio Garcia-Rubio, Farnaz Daneshnia, Macit Ilkit, Teun Boekhout, Toni Gabaldon, David S. Perlin
Published in: Journal of Fungi, Issue 6, 2024, Page(s) 138, ISSN 2309-608X
Publisher: MDPI AG
DOI: 10.3390/jof6030138

Diversity of Secondary Metabolism in Aspergillus nidulans Clinical Isolates

Author(s): Drott MT, Bastos RW, Rokas A, Ries LNA, Gabaldón T, Goldman GH, Keller NP, Greco C.
Published in: mSphere, 2020, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/msphere.00156-20

Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

Author(s): Ana Cristina Colabardini, Fang Wang, Zhengqiang Miao, Lakhansing Pardeshi, Clara Valero, Patrícia Alves de Castro, Daniel Yuri Akiyama, Kaeling Tan, Luisa Czamanski Nora, Rafael Silva-Rocha, Marina Marcet-Houben, Toni Gabaldón, Taicia Fill, Koon Ho Wong, Gustavo H. Goldman
Published in: PLOS Genetics, Issue 18, 2023, Page(s) e1010001, ISSN 1553-7404
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pgen.1010001

A hybrid approach to assess the structural impact of long noncoding RNA mutations uncovers key NEAT1 interactions in colorectal cancer

Author(s): Efe Aydın; Ester Saus; Uciel Chorostecki; Toni Gabaldón
Published in: IUBMB Life, 2023, ISSN 1521-6543
Publisher: Taylor & Francis
DOI: 10.1002/iub.2710

Positive selection in gamete interaction proteins in Carnivora

Author(s): Pisciottano F, Campos MC, Penna C, Bruque CD, Gabaldón T, Saragüeta P.
Published in: Molecular ecology, 2024, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.17263

PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.

Author(s): Diego Fuentes; Manuel Molina; Uciel Chorostecki; Salvador Capella-Gutierrez; Marina Marcet-Houben; Toni Gabaldón
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab966