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1. Functional and evolutionary significance of unknown genes from uncultivated taxa

Author

Rodríguez del Río, Álvaro, Giner-Lamia, Joaquín, Cantalapiedra, Carlos P., Botas, Jorge, Deng, Ziqi, Hernández-Plaza, Ana, Munar-Palmer, Martí, Santamaría-Hernando, Saray, Rodríguez-Herva, José J., Ruscheweyh, Hans-Joachim, Paoli, Lucas, Schmidt, Thomas S. B., Sunagawa, Shinichi, Bork, Peer, López-Solanilla, Emilia, Coelho, Luis Pedro, and Huerta-Cepas, Jaime

Published
2024
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2. Functional and evolutionary significance of unknown genes from uncultivated taxa

Author

Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Fundación la Caixa, Silicon Valley Community Foundation, Swiss National Science Foundation, ETH Zurich, Rodríguez, Alvaro [0000-0003-3907-3904], Giner-Lamia, Joaquín [0000-0003-1553-8295], Cantalapiedra, Carlos P [0000-0001-5263-533X], Botas, Jorge [0000-0001-7292-8981], Hernández-Plaza, Ana [0000-0002-9844-7999], Munar-Palmer, Martí [0000-0002-8898-4483], Santamaría-Hernando, Saray [0000-0001-6763-3839], Rodríguez-Herva, José J. [0000-0001-9962-2261], Ruscheweyh, Hans-Joachim [0000-0001-7473-6086], Paoli, Lucas [0000-0003-0771-8309], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Sunagawa, Shinichi [0000-0003-3065-0314], Bork, Peer [0000-0002-2627-833X], López-Solanilla, Emilia [0000-0002-8578-7433], Coelho, Luis Pedro [0000-0002-9280-7885], Huerta-Cepas, Jaime [0000-0003-4195-5025], Rodríguez, Alvaro, Giner-Lamia, Joaquín, Cantalapiedra, Carlos P, Botas, Jorge, Deng, Ziqi, Hernández-Plaza, Ana, Munar-Palmer, Martí, Santamaría-Hernando, Saray, Rodríguez-Herva, José J., Ruscheweyh, Hans-Joachim, Paoli, Lucas, Schmidt, Thomas Sebastian, Sunagawa, Shinichi, Bork, Peer, López-Solanilla, Emilia, Coelho, Luis Pedro, Huerta-Cepas, Jaime, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Fundación la Caixa, Silicon Valley Community Foundation, Swiss National Science Foundation, ETH Zurich, Rodríguez, Alvaro [0000-0003-3907-3904], Giner-Lamia, Joaquín [0000-0003-1553-8295], Cantalapiedra, Carlos P [0000-0001-5263-533X], Botas, Jorge [0000-0001-7292-8981], Hernández-Plaza, Ana [0000-0002-9844-7999], Munar-Palmer, Martí [0000-0002-8898-4483], Santamaría-Hernando, Saray [0000-0001-6763-3839], Rodríguez-Herva, José J. [0000-0001-9962-2261], Ruscheweyh, Hans-Joachim [0000-0001-7473-6086], Paoli, Lucas [0000-0003-0771-8309], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Sunagawa, Shinichi [0000-0003-3065-0314], Bork, Peer [0000-0002-2627-833X], López-Solanilla, Emilia [0000-0002-8578-7433], Coelho, Luis Pedro [0000-0002-9280-7885], Huerta-Cepas, Jaime [0000-0003-4195-5025], Rodríguez, Alvaro, Giner-Lamia, Joaquín, Cantalapiedra, Carlos P, Botas, Jorge, Deng, Ziqi, Hernández-Plaza, Ana, Munar-Palmer, Martí, Santamaría-Hernando, Saray, Rodríguez-Herva, José J., Ruscheweyh, Hans-Joachim, Paoli, Lucas, Schmidt, Thomas Sebastian, Sunagawa, Shinichi, Bork, Peer, López-Solanilla, Emilia, Coelho, Luis Pedro, and Huerta-Cepas, Jaime

Abstract

Many of the Earth's microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies1. Here we analysed 149,842 environmental genomes from multiple habitats2-6 and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalogue is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes and orders, probably representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework that we used for experimental validatation of a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.

Published
2024

3. eggNOG 6.0: enabling comparative genomics across 12 535 organisms

Author

Agencia Estatal de Investigación (España), European Commission, Silicon Valley Community Foundation, Novo Nordisk Foundation, Swiss Institute of Bioinformatics, Hernández-Plaza, Ana [0000-0002-9844-7999], Szklarczyk, Damian [0000-0002-4052-5069], Botas, Jorge [0000-0001-7292-8981], Cantalapiedra, Carlos P [0000-0001-5263-533X], Giner-Lamia, Joaquín [0000-0003-1553-8295], Mende, Daniel R. [0000-0001-6831-4557], Kirsch, Rebecca [0000-0003-1126-0089], Rattei, Thomas [0000-0002-0592-7791], Letunic, Ivica [0000-0003-3560-4288], Jensen, Lars J. [0000-0001-7885-715X], Bork, Peer [0000-0002-2627-833X], von Mering, Christian [0000-0001-7734-9102], Huerta-Cepas, Jaime [0000-0003-4195-5025], Hernández-Plaza, Ana, Szklarczyk, Damian, Botas, Jorge, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Mende, Daniel R., Kirsch, Rebecca, Rattei, Thomas, Letunic, Ivica, Jensen, Lars J., Bork, Peer, von Mering, Christian, Huerta-Cepas, Jaime, Agencia Estatal de Investigación (España), European Commission, Silicon Valley Community Foundation, Novo Nordisk Foundation, Swiss Institute of Bioinformatics, Hernández-Plaza, Ana [0000-0002-9844-7999], Szklarczyk, Damian [0000-0002-4052-5069], Botas, Jorge [0000-0001-7292-8981], Cantalapiedra, Carlos P [0000-0001-5263-533X], Giner-Lamia, Joaquín [0000-0003-1553-8295], Mende, Daniel R. [0000-0001-6831-4557], Kirsch, Rebecca [0000-0003-1126-0089], Rattei, Thomas [0000-0002-0592-7791], Letunic, Ivica [0000-0003-3560-4288], Jensen, Lars J. [0000-0001-7885-715X], Bork, Peer [0000-0002-2627-833X], von Mering, Christian [0000-0001-7734-9102], Huerta-Cepas, Jaime [0000-0003-4195-5025], Hernández-Plaza, Ana, Szklarczyk, Damian, Botas, Jorge, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Mende, Daniel R., Kirsch, Rebecca, Rattei, Thomas, Letunic, Ivica, Jensen, Lars J., Bork, Peer, von Mering, Christian, and Huerta-Cepas, Jaime

Abstract

The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de.

Published
2023

4. Functional and evolutionary significance of unknown genes from uncultivated taxa

Author

Rodríguez del Río, Álvaro, primary, Giner-Lamia, Joaquín, additional, Cantalapiedra, Carlos P., additional, Botas, Jorge, additional, Deng, Ziqi, additional, Hernández-Plaza, Ana, additional, Munar-Palmer, Martí, additional, Santamaría-Hernando, Saray, additional, Rodríguez-Herva, José J., additional, Ruscheweyh, Hans-Joachim, additional, Paoli, Lucas, additional, Schmidt, Thomas S. B., additional, Sunagawa, Shinichi, additional, Bork, Peer, additional, López-Solanilla, Emilia, additional, Coelho, Luis Pedro, additional, and Huerta-Cepas, Jaime, additional

Published
2023
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5. eggNOG 6.0: enabling comparative genomics across 12 535 organisms

Author

Hernández-Plaza, Ana, Szklarczyk, Damian, Botas, Jorge, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Mende, Daniel R, Kirsch, Rebecca, Rattei, Thomas, Letunic, Ivica, Jensen, Lars J, Bork, Peer, von Mering, Christian, Huerta-Cepas, Jaime, Medical Microbiology and Infection Prevention, AII - Infectious diseases, Agencia Estatal de Investigación (España), European Commission, Silicon Valley Community Foundation, Novo Nordisk Foundation, Swiss Institute of Bioinformatics, Hernández-Plaza, Ana, Szklarczyk, Damian, Botas, Jorge, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Mende, Daniel R., Kirsch, Rebecca, Rattei, Thomas, Letunic, Ivica, Jensen, Lars J., Bork, Peer, von Mering, Christian, Huerta-Cepas, Jaime, and University of Zurich

Subjects
UFSP13-7 Evolution in Action: From Genomes to Ecosystems, Genetics, 570 Life sciences, biology, 10124 Institute of Molecular Life Sciences
Abstract

6 Pág., The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de., National Programme for Fostering Excellence in Scientific and Technical Research [PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE to J.H.-C., J.G.-L.]; Chan Zuckerberg Initiative DAF [2020-218584]; Silicon Valley Community Foundation (to J.B. and J.H.C.); Severo Ochoa Centres of Excellence Programme from the State Research Agency (AEI) of Spain [SEV-2016–0672 (2017–2021) to C.P.C.]; Research Technical Support Staff Aid [PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.]; Novo Nordisk Foundation [NNF14CC0001 to R.K., L.J.J.]; SIB Swiss Institute of Bioinformatics (to D.S. and C.vM.). Funding for open access charge: Institutional CSIC and EMBL agreements.

Published
2023
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6. PhyloCloud: an online platform for making sense of phylogenomic data

Author

Silicon Valley Community Foundation, Agencia Estatal de Investigación (España), Deng, Ziqi [0000-0001-5347-3846], Botas, Jorge [0000-0001-7292-8981], Cantalapiedra, Carlos P [0000-0001-5263-533X], Hernández-Plaza, Ana [0000-0002-9844-7999], Burguet-Castell, Jordi [0000-0002-9198-5380], Huerta-Cepas, Jaime [0000-0003-4195-5025], Deng, Ziqi, Botas, Jorge, Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Burguet-Castell, Jordi, Huerta-Cepas, Jaime, Silicon Valley Community Foundation, Agencia Estatal de Investigación (España), Deng, Ziqi [0000-0001-5347-3846], Botas, Jorge [0000-0001-7292-8981], Cantalapiedra, Carlos P [0000-0001-5263-533X], Hernández-Plaza, Ana [0000-0002-9844-7999], Burguet-Castell, Jordi [0000-0002-9198-5380], Huerta-Cepas, Jaime [0000-0003-4195-5025], Deng, Ziqi, Botas, Jorge, Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Burguet-Castell, Jordi, and Huerta-Cepas, Jaime

Published
2022

7. Weed vegetation, crop yield and quality and management of 26 wheat fields of Mediterranean Spain

Author

Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), European Commission, Hernández-Plaza, Ana [eva.hernandez@inia.csic.es], Hernández-Plaza, Ana, Bastida, F., Gibson, David J., Barro Losada, Francisco, Giménez, María J., Pallavicini, Yésica, Izquierdo, Jordi, González-Andújar, José Luis, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), European Commission, Hernández-Plaza, Ana [eva.hernandez@inia.csic.es], Hernández-Plaza, Ana, Bastida, F., Gibson, David J., Barro Losada, Francisco, Giménez, María J., Pallavicini, Yésica, Izquierdo, Jordi, and González-Andújar, José Luis

Abstract

Weed community structure, including composition and taxonomic and functional diversity, may explain variability in crop quality, adding to the variability accounted for by management, climatic and genetic factors. Focusing on Mediterranean rainfed wheat crops, we sampled weed communities from 26 fields in Spain that were either organically or conventionally managed. Weed communities were characterized by their abundance and taxonomic, compositional and trait-based measures. Grain protein concentration and the glutenin-to-gliadin ratio were used as indicators of wheat grain quality. Linear mixed-effects models were used to analyze the relationship between crop quality and weed community variables, while accounting for environmental factors. Nitrogen fertilization, previous crop and precipitation explained an important part of wheat grain protein concentration (R2marginal = 0.39) and composition (R2marginal = 0.26). Weed community measures had limited effects on grain quality (increasing R2marginal of models by 1% on average). The weed effects were related to the composition and the functional structure of their communities but not to their abundance. Environmental conditions promoting higher protein concentration also selected for weed species with competitive attributes, whereas the role of weed functional diversity depended on the functional trait and on the resource limiting crop grain quality. Understanding the mechanisms of weed effects on crop quality could aid in designing sustainable weed management practices.

Published
2022

8. eggNOG 6.0:enabling comparative genomics across 12 535 organisms

Author

Hernández-Plaza, Ana, Szklarczyk, Damian, Botas, Jorge, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Mende, Daniel R, Kirsch, Rebecca, Rattei, Thomas, Letunic, Ivica, Jensen, Lars J, Bork, Peer, von Mering, Christian, Huerta-Cepas, Jaime, Hernández-Plaza, Ana, Szklarczyk, Damian, Botas, Jorge, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Mende, Daniel R, Kirsch, Rebecca, Rattei, Thomas, Letunic, Ivica, Jensen, Lars J, Bork, Peer, von Mering, Christian, and Huerta-Cepas, Jaime

Abstract

The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de.

Published
2023

9. eggNOG 6.0: enabling comparative genomics across 12 535 organisms

Author

Hernández-Plaza, Ana; https://orcid.org/0000-0002-9844-7999, Szklarczyk, Damian; https://orcid.org/0000-0002-4052-5069, Botas, Jorge; https://orcid.org/0000-0001-7292-8981, Cantalapiedra, Carlos P; https://orcid.org/0000-0001-5263-533X, Giner-Lamia, Joaquín; https://orcid.org/0000-0003-1553-8295, Mende, Daniel R; https://orcid.org/0000-0001-6831-4557, Kirsch, Rebecca, Rattei, Thomas; https://orcid.org/0000-0002-0592-7791, Letunic, Ivica; https://orcid.org/0000-0003-3560-4288, Jensen, Lars J; https://orcid.org/0000-0001-7885-715X, Bork, Peer; https://orcid.org/0000-0002-2627-833X, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, Huerta-Cepas, Jaime; https://orcid.org/0000-0003-4195-5025, Hernández-Plaza, Ana; https://orcid.org/0000-0002-9844-7999, Szklarczyk, Damian; https://orcid.org/0000-0002-4052-5069, Botas, Jorge; https://orcid.org/0000-0001-7292-8981, Cantalapiedra, Carlos P; https://orcid.org/0000-0001-5263-533X, Giner-Lamia, Joaquín; https://orcid.org/0000-0003-1553-8295, Mende, Daniel R; https://orcid.org/0000-0001-6831-4557, Kirsch, Rebecca, Rattei, Thomas; https://orcid.org/0000-0002-0592-7791, Letunic, Ivica; https://orcid.org/0000-0003-3560-4288, Jensen, Lars J; https://orcid.org/0000-0001-7885-715X, Bork, Peer; https://orcid.org/0000-0002-2627-833X, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, and Huerta-Cepas, Jaime; https://orcid.org/0000-0003-4195-5025

Abstract

The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de.

Published
2023

10. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Author

Agencia Estatal de Investigación (España), European Commission, Cantalapiedra, Carlos P [0000-0001-5263-533X], Hernández-Plaza, Ana [0000-0002-9844-7999], Letunic, Ivica [0000-0003-3560-4288], Bork, Peer [0000-0002-2627-833X], Huerta-Cepas, Jaime [0000-0003-4195-5025], Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Letunic, Ivica, Bork, Peer, Huerta-Cepas, Jaime, Agencia Estatal de Investigación (España), European Commission, Cantalapiedra, Carlos P [0000-0001-5263-533X], Hernández-Plaza, Ana [0000-0002-9844-7999], Letunic, Ivica [0000-0003-3560-4288], Bork, Peer [0000-0002-2627-833X], Huerta-Cepas, Jaime [0000-0003-4195-5025], Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Letunic, Ivica, Bork, Peer, and Huerta-Cepas, Jaime

Abstract

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.

Published
2021

11. eggNOG 6.0: enabling comparative genomics across 12 535 organisms

Author

Hernández-Plaza, Ana, primary, Szklarczyk, Damian, additional, Botas, Jorge, additional, Cantalapiedra, Carlos P, additional, Giner-Lamia, Joaquín, additional, Mende, Daniel R, additional, Kirsch, Rebecca, additional, Rattei, Thomas, additional, Letunic, Ivica, additional, Jensen, Lars J, additional, Bork, Peer, additional, von Mering, Christian, additional, and Huerta-Cepas, Jaime, additional

Published
2022
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13. The Quest for Orthologs benchmark service and consensus calls in 2020

Author

Swiss Institute of Bioinformatics, European Commission, Agencia Estatal de Investigación (España), Comunidad de Madrid, Gouvernement de la République française, Altenhoff, Adrian M [0000-0001-7492-1273], Garrayo-Ventas, Javier [0000-0003-0015-1573], Emms, David [0000-0002-9065-8978], Glover, Natasha M [0000-0003-1811-4340], Hernández-Plaza, Ana [0000-0002-9844-7999], Nevers, Yannis [0000-0002-8604-2943], Sundesha, Vicky [0000-0001-7667-6435], Szklarczyk, Damian [0000-0002-4052-5069], Codó, Laia [0000-0002-6797-8746], Gelpi, Josep Ll [0000-0002-0566-7723], Huerta-Cepas, Jaime [0000-0003-4195-5025], Lecompte, Odile [0000-0002-2005-460X], Muffato, Matthieu [0000-0002-7860-3560], Capella-Gutierrez, Salvador [0000-0002-0309-604X], Sonnhammer, Erik [0000-0002-9015-5588], Dessimoz, Christophe [0000-0002-2170-853X], Altenhoff, Adrian M, Garrayo-Ventas, Javier, Cosentino, Salvatore, Emms, David, Glover, Natasha M, Hernández-Plaza, Ana, Nevers, Yannis, Sundesha, Vicky, Szklarczyk, Damian, Fernández, José M, Codó, Laia, Gelpí, Josep Lluis, Huerta-Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martín, María Jesús, Capella-Gutierrez, Salvador, Thomas, Paul D, Sonnhammer, Erik, Dessimoz, Christophe, Swiss Institute of Bioinformatics, European Commission, Agencia Estatal de Investigación (España), Comunidad de Madrid, Gouvernement de la République française, Altenhoff, Adrian M [0000-0001-7492-1273], Garrayo-Ventas, Javier [0000-0003-0015-1573], Emms, David [0000-0002-9065-8978], Glover, Natasha M [0000-0003-1811-4340], Hernández-Plaza, Ana [0000-0002-9844-7999], Nevers, Yannis [0000-0002-8604-2943], Sundesha, Vicky [0000-0001-7667-6435], Szklarczyk, Damian [0000-0002-4052-5069], Codó, Laia [0000-0002-6797-8746], Gelpi, Josep Ll [0000-0002-0566-7723], Huerta-Cepas, Jaime [0000-0003-4195-5025], Lecompte, Odile [0000-0002-2005-460X], Muffato, Matthieu [0000-0002-7860-3560], Capella-Gutierrez, Salvador [0000-0002-0309-604X], Sonnhammer, Erik [0000-0002-9015-5588], Dessimoz, Christophe [0000-0002-2170-853X], Altenhoff, Adrian M, Garrayo-Ventas, Javier, Cosentino, Salvatore, Emms, David, Glover, Natasha M, Hernández-Plaza, Ana, Nevers, Yannis, Sundesha, Vicky, Szklarczyk, Damian, Fernández, José M, Codó, Laia, Gelpí, Josep Lluis, Huerta-Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martín, María Jesús, Capella-Gutierrez, Salvador, Thomas, Paul D, Sonnhammer, Erik, and Dessimoz, Christophe

Abstract

The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.

Published
2020

14. The quest for orthologs benchmark service and consensus calls in 2020

Author

Altenhoff, Adrian M, Garrayo-Ventas, Javier, Cosentino, Salvatore, Emms, David, Glover, Natasha M, Hernández-Plaza, Ana, Nevers, Yannis, Sundesha, Vicky, Szklarczyk, Damian, Fernández, José M, Codó, Laia, Gelpí, Josep Lluis, Huerta-Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martin, Maria J, Capella-Gutierrez, Salvador, Thomas, Paul D, Sonnhammer, Erik, Dessimoz, Christophe, Swiss Institute of Bioinformatics, European Commission, Agencia Estatal de Investigación (España), Comunidad de Madrid, Gouvernement de la République française, Altenhoff, Adrian M, Garrayo-Ventas, Javier, Emms, David, Glover, Natasha M, Hernández-Plaza, Ana, Nevers, Yannis, Sundesha, Vicky, Szklarczyk, Damian, Codó, Laia, Gelpi, Josep Ll, Huerta-Cepas, Jaime, Lecompte, Odile, Muffato, Matthieu, Capella-Gutierrez, Salvador, Sonnhammer, Erik, Dessimoz, Christophe, Barcelona Supercomputing Center, Altenhoff, Adrian M [0000-0001-7492-1273], Garrayo-Ventas, Javier [0000-0003-0015-1573], Emms, David [0000-0002-9065-8978], Glover, Natasha M [0000-0003-1811-4340], Hernández-Plaza, Ana [0000-0002-9844-7999], Nevers, Yannis [0000-0002-8604-2943], Sundesha, Vicky [0000-0001-7667-6435], Szklarczyk, Damian [0000-0002-4052-5069], Codó, Laia [0000-0002-6797-8746], Gelpi, Josep Ll [0000-0002-0566-7723], Huerta-Cepas, Jaime [0000-0003-4195-5025], Lecompte, Odile [0000-0002-2005-460X], Muffato, Matthieu [0000-0002-7860-3560], Capella-Gutierrez, Salvador [0000-0002-0309-604X], Sonnhammer, Erik [0000-0002-9015-5588], and Dessimoz, Christophe [0000-0002-2170-853X]

Subjects
Filogènia, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], Genòmica, Proteomes, Comparative genomics, Proteins, Molecular evolution, Genomics, Quest for Orthologs consortium, Proteïnes, Phylogeny, Genòmica -- Informàtica, Orthologs
Abstract

Departamento de Biotecnología (INIA), The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases., Service and Infrastructure grant from the Swiss Institute of Bioinformatics [to C.D.]; NSF [1917302 to P.D.T.]; NIH NHGRI [HG002273, HG010859 to P.D.T.]; INB [PT17/0009/0001 - ISCIII-SGEFI/ERDF to J.G.V., V.S., J.M.F., L.C., J.L.G. and S.C.G.]; H2020 ELIXIR-EXCELERATE [676559 to J.G.V., V.S., J.M.F., L.C., J.L.G. and S.C.G]; ELIXIR, the research infrastructure for life-science data [to J.G.V., V.S., J.M.F., L.C., J.L.G. and S.C.G]; Ministerio de Ciencia, Innovación y Universidades [PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE to J.H.C.]; European Union's Horizon 2020 Research and Innovation Programme [686070 to J.H.C. and D.S, and 637765 to D.M.E. and S.K.]; Consejería de Educación, Juventud y Deporte de la Comunidad de Madrid and Fondo Social Europeo [PEJ-2017-AI/TIC-7514 to A.H.P.]; IdEX Unistra in the framework of the Investments for the future program of the French government [to O.L.]; National Institutes of Health (NIH) [U24HG007822 to M.J.M.]; European Molecular Biology Laboratory (EMBL) [core funds to M.J.M and M.M.]; Wellcome Trust [WT108749/Z/15/Z to M.M.]; S.K. is a royal Society University Research Fellow; Swiss National Science Foundation [183723 to C.D.]. Funding for open access charge: Swiss National Science Foundation.

Published
2020

15. Functional and evolutionary significance of unknown genes from uncultivated taxa

Author

Rodríguez del Río, Álvaro, primary, Giner-Lamia, Joaquín, additional, Cantalapiedra, Carlos P., additional, Botas, Jorge, additional, Deng, Ziqi, additional, Hernández-Plaza, Ana, additional, Paoli, Lucas, additional, Schmidt, Thomas S.B., additional, Sunagawa, Shinichi, additional, Bork, Peer, additional, Coelho, Luis Pedro, additional, and Huerta-Cepas, Jaime, additional

Published
2022
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16. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Author

Musser, Jacob M., primary, Schippers, Klaske J., additional, Nickel, Michael, additional, Mizzon, Giulia, additional, Kohn, Andrea B., additional, Pape, Constantin, additional, Ronchi, Paolo, additional, Papadopoulos, Nikolaos, additional, Tarashansky, Alexander J., additional, Hammel, Jörg U., additional, Wolf, Florian, additional, Liang, Cong, additional, Hernández-Plaza, Ana, additional, Cantalapiedra, Carlos P., additional, Achim, Kaia, additional, Schieber, Nicole L., additional, Pan, Leslie, additional, Ruperti, Fabian, additional, Francis, Warren R., additional, Vargas, Sergio, additional, Kling, Svenja, additional, Renkert, Maike, additional, Polikarpov, Maxim, additional, Bourenkov, Gleb, additional, Feuda, Roberto, additional, Gaspar, Imre, additional, Burkhardt, Pawel, additional, Wang, Bo, additional, Bork, Peer, additional, Beck, Martin, additional, Schneider, Thomas R., additional, Kreshuk, Anna, additional, Wörheide, Gert, additional, Huerta-Cepas, Jaime, additional, Schwab, Yannick, additional, Moroz, Leonid L., additional, and Arendt, Detlev, additional

Published
2021
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19. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Author

Huerta-Cepas, Jaime [0000-0003-4195-5025], Hernández-Plaza, Ana, Musser, Jacob M., Schippers, Klaske J., Nickel, Michael, Mizzon, Giulia, Kohn, Andrea B., Pape, Constantin, Ronchi, Paolo, Papadopoulos, Nikolaos, Tarashansky, Alexander J., Hammel, Jörg U., Wolf, Florian, Liang, Cong, Cantalapiedra, Carlos P, Achim, Kaia, Schieber, Nicole L., Pan, Leslie, Ruperti, Fabian, Francis, Warren R., Vargas, Sergio, Kling, Svenja, Renkert, Maike, Polikarpov, Maxim, Bourenkov, Gleb, Feuda, Roberto, Gaspar, Imre, Burkhardt, Pawel, Wang, Bo, Bork, Peer, Beck, Martin, Schneider, Thomas R., Kreshuk, Anna, Wörheide, Gert, Huerta-Cepas, Jaime, Moroz, Leonid L., Arendt, Detlev, Huerta-Cepas, Jaime [0000-0003-4195-5025], Hernández-Plaza, Ana, Musser, Jacob M., Schippers, Klaske J., Nickel, Michael, Mizzon, Giulia, Kohn, Andrea B., Pape, Constantin, Ronchi, Paolo, Papadopoulos, Nikolaos, Tarashansky, Alexander J., Hammel, Jörg U., Wolf, Florian, Liang, Cong, Cantalapiedra, Carlos P, Achim, Kaia, Schieber, Nicole L., Pan, Leslie, Ruperti, Fabian, Francis, Warren R., Vargas, Sergio, Kling, Svenja, Renkert, Maike, Polikarpov, Maxim, Bourenkov, Gleb, Feuda, Roberto, Gaspar, Imre, Burkhardt, Pawel, Wang, Bo, Bork, Peer, Beck, Martin, Schneider, Thomas R., Kreshuk, Anna, Wörheide, Gert, Huerta-Cepas, Jaime, Moroz, Leonid L., and Arendt, Detlev

Abstract

The evolutionary origin of metazoan cell types such as neurons and muscles is not known. Using whole-body single-cell RNA sequencing in a sponge, an animal without nervous system and musculature, we identified 18 distinct cell types. These include nitric oxide-sensitive contractile pinacocytes, amoeboid phagocytes, and secretory neuroid cells that reside in close contact with digestive choanocytes that express scaffolding and receptor proteins. Visualizing neuroid cells by correlative x-ray and electron microscopy revealed secretory vesicles and cellular projections enwrapping choanocyte microvilli and cilia. Our data show a communication system that is organized around sponge digestive chambers, using conserved modules that became incorporated into the pre- and postsynapse in the nervous systems of other animals.

Published
2021

20. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Author

Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Huerta Cepas, Jaime, Letunic, Ivica, Bork, Peer, Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Huerta Cepas, Jaime, Letunic, Ivica, and Bork, Peer

Abstract

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnogmapper.embl.de.

Published
2021

21. The Quest for Orthologs benchmark service and consensus calls in 2020

Author

Altenhoff, Adrian M, primary, Garrayo-Ventas, Javier, primary, Cosentino, Salvatore, primary, Emms, David, primary, Glover, Natasha M, primary, Hernández-Plaza, Ana, primary, Nevers, Yannis, primary, Sundesha, Vicky, primary, Szklarczyk, Damian, primary, Fernández, José M, primary, Codó, Laia, primary, for Orthologs Consortium, the Quest, primary, Gelpi, Josep Ll, primary, Huerta-Cepas, Jaime, primary, Iwasaki, Wataru, primary, Kelly, Steven, primary, Lecompte, Odile, primary, Muffato, Matthieu, primary, Martin, Maria J, primary, Capella-Gutierrez, Salvador, primary, Thomas, Paul D, primary, Sonnhammer, Erik, primary, and Dessimoz, Christophe, primary

Published
2020
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22. The Quest for Orthologs benchmark service and consensus calls in 2020

Author

Altenhoff, Adrian M., Garrayo-Ventas, Javier, Cosentino, Salvatore, Emms, David, Glover, Natasha M., Hernández-Plaza, Ana, Nevers, Yannis, Sundesha, Vicky, Szklarczyk, Damian, Fernández, José M., Codó, Laia, Li Gelpi, Josep, Huerta-Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martin, Maria J., Capella-Gutierrez, Salvador, Thomas, Paul D., Sonnhammer, Erik, Dessimoz, Christophe, Altenhoff, Adrian M., Garrayo-Ventas, Javier, Cosentino, Salvatore, Emms, David, Glover, Natasha M., Hernández-Plaza, Ana, Nevers, Yannis, Sundesha, Vicky, Szklarczyk, Damian, Fernández, José M., Codó, Laia, Li Gelpi, Josep, Huerta-Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martin, Maria J., Capella-Gutierrez, Salvador, Thomas, Paul D., Sonnhammer, Erik, and Dessimoz, Christophe

Abstract

The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.

Published
2020
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23. The quest for orthologs benchmark service and consensus calls in 2020

Author

Barcelona Supercomputing Center, Altenhoff, Adrian M, Garrayo Ventas, Javier, Consentino, Salvatore, Emms, David, Glover, Natasha M, Hernández Plaza, Ana, Nevers, Yannis, Szklarczyk, Damian, Fernández González, Jose María, Codó, Laia, Gelpi, Josep, Huertas Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martín, María Jesús, Capella Gutiérrez, Salvador, Thomas, Paul D., Sonnhammer, Erik, Dessimoz, Christophe, the Quest for Orthologs Consortium, Barcelona Supercomputing Center, Altenhoff, Adrian M, Garrayo Ventas, Javier, Consentino, Salvatore, Emms, David, Glover, Natasha M, Hernández Plaza, Ana, Nevers, Yannis, Szklarczyk, Damian, Fernández González, Jose María, Codó, Laia, Gelpi, Josep, Huertas Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martín, María Jesús, Capella Gutiérrez, Salvador, Thomas, Paul D., Sonnhammer, Erik, Dessimoz, Christophe, and the Quest for Orthologs Consortium

Abstract

The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases., Service and Infrastructure grant from the Swiss Institute of Bioinformatics [to C.D.]; NSF [1917302 to P.D.T.]; NIH NHGRI [HG002273, HG010859 to P.D.T.]; INB [PT17/0009/0001 - ISCIII-SGEFI/ERDF to J.G.V., V.S., J.M.F., L.C., J.L.G. and S.C.G.]; H2020 ELIXIR-EXCELERATE [676559 to J.G.V., V.S., J.M.F., L.C., J.L.G. and S.C.G]; ELIXIR, the research infrastructure for life-science data [to J.G.V., V.S., J.M.F., L.C., J.L.G. and S.C.G]; Ministerio de Ciencia, Innovación y Universidades [PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE to J.H.C.]; European Union's Horizon 2020 Research and Innovation Programme [686070 to J.H.C. and D.S, and 637765 to D.M.E. and S.K.]; Consejería de Educación, Juventud y Deporte de la Comunidad de Madrid and Fondo Social Europeo [PEJ-2017-AI/TIC-7514 to A.H.P.]; IdEX Unistra in the framework of the Investments for the future program of the French government [to O.L.]; National Institutes of Health (NIH) [U24HG007822 to M.J.M.]; European Molecular Biology Laboratory (EMBL) [core funds to M.J.M and M.M.]; Wellcome Trust [WT108749/Z/15/Z to M.M.]; S.K. is a royal Society University Research Fellow; Swiss National Science Foundation [183723 to C.D.]. Funding for open access charge: Swiss National Science Foundation., Peer Reviewed, Postprint (published version)

Published
2020

24. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Author

European Commission, Comunidad de Madrid, Agencia Estatal de Investigación (España), Mende, Daniel R. [0000-0001-6831-4557], Letunic, Ivica [0000-0003-3560-4288], Maistrenko, Oleksandr M. [0000-0003-1961-7548], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Milanese, Alessio [0000-0002-7050-2239], Paoli, Lucas [0000-0003-0771-8309], Orakov, Askarbek [0000-0001-6823-5269], Forslund, Sofía K. [0000-0003-4285-6993], Sunagawa, Shinichi [0000-0003-3065-0314], Zeller, Georg [0000-0003-1429-7485], Huerta-Cepas, Jaime [0000-0003-4195-5025], Coelho, Luis Pedro [0000-0002-9280-7885], Bork, Peer [0000-0002-2627-833X], Mende, Daniel R., Letunic, Ivica, Maistrenko, Oleksandr M., Schmidt, Thomas Sebastian, Milanese, Alessio, Paoli, Lucas, Hernández-Plaza, Ana, Orakov, Askarbek, Forslund, Sofía K., Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, Coelho, Luis Pedro, Bork, Peer, European Commission, Comunidad de Madrid, Agencia Estatal de Investigación (España), Mende, Daniel R. [0000-0001-6831-4557], Letunic, Ivica [0000-0003-3560-4288], Maistrenko, Oleksandr M. [0000-0003-1961-7548], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Milanese, Alessio [0000-0002-7050-2239], Paoli, Lucas [0000-0003-0771-8309], Orakov, Askarbek [0000-0001-6823-5269], Forslund, Sofía K. [0000-0003-4285-6993], Sunagawa, Shinichi [0000-0003-3065-0314], Zeller, Georg [0000-0003-1429-7485], Huerta-Cepas, Jaime [0000-0003-4195-5025], Coelho, Luis Pedro [0000-0002-9280-7885], Bork, Peer [0000-0002-2627-833X], Mende, Daniel R., Letunic, Ivica, Maistrenko, Oleksandr M., Schmidt, Thomas Sebastian, Milanese, Alessio, Paoli, Lucas, Hernández-Plaza, Ana, Orakov, Askarbek, Forslund, Sofía K., Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, Coelho, Luis Pedro, and Bork, Peer

Abstract

Microbiology depends on the availability of annotated microbial genomes for many applications. Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. In addition, newer concepts such as the pan-genome concept are still being implemented to help answer biological questions. Hence, we present proGenomes2, which provides 87 920 high-quality genomes in a user-friendly and interactive manner. Genome sequences and annotations can be retrieved individually or by taxonomic clade. Every genome in the database has been assigned to a species cluster and most genomes could be accurately assigned to one or multiple habitats. In addition, general functional annotations and specific annotations of antibiotic resistance genes and single nucleotide variants are provided. In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database. The database is available at http://progenomes.embl.de/.

Published
2020

25. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Author

Mende, Daniel R, primary, Letunic, Ivica, additional, Maistrenko, Oleksandr M, additional, Schmidt, Thomas S B, additional, Milanese, Alessio, additional, Paoli, Lucas, additional, Hernández-Plaza, Ana, additional, Orakov, Askarbek N, additional, Forslund, Sofia K, additional, Sunagawa, Shinichi, additional, Zeller, Georg, additional, Huerta-Cepas, Jaime, additional, Coelho, Luis Pedro, additional, and Bork, Peer, additional

Published
2019
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26. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Author

Musser, Jacob M., primary, Schippers, Klaske J., additional, Nickel, Michael, additional, Mizzon, Giulia, additional, Kohn, Andrea B., additional, Pape, Constantin, additional, Hammel, Jörg U., additional, Wolf, Florian, additional, Liang, Cong, additional, Hernández-Plaza, Ana, additional, Achim, Kaia, additional, Schieber, Nicole L., additional, Francis, Warren R., additional, Vargas R., Sergio, additional, Kling, Svenja, additional, Renkert, Maike, additional, Feuda, Roberto, additional, Gaspar, Imre, additional, Burkhardt, Pawel, additional, Bork, Peer, additional, Beck, Martin, additional, Kreshuk, Anna, additional, Wörheide, Gert, additional, Huerta-Cepas, Jaime, additional, Schwab, Yannick, additional, Moroz, Leonid L., additional, and Arendt, Detlev, additional

Published
2019
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27. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Author

Huerta-Cepas, Jaime, Szklarczyk, Damian, Heller, Davide, Hernández-Plaza, Ana, Forslund, Sofia K, Cook, Helen, Mende, Daniel R, Letunic, Ivica, Rattei, Thomas, Jensen, Lars J, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, Bork, Peer, Huerta-Cepas, Jaime, Szklarczyk, Damian, Heller, Davide, Hernández-Plaza, Ana, Forslund, Sofia K, Cook, Helen, Mende, Daniel R, Letunic, Ivica, Rattei, Thomas, Jensen, Lars J, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, and Bork, Peer

Abstract

eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de.

Published
2019

28. eggNOG 5.0:a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Author

Huerta-Cepas, Jaime, Szklarczyk, Damian, Heller, Davide, Hernández-Plaza, Ana, Forslund, Sofia K, Cook, Helen, Mende, Daniel R, Letunic, Ivica, Rattei, Thomas, Jensen, Lars J, von Mering, Christian, Bork, Peer, Huerta-Cepas, Jaime, Szklarczyk, Damian, Heller, Davide, Hernández-Plaza, Ana, Forslund, Sofia K, Cook, Helen, Mende, Daniel R, Letunic, Ivica, Rattei, Thomas, Jensen, Lars J, von Mering, Christian, and Bork, Peer

Abstract

eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de.

Published
2019

29. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Author

Huerta-Cepas, Jaime, primary, Szklarczyk, Damian, additional, Heller, Davide, additional, Hernández-Plaza, Ana, additional, Forslund, Sofia K, additional, Cook, Helen, additional, Mende, Daniel R, additional, Letunic, Ivica, additional, Rattei, Thomas, additional, Jensen, Lars J, additional, von Mering, Christian, additional, and Bork, Peer, additional

Published
2018
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31. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Author

Mende, Daniel R., Letunic, Ivica, Maistrenko, Oleksandr M., Schmidt, Thomas S.B., Milanese, Alessio, Paoli, Lucas, Hernández-Plaza, Ana, Orakov, Askarbek N, Forslund, Sofia K., Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, Coelho, Luis P., and Bork, Peer

Subjects
2. Zero hunger
Abstract

Microbiology depends on the availability of annotated microbial genomes for many applications. Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. In addition, newer concepts such as the pan-genome concept are still being implemented to help answer biological questions. Hence, we present proGenomes2, which provides 87 920 high-quality genomes in a user-friendly and interactive manner. Genome sequences and annotations can be retrieved individually or by taxonomic clade. Every genome in the database has been assigned to a species cluster and most genomes could be accurately assigned to one or multiple habitats. In addition, general functional annotations and specific annotations of antibiotic resistance genes and single nucleotide variants are provided. In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database. The database is available at http://progenomes.embl.de/., Nucleic Acids Research, 48, ISSN:1362-4962, ISSN:0301-5610

32. PhyloCloud: an online platform for making sense of phylogenomic data

Author

Jorge Botas, Ana Hernandez-Plaza, Jordi Burguet-Castell, Jaime Huerta-Cepas, Carlos Pérez Cantalapiedra, Ziqi Deng, Silicon Valley Community Foundation, Agencia Estatal de Investigación (España), Deng, Ziqi, Botas, Jorge, Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Burguet-Castell, Jordi, Huerta-Cepas, Jaime, Deng, Ziqi [0000-0001-5347-3846], Botas, Jorge [0000-0001-7292-8981], Cantalapiedra, Carlos P [0000-0001-5263-533X], Hernández-Plaza, Ana [0000-0002-9844-7999], Burguet-Castell, Jordi [0000-0002-9198-5380], and Huerta-Cepas, Jaime [0000-0003-4195-5025]

Subjects
Genetics
Abstract

6 Pág., [2020-218584], Chan Zuckerberg Initiative DAF an advised fund of Silicon Valley Community Foundation (to J.B., J.BC, and J.HC); [PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE], National Programme for Fostering Excellence in Scientific and Technical Research (to J.HC) [SEV-2016-0672-18-2:PRE2018-084075] FPI-Severo Ochoa predoctoral fellowship (to Z.D); [SEV-2016-0672 (2017–2021)] Severo Ochoa Centres of Excellence Programme from the State [2020-218584], Chan Zuckerberg Initiative DAF an 2018-098073-A-I00 MCIU/AEI/FEDER, UE], National Programme for Fostering Excellence in Scientific and Technical Research (to J.HC) [SEV-2016-0672-18-2:PRE2018-084075] FPI-Severo Ochoa predoctoral fellowship (to Z.D); [SEV-2016-0672 (2017–2021)] Severo Ochoa Centres of Excellence Programme from the State [2020-218584], Chan Zuckerberg Initiative DAF an advised fund of Silicon Valley Community Founda tion (to J.B., J.BC, and J.HC); [PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE], National Programme for Fostering Excellence in Scientific and Technical Re search (to J.HC) [SEV-2016-0672-18-2:PRE2018-084075] FPI-Severo Ochoa predoctoral fellowship (to Z.D); [SEV-2016-0672 (2017–2021)] Severo Ochoa Centres of Excellence Programme from the State Research.

Published
2022

33. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Author

Ana Hernández-Plaza, Jaime Huerta-Cepas, Ivica Letunic, Peer Bork, Carlos Pérez Cantalapiedra, Agencia Estatal de Investigación (España), European Commission, Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Letunic, Ivica, Bork, Peer, Huerta-Cepas, Jaime, Cantalapiedra, Carlos P [0000-0001-5263-533X], Hernández-Plaza, Ana [0000-0002-9844-7999], Letunic, Ivica [0000-0003-3560-4288], Bork, Peer [0000-0002-2627-833X], and Huerta-Cepas, Jaime [0000-0003-4195-5025]

Subjects
Bioinformatics, Gene prediction, Computational biology, Biology, AcademicSubjects/SCI01180, Genome, 03 medical and health sciences, Databases, Genetic, Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Domain prediction, 030302 biochemistry & molecular biology, AcademicSubjects/SCI01130, Molecular Sequence Annotation, Functional annotation, Genomics, Resources, Computational genomics, Workflow, Metagenomics, Metagenome, Pairwise comparison, Scale (map), Software
Abstract

Centro de Biotecnología y Genómica de Plantas (CBGP), Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de., This research was supported by the National Programme for Fostering Excellence in Scientific and Technical Research (Grant No. PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE, to J.H.C.) and the Severo Ochoa Centres of Excellence Programme (Grant No. SEV-2016-0672 (2017–2021) to C.P.C.) from the State Research Agency (AEI) of Spain, as well as a Research Technical Support Staff Aid (PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.); European Research Council grant MicroBioS (ERC-2014-AdG)—GA669830 (to P.B.). Cloud computing is supported by BMBF (de.NBI network #031A537B)., 5 Pág.

Published
2021

34. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.

Author

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, and Bork P

Subjects
Animals, Classification, Eukaryota genetics, Gene Duplication, Gene Ontology, Genes, Viral, Genome, Humans, Molecular Sequence Annotation, Proteome, Sequence Alignment, Structure-Activity Relationship, Conserved Sequence, Databases, Genetic, Evolution, Molecular, Phylogeny, Sequence Homology
Abstract

eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de.

Published
2019
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