An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms

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  • dc.contributor.author Reyes Prieto, Mariana
  • dc.contributor.author Vargas Chavez, Carlos Alberto
  • dc.contributor.author Llabrés, Mercè
  • dc.contributor.author Palmer, Pere
  • dc.contributor.author Latorre, Amparo
  • dc.contributor.author Moya, Andrés
  • dc.date.accessioned 2021-04-27T08:24:18Z
  • dc.date.available 2021-04-27T08:24:18Z
  • dc.date.issued 2020
  • dc.description.abstract The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished bacterial genomes exclusively. It originally consisted of three modules where users could search for the bacteria involved in a specific symbiotic relationship, their genomes and their genes (including their orthologs). In this update, we present an additional module that includes a representation of the metabolic network of each organism included in the database, as Directed Acyclic Graphs (MetaDAGs). This module provides unique opportunities to explore the metabolism of each individual organism and/or to evaluate the shared and joint metabolic capabilities of the organisms of the same genera included in our listing, allowing users to construct predictive analyses of metabolic associations and complementation between systems. We also report a ~25% increase in manually curated content in the database, i.e. bacterial genomes and their associations, with a final count of 2328 bacterial genomes associated to 498 hosts. We describe new querying possibilities for all the modules, as well as new display features for the MetaDAGs module, providing a relevant range of content and utility. This update continues to improve SymGenDB and can help elucidate the mechanisms by which organisms depend on each other.en
  • dc.description.sponsorship National Board of Science and Technology of México (CONACYT) (538243 to M.R.P.); FPI fellowship from the Ministry of Economy and Competitiveness (BES-2013-063548 to C.V.C.); Spanish Ministry of Science, Innovation and Universities and the European Regional Development Fund through projects DPI2015-67082-P and PGC2018-096956-B-C43 (FEDER/MICINN/AEI) and the Spanish Ministry of Economy and Competitiveness (projects SAF2012-31187, SAF2013-49788-EXP, SAF2015-65878-R and BFU2015-64322-C2-1-R, co-financed by FEDER funds); Carlos III Institute of Health (projects PIE14/00045 and AC15/00022); Generalitat Valenciana (project Prometeo/2018/A/133); Asociación Española contra el Cáncer (project AECC 2017-1485) and co-financed by the European Regional Development Fund (ERDF). The funders had no role in study design, data collection and analysis, decision to publish or preparation of any of the work.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Reyes-Prieto M, Vargas-Chávez C, Llabrés M, Palmer P, Latorre A, Moya A. An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms. Database. 2020 Feb 13;2020:baz160. DOI: 10.1093/database/baz160
  • dc.identifier.doi http://dx.doi.org/10.1093/database/baz160
  • dc.identifier.issn 1758-0463
  • dc.identifier.uri http://hdl.handle.net/10230/47225
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Database. 2020 Feb 13;2020:baz160
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BES-2013-063548
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/DPI2015-67082-P
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-096956-B-C43
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SAF2012-31187
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2013-49788-EXP
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2015-65878-R
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-64322-C2-1-R
  • dc.rights © The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.title An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organismsen
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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