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      PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

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          Abstract

          PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes a broad set of genomes, data types and analysis tools available to researchers through a user-friendly website, an API, and bulk downloads. In this latest release of the PLAZA platform, we are integrating a record number of 134 high-quality plant genomes, split up over two instances: PLAZA Dicots 5.0 and PLAZA Monocots 5.0. This number of genomes corresponds with a massive expansion in the number of available species when compared to PLAZA 4.0, which offered access to 71 species, a 89% overall increase. The PLAZA 5.0 release contains information for 5 882 730 genes, and offers pre-computed gene families and phylogenetic trees for 5 274 684 protein-coding genes. This latest release also comes with a set of new and updated features: a new BED import functionality for the workbench, improved interactive visualizations for functional enrichments and genome-wide mapping of gene sets, and a fully redesigned and extended API. Taken together, this new version offers extended support for plant biologists working on different families within the green plant lineage and provides an efficient and versatile toolbox for plant genomics. All PLAZA releases are accessible from the portal website: https://bioinformatics.psb.ugent.be/plaza/.

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          The Gene Ontology resource: enriching a GOld mine

          Jurg Bahler, Christopher Tabone (2021)
          Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.
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            Phytozome: a comparative platform for green plant genomics

            David Goodstein, Shengqiang Shu, Russell Howson … (2011)
            The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.
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              The InterPro protein families and domains database: 20 years on

              Matthias Blum, Hsin-Yu Chang, Sara Chuguransky … (2020)
              Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.
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                Author and article information

                Contributors
                Michiel Van Bel:
                ORCID: https://orcid.org/0000-0002-1873-2563
                Francesca Silvestri
                Eric M Weitz:
                ORCID: https://orcid.org/0000-0001-6622-6350
                Lukasz Kreft:
                ORCID: https://orcid.org/0000-0001-7620-4657
                Alexander Botzki:
                ORCID: https://orcid.org/0000-0001-6691-4233
                Frederik Coppens:
                ORCID: https://orcid.org/0000-0001-6565-5145
                Klaas Vandepoele:
                ORCID: https://orcid.org/0000-0003-4790-2725
                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: 07 January 2022
                Publication date (Electronic): 08 November 2021
                Publication date PMC-release: 08 November 2021
                Volume: 50
                Issue: D1
                Pages: D1468-D1474
                Affiliations
                Department of Plant Biotechnology and Bioinformatics, Ghent University , Technologiepark 71, 9052 Ghent, Belgium
                VIB Center for Plant Systems Biology , Technologiepark 71, 9052 Ghent, Belgium
                Department of Plant Biotechnology and Bioinformatics, Ghent University , Technologiepark 71, 9052 Ghent, Belgium
                VIB Center for Plant Systems Biology , Technologiepark 71, 9052 Ghent, Belgium
                Data Sciences Platform, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA
                Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Pawińskiego 5A 02-106 Warsaw, Poland
                VIB Bioinformatics Core , 9052 Ghent, Belgium
                Department of Plant Biotechnology and Bioinformatics, Ghent University , Technologiepark 71, 9052 Ghent, Belgium
                VIB Center for Plant Systems Biology , Technologiepark 71, 9052 Ghent, Belgium
                Department of Plant Biotechnology and Bioinformatics, Ghent University , Technologiepark 71, 9052 Ghent, Belgium
                VIB Center for Plant Systems Biology , Technologiepark 71, 9052 Ghent, Belgium
                Bioinformatics Institute Ghent, Ghent University , Technologiepark 71, 9052 Ghent, Belgium
                Author notes
                To whom correspondence should be addressed. Tel: +32 93313822; Email: klaas.vandepoele@ 123456psb.vib-ugent.be
                Author information
                https://orcid.org/0000-0002-1873-2563
                https://orcid.org/0000-0001-6622-6350
                https://orcid.org/0000-0001-7620-4657
                https://orcid.org/0000-0001-6691-4233
                https://orcid.org/0000-0001-6565-5145
                https://orcid.org/0000-0003-4790-2725
                Article
                Publisher ID: gkab1024
                DOI: 10.1093/nar/gkab1024
                PMC ID: 8728282
                PubMed ID: 34747486
                SO-VID: 15137d03-9d22-4e45-9168-4a0c2cf2577e
                Copyright © © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 13 October 2021
                Date revision received : 12 October 2021
                Date received : 16 September 2021
                Page count
                Pages: 7
                Funding
                Funded by: Research Foundation Flanders, DOI 10.13039/501100003130;
                Award ID: I002819N
                Funded by: Ghent University, DOI 10.13039/501100004385;
                Award ID: BOF24Y2019001901
                Funded by: VIB, DOI 10.13039/501100004727;
                Categories
                Subject: AcademicSubjects/SCI00010
                Subject: Database Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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