pico‐PLAZA, a genome database of microbial photosynthetic eukaryotes
Identifieur interne : 000381 ( Main/Exploration ); précédent : 000380; suivant : 000382pico‐PLAZA, a genome database of microbial photosynthetic eukaryotes
Auteurs : Klaas Vandepoele [Belgique] ; Michiel Van Bel [Belgique] ; Guilhem Richard [France] ; Sofie Van Landeghem [Belgique] ; Bram Verhelst [Belgique] ; Hervé Moreau [France] ; Yves Van De Peer [Belgique] ; Nigel Grimsley [France] ; Gwenael Piganeau [France]Source :
- Environmental Microbiology [ 1462-2912 ] ; 2013-08.
Abstract
With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user‐defined sequences or gene lists remains a major challenge. pico‐PLAZA is a web‐based resource (http://bioinformatics.psb.ugent.be/pico‐plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text‐mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non‐expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico‐PLAZA can be used to functionally characterize large‐scale EST/RNA‐Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.
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DOI: 10.1111/1462-2920.12174
Affiliations:
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xml:lang="fr">France</country><wicri:regionArea>CNRS, UMR 7232, Observatoire Océanologique, Banyuls‐sur‐Mer</wicri:regionArea><wicri:noRegion>Banyuls‐sur‐Mer</wicri:noRegion><wicri:noRegion>Banyuls‐sur‐Mer</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">France</country><wicri:regionArea>UPMC Univ Paris 06, UMR 7232, Observatoire Océanologique, Banyuls‐sur‐Mer</wicri:regionArea><wicri:noRegion>Banyuls‐sur‐Mer</wicri:noRegion><wicri:noRegion>Banyuls‐sur‐Mer</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j">Environmental Microbiology</title><title level="j" type="abbrev">Environ Microbiol</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><date type="published" when="2013-08">2013-08</date><biblScope unit="volume">15</biblScope><biblScope unit="issue">8</biblScope><biblScope unit="page" from="2147">2147</biblScope><biblScope unit="page" to="2153">2153</biblScope></imprint><idno type="ISSN">1462-2912</idno></series><idno type="istex">F40BD7F63800F1623E9521F4F517A2697BE3E02F</idno><idno type="DOI">10.1111/1462-2920.12174</idno><idno type="ArticleID">EMI12174</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1462-2912</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user‐defined sequences or gene lists remains a major challenge. pico‐PLAZA is a web‐based resource (http://bioinformatics.psb.ugent.be/pico‐plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text‐mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non‐expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico‐PLAZA can be used to functionally characterize large‐scale EST/RNA‐Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.</div></front></TEI><affiliations><list><country><li>Belgique</li><li>France</li></country></list><tree><country name="Belgique"><noRegion><name sortKey="Vandepoele, Klaas" sort="Vandepoele, Klaas" uniqKey="Vandepoele K" first="Klaas" last="Vandepoele">Klaas Vandepoele</name></noRegion><name sortKey="Van Bel, Michiel" sort="Van Bel, Michiel" uniqKey="Van Bel M" first="Michiel" last="Van Bel">Michiel Van Bel</name><name sortKey="Van Bel, Michiel" sort="Van Bel, Michiel" uniqKey="Van Bel M" first="Michiel" last="Van Bel">Michiel Van Bel</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Van Landeghem, Sofie" sort="Van Landeghem, Sofie" uniqKey="Van Landeghem S" first="Sofie" last="Van Landeghem">Sofie Van Landeghem</name><name sortKey="Van Landeghem, Sofie" sort="Van Landeghem, Sofie" uniqKey="Van Landeghem S" first="Sofie" last="Van Landeghem">Sofie Van Landeghem</name><name sortKey="Vandepoele, Klaas" sort="Vandepoele, Klaas" uniqKey="Vandepoele K" first="Klaas" last="Vandepoele">Klaas Vandepoele</name><name sortKey="Verhelst, Bram" sort="Verhelst, Bram" uniqKey="Verhelst B" first="Bram" last="Verhelst">Bram Verhelst</name><name sortKey="Verhelst, Bram" sort="Verhelst, Bram" uniqKey="Verhelst B" first="Bram" last="Verhelst">Bram Verhelst</name></country><country name="France"><noRegion><name sortKey="Richard, Guilhem" sort="Richard, Guilhem" uniqKey="Richard G" first="Guilhem" last="Richard">Guilhem Richard</name></noRegion><name sortKey="Grimsley, Nigel" sort="Grimsley, Nigel" uniqKey="Grimsley N" first="Nigel" last="Grimsley">Nigel Grimsley</name><name sortKey="Grimsley, Nigel" sort="Grimsley, Nigel" uniqKey="Grimsley N" first="Nigel" last="Grimsley">Nigel Grimsley</name><name sortKey="Moreau, Herve" sort="Moreau, Herve" uniqKey="Moreau H" first="Hervé" last="Moreau">Hervé Moreau</name><name sortKey="Moreau, Herve" sort="Moreau, Herve" uniqKey="Moreau H" first="Hervé" last="Moreau">Hervé Moreau</name><name sortKey="Piganeau, Gwenael" sort="Piganeau, Gwenael" uniqKey="Piganeau G" first="Gwenael" last="Piganeau">Gwenael Piganeau</name><name sortKey="Piganeau, Gwenael" sort="Piganeau, Gwenael" uniqKey="Piganeau G" first="Gwenael" last="Piganeau">Gwenael Piganeau</name><name sortKey="Richard, Guilhem" sort="Richard, Guilhem" uniqKey="Richard G" first="Guilhem" last="Richard">Guilhem Richard</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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