Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database
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Transcriptome analyses plus release of the PhyloFish database; a domain genomics resource, not infrastructure of the research ecosystem in the metaresearch sense.
This describes a genomics database resource and is an infrastructure announcement rather than an analytic study.
Domain genomics resource (PhyloFish) for fish gene evolution; uses a database tool rather than studying research infrastructure.
Résumé
With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.
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La notice
- Revue
- BMC Genomics
- Thématique
- Genomics and Phylogenetic Studies
- Domaine
- Biochemistry, Genetics and Molecular Biology
- Établissements canadiens
- —
- Organismes subventionnaires
- National Institutes of HealthInstitut National de la Recherche AgronomiqueAgence Nationale de la RechercheAgentschap voor Natuur en BosCentre National de la Recherche ScientifiqueUniversité de Pau et des Pays de l'AdourUniversité Laval
- Mots-clés
- BiologyGene duplicationGeneEvolutionary biologyLineage (genetic)GenomeTranscriptomeVertebrateGene expressionPhylogeneticsConcerted evolutionDNA microarrayDatabaseGenetics
- Résumé présent dans OpenAlex
- oui