Abstract
BackgroundwFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Commonly known as the water-flea, Daphnia's ecological merit is unequaled among metazoans, largely because of its sentinel role within freshwater ecosystems and over 200 years of biological investigations. By consequence, the Daphnia Genomics Consortium (DGC) has launched an interdisciplinary research program to create the resources needed to study genes that affect ecological and evolutionary success in natural environments.DiscussionThese tools include the genome database wFleaBase, which currently contains functions to search and extract information from expressed sequenced tags, genome survey sequences and full genome sequencing projects. This new database is built primarily from core components of the Generic Model Organism Database project, and related bioinformatics tools.SummaryOver the coming year, preliminary genetic maps and the nearly complete genomic sequence of Daphnia pulex will be integrated into wFleaBase, including gene predictions and ortholog assignments based on sequence similarities with eukaryote genes of known function. wFleaBase aims to serve a large ecological and evolutionary research community. Our challenge is to rapidly expand its content and to ultimately integrate genetic and functional genomic information with population-level responses to environmental challenges. URL: .
Highlights
WFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia
The micro-crustacean Daphnia is a ubiquitous resident of inland waters within all continents of the globe and is the subject of study for numerous biological disciplines including limnology, ecology, physiology, toxicology, population genetics and evolution
As the principal grazers of algae and the primary forage of fish, Daphnia are key members of aquatic food webs and are sampled in great numbers. These animals inhabit remarkably diverse environments and show striking patterns of convergent evolution linked to specific habitat transitions [1]. Their mode of reproduction is convenient for experimental genetics, providing both longterm clonal lineages and controlled outbred populations by manipulating the environmental cues required for the induction of male production and for mating [2]
Summary
These tools include the genome database wFleaBase, which currently contains functions to search and extract information from expressed sequenced tags, genome survey sequences and full genome sequencing projects. This new database is built primarily from core components of the Generic Model Organism Database project, and related bioinformatics tools. Summary: Over the coming year, preliminary genetic maps and the nearly complete genomic sequence of Daphnia pulex will be integrated into wFleaBase, including gene predictions and ortholog assignments based on sequence similarities with eukaryote genes of known function. Our challenge is to rapidly expand its content and to integrate genetic and functional genomic information with population-level responses to environmental challenges.
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