Daphnia pulex Assembly and Gene Annotation
About Daphnia pulex
Daphnia pulex, the common water flea, is a microcrustacean arthropod (typically 0.2-3.0 mm long) found ubiquitously in freshwater around the globe, predominately in small ponds and ephemeral pools. D. pulex live for around 10-30 days, but can live up to 100 days in the absence of predation. Their anatomy is easily studied, due to the see-through carapce which reveals the internal organs at work.
Daphnia pulex is sensitive to environmental changes and exhibits context-dependent responses (e.g. switching from clonal to sexual reproduction, or rapidly changing haemoglobin levels) that make it a sensible agent to assess the ecological impact of environmental fluctuations. Predation can induce a range of morphological changes in D. pulex. In response to kairomones (chemicals released by predatory insect larvae), D. pulex develop small protusions (neckteeth) that act as a defence mechanism. It can also change size to avoid either detection by larger vertebrate predators, or consumption by smaller invertebrate predators.
In addition to its usefulness in a variety of research areas (including ecology, toxicology, and physiology), in evolutionary terms Daphnia pulex is important as a representative of the sister group to the insects, and can highlight genes present in the pancrustacean common ancestor.
Picture credit: Dr Paul D.N. Hebert (University of Guelph)
Daphnia pulex was the first published crustacean genome, and was sequenced and assembled by the Joint Genome Institute . The assembly was sequenced to 8.7x coverage, and assembled with the JGI software, JAZZ.
Gene models were predicted using ab initio and homology-based methods (FGENESH, GENEWISE, SNAP, PASA and Gnomon). The automated annotation was followed by a distributed community-wide manual curation. Since release 22 (March 2014), Ensembl Genomes has displayed the ENA gene set; this gene set is a subset of the original JGI gene set, therefore all genes contain a JGI cross reference. Between Ensembl Genomes release 21 and release 22, 304 protein-coding genes were removed, and 23 new pseudogenes were imported. Non-coding RNA genes were added using the Ensembl Genomes pipeline, and BLAST hits and protein features have been computed. Additional data is available at wFleaBase .
- The ecoresponsive genome of Daphnia
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK et al. 2011. Science. 331:555-561.
- wFleaBase: the Daphnia genome
Colbourne JK, Singan VR, Gilbert DG. 2005. BMC Bioinformatics. 6:45.
General information about this species can be found in Wikipedia.
|Assembly||V1.0, INSDC Assembly GCA_000187875.1, Feb 2011|
|Golden Path Length||197,206,209|
|Data source||Joint Genome Institute|
|Non coding genes||2,436|
|Small non coding genes||2,435|
|Long non coding genes||1|