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 [1]. 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 [2].


  1. The ecoresponsive genome of Daphnia pulex.
    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.
  2. wFleaBase: the Daphnia genome database.
    Colbourne JK, Singan VR, Gilbert DG. 2005. BMC Bioinformatics. 6:45.

More information

General information about this species can be found in Wikipedia.



AssemblyV1.0, INSDC Assembly GCA_000187875.1, Feb 2011
Database version93.1
Base Pairs158,609,466
Golden Path Length197,206,209
Genebuild byEnsemblMetazoa
Genebuild methodGenerated from ENA annotation
Data sourceJGI

Gene counts

Coding genes30,590
Non coding genes2,436
Small non coding genes2,435
Long non coding genes1
Gene transcripts33,070

About this species