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The components of the Daphnia pulex immune system as revealed by complete genome sequencing

Seanna J McTaggart1*, Claire Conlon1, John K Colbourne2, Mark L Blaxter1 and Tom J Little1

Author Affiliations

1 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK

2 Center for Genomics and Bioinformatics, Indiana University, Bloomington, USA

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BMC Genomics 2009, 10:175  doi:10.1186/1471-2164-10-175

Published: 22 April 2009



Branchiopod crustaceans in the genus Daphnia are key model organisms for investigating interactions between genes and the environment. One major theme of research on Daphnia species has been the evolution of resistance to pathogens and parasites, but lack of knowledge of the Daphnia immune system has limited the study of immune responses. Here we provide a survey of the immune-related genome of D. pulex, derived from the newly completed genome sequence. Genes likely to be involved in innate immune responses were identified by comparison to homologues from other arthropods. For each candidate, the gene model was refined, and we conducted an analysis of sequence divergence from homologues from other taxa.

Results and conclusion

We found that some immune pathways, in particular the TOLL pathway, are fairly well conserved between insects and Daphnia, while other elements, in particular antimicrobial peptides, could not be recovered from the genome sequence. We also found considerable variation in gene family copy number when comparing Daphnia to insects and present phylogenetic analyses to shed light on the evolution of a range of conserved immune gene families.