| Summary: | <p>Abstract</p> <p>Background</p> <p>Branchiopod crustaceans in the genus <it>Daphnia </it>are key model organisms for investigating interactions between genes and the environment. One major theme of research on <it>Daphnia </it>species has been the evolution of resistance to pathogens and parasites, but lack of knowledge of the <it>Daphnia </it>immune system has limited the study of immune responses. Here we provide a survey of the immune-related genome of <it>D. pulex</it>, 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.</p> <p>Results and conclusion</p> <p>We found that some immune pathways, in particular the TOLL pathway, are fairly well conserved between insects and <it>Daphnia</it>, 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 <it>Daphnia </it>to insects and present phylogenetic analyses to shed light on the evolution of a range of conserved immune gene families.</p>
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