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Background 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.

Background Understanding which parts of the genome have been most influenced by adaptive evolution remains an unsolved puzzle. Some evidence suggests that selection has the greatest impact on regions of the genome that interact with other evolving genomes, including loci that are involved in host-parasite co-evolutionary processes. In this study, we used a population genetic approach to test this hypothesis by comparing DNA sequences of 30 putative immune system genes in the crustacean Daphnia pulex with 24 non-immune system genes. Results In support of the hypothesis, results from a multilocus extension of the McDonald-Kreitman (MK) test indicate that immune system genes as a class have experienced more adaptive evolution than non-immune system genes. However, not all immune system genes show evidence of adaptive evolution. Additionally, we apply single locus MK tests and calculate population genetic parameters at all loci in order to characterize the mode of selection (directional versus balancing) in the genes that show the greatest deviation from neutral evolution. Conclusions Our data are consistent with the hypothesis that immune system genes undergo more adaptive evolution than non-immune system genes, possibly as a result of host-parasite arms races. The results of these analyses highlight several candidate loci undergoing adaptive evolution that could be targeted in future studies.

Background Little is known about invertebrate responses to DNA viruses. Here, we infect a commercially important pest moth species Plodia interpunctella with its naturally infecting DNA virus. We sequenced, assembled and annotated the complete transcriptome of the moth, and a partial transcriptome of the virus. We then tested for differential gene expression between moths that were exposed to the virus and controls. Results We found 51 genes that were differentially expressed in moths exposed to a DNA baculovirus compared to controls. Gene set enrichment analysis revealed that cuticle proteins were significantly overrepresented in this group of genes. Interestingly, 6 of the 7 differentially expressed cuticle proteins were downregulated, suggesting that baculoviruses are able to manipulate its host’s response. In fact, an additional 29 of the 51 genes were also downregulated in exposed compared with control animals, including a gram-negative binding protein. In contrast, genes involved in transposable element movement were upregulated after infection. Conclusions We present the first experiment to measure genome-wide gene expression in an insect after infection with a natural DNA virus. Our results indicate that cuticle proteins might be key genes underpinning the response to DNA viruses. Furthermore, the large proportion of genes that were downregulated after viral exposure suggests that this virus is actively manipulating the insect immune response. Finally, it appears that transposable element activity might increase during viral invasion. Combined, these results provide much needed host candidate genes that respond to DNA viral invaders.

Ribosomal (r)DNA undergoes concerted evolution, the mechanisms of which are unequal crossing over and gene conversion. Despite the fundamental importance of these mechanisms to the evolution of rDNA, their rates have been estimated only in a few model species. We estimated recombination rate in rDNA by quantifying the relative frequency of intraindividual length variants in an expansion segment of the 18S rRNA gene of the cladoceran crustacean, Daphnia obtusa, in four apomictically propagated lines. We also used quantitative PCR to estimate rDNA copy number. The apomictic lines were sampled every 5 generations for 90 generations, and we considered each significant change in the frequency distribution of length variants between time intervals to be the result of a recombination event. Using this method, we calculated the recombination rate for this region to be 0.02–0.06 events/generation on the basis of three different estimates of rDNA copy number. In addition, we observed substantial changes in rDNA copy number within and between lines. Estimates of haploid copy number varied from 53 to 233, with a mean of 150. We also measured the relative frequency of length variants in 30 lines at generations 5, 50, and 90. Although length variant frequencies changed significantly within and between lines, the overall average frequency of each length variant did not change significantly between the three generations sampled, suggesting that there is little or no bias in the direction of change due to recombination.

Expansion segments in ribosomal DNA (rDNA) can show length variation at the level of the individual, yet our understanding of the evolutionary forces shaping this variation is incomplete. Previous studies of expansion segment 43/e4 of the 18S rRNA gene in Daphnia obtusa have examined this variation in six individuals; however, it is not known if the variation documented at this locus is representative of variation across the species' geographic range. Furthermore, it is unclear whether length variants found in multiple individuals share common ancestry, or were generated de novo through recombination. We quantified expansion segment length variant frequencies in 134 individual D. obtusa from 33 populations at 15 sites across the species range in the US, and used a phylogeographic approach to determine whether recombination continues to add to the standing crop of variation at this locus. We identified seven length variants across the sampling range, which spans almost 3000 km. Based on the phylogeographic distribution of length variants in the expansion segment, we conclude that they are shared ancient polymorphisms that have persisted despite the operation of molecular mechanisms that cause the concerted evolution of multigene families such as rDNA.

Background Infection outcome in some coevolving host-pathogens is characterised by host-pathogen genetic interactions, where particular host genotypes are susceptible only to a subset of pathogen genotypes. To identify candidate genes responsible for the infection status of the host, we exposed a Daphnia magna host genotype to two bacterial strains of Pasteuria ramosa, one of which results in infection, while the other does not. At three time points (four, eight and 12 h) post pathogen exposure, we sequenced the complete transcriptome of the hosts using RNA-Seq (Illumina). Results We observed a rapid and transient response to pathogen treatment. Specifically, at the four-hour time point, eight genes were differentially expressed. At the eight-hour time point, a single gene was differentially expressed in the resistant combination only, and no genes were differentially expressed at the 12-h time point. Conclusions We found that pathogen-associated transcriptional activity is greatest soon after exposure. Genome-wide resistant combinations were more likely to show upregulation of genes, while susceptible combinations were more likely to be downregulated, relative to controls. Our results also provide several novel candidate genes that may play a pivotal role in determining infection outcomes.

Theory predicts that partially asexual organisms may make the “best of both worlds”: for the most part, they avoid the costs of sexual reproduction, while still benefiting from an enhanced efficiency of selection compared to obligately asexual organisms. There is, however, little empirical data on partially asexual organisms to test this prediction. Here we examine patterns of nucleotide diversity at eight nuclear loci in continentwide samples of two species of cyclically parthenogenetic Daphnia to assess the effect of partial asexual reproduction on effective population size and amount of recombination. Both species have high nucleotide diversities and show abundant evidence for recombination, yielding large estimates of effective population sizes (300,000–600,000). This suggests that selection will act efficiently even on mutations with small selection coefficients. Divergence between the two species is less than one-tenth of previous estimates, which were derived using a mitochondrial molecular clock. As the two species investigated are among the most distantly related species of the genus, this suggests that the genus Daphnia may be considerably younger than previously thought. Daphnia has recently received increased attention because it is being developed as a model organism for ecological and evolutionary genomics. Our results confirm the attractiveness of Daphnia as a model organism, because the high nucleotide diversity and low linkage disequilibrium suggest that fine-scale mapping of genes affecting phenotypes through association studies should be feasible.

In insects, the homologue of the Down syndrome cell adhesion molecule (Dscam) is a unique case of a single-locus gene whose expression has extensive somatic diversification in both the nervous and immune systems. How this situation evolved is best understood through comparative studies. We describe structural, expression, and evolutionary aspects of a Dscam homolog in 2 species of the crustacean Daphnia. The Dscam of Daphnia generates up to 13,000 different transcripts by the alternative splicing of variable exons. This extends the taxonomic range of a highly diversified Dscam beyond the insects. Additionally, we have identified 4 alternative forms of the cytoplasmic tail that generate isoforms with or without inhibitory or activating immunoreceptor tyrosine-based motifs (ITIM and ITAM respectively), something not previously reported in insect's Dscam. In Daphnia, we detected exon usage variability in both the brain and hemocytes (the effector cells of immunity), suggesting that Dscam plays a role in the nervous and immune systems of crustaceans, as it does in insects. Phylogenetic analysis shows a high degree of amino acid conservation between Daphnia and insects except in the alternative exons, which diverge greatly between these taxa. Our analysis shows that the variable exons diverged before the split of the 2 Daphnia species and is in agreement with the nearest-neighbor model for the evolution of the alternative exons. The genealogy of the Dscam gene family from vertebrates and invertebrates confirmed that the highly diversified form of the gene evolved from a nondiversified form before the split of insects and crustaceans. [PUBLICATION ABSTRACT]

Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A. aequalis with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of A. aequalis is more similar to Hordeum vulgare rather than the more closely related Alopecurus myosuroides .