Nuclear and mitochondrial genome assemblies for the endangered wood-decaying fungus Somion occarium.

Somion occarium is a wood-decaying bracket fungus belonging to an order known to be rich in useful chemical compounds. Despite its widespread distribution, S. occarium has been assessed as endangered on at least one national Red List, presumably due to loss of old-growth forest habitat.

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

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.

The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion.

We present a reference genome assembly from an individual male Violet Carpenter Bee (Xylocopa violacea, Linnaeus 1758). The assembly is 1.02 gigabases in span.

COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project.

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland.

Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids.

The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the "universal" genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled.

Mitogenome phylogeographic analysis of a planktonic crustacean.

Phylogeography places population genetics in an explicitly spatial context, and in doing so attempts to reconstruct the historical and contemporary evolutionary processes acting across a species range through space and time. Here we present the phylogeographical structure of Daphnia magna as determined for full mitochondrial genomes from samples of 60 populations throughout much of the species known range, including Europe, the Middle East, and Asia. Contrary to previous analyses, the present analysis of the mitochondrial genome reveals coarse-grained (continental scale) evidence for spatial structure, and in particular a deep split between Western Eurasia and East Asian D.

Transcriptome profiling during a natural host-parasite interaction.

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).

Novel insights into the insect trancriptome response to a natural DNA virus.

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.

The development of pathogen resistance in Daphnia magna: implications for disease spread in age-structured populations.

Immunity in vertebrates is well established to develop with time, but the ontogeny of defence in invertebrates is markedly less studied. Yet, age-specific capacity for defence against pathogens, coupled with age structure in populations, has widespread implications for disease spread. Thus, we sought to determine the susceptibility of hosts of different ages in an experimental invertebrate host-pathogen system.

Immune genes undergo more adaptive evolution than non-immune system genes in Daphnia pulex.

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.

Length variation in 18S rRNA expansion segment 43/e4 of Daphnia obtusa: ancient or recurring polymorphism?

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.

An ancient immunity gene duplication in Daphnia magna: RNA expression and sequence analysis of two nitric oxide synthase genes.

NO (nitric oxide) is a highly reactive free radical gas thought to play a major role in the invertebrate immune response by harming pathogens and limiting their growth. Here we report on studies of nitric oxide synthase (NOS) genes in the crustacean Daphnia, one of the few non-insect arthropod models used to study host-pathogen interactions. While the NOS gene is found as a single copy in other invertebrates, we found two copies (NOS1 and NOS2), which a phylogenetic reconstruction showed to be the result of an ancient duplication event.

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

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.

Nucleotide polymorphism and within-gene recombination in Daphnia magna and D. pulex, two cyclical parthenogens.

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.

The Dscam homologue of the crustacean Daphnia is diversified by alternative splicing like in insects.

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.

Selection on the structural stability of a ribosomal RNA expansion segment in Daphnia obtusa.

The high rate of sequence divergence in nuclear ribosomal RNA (rRNA) expansion segments offers a unique opportunity to study the importance of natural selection in their evolution. To this end, we polymerase chain reaction amplified and cloned a 589-nt fragment of the 18S rRNA gene containing expansion segments 43/e1 and 43/e4 from six individual Daphnia obtusa from four populations. We screened 2,588 clones using single-stranded conformation polymorphism analysis and identified 103 unique haplotype sequences.