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Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms. The knowledge of the function of aquaporins in crustaceans is, however, limited and nothing is known about them in barnacles. We here present the repertoire of aquaporins from a thecostracan crustacean, the barnacle B. improvisus, based on genome and transcriptome sequencing. Our analyses reveal that B. improvisus contains eight genes for aquaporins. Phylogenetic analysis showed that they represented members of the classical water aquaporins (Aqp1, Aqp2), the aquaglyceroporins (Glp1, Glp2), the unorthodox aquaporin (Aqp12) and the arthropod-specific big brain aquaporin (Bib). Interestingly, we also found two big brain-like proteins (BibL1 and BibL2) constituting a new group of aquaporins not yet described in arthropods. In addition, we found that the two water-specific aquaporins were expressed as C-terminal splice variants. Heterologous expression of some of the aquaporins followed by functional characterization showed that Aqp1 transported water and Glp2 water and glycerol, agreeing with the predictions of substrate specificity based on 3D modeling and phylogeny. To investigate a possible role for the B. improvisus aquaporins in osmoregulation, mRNA expression changes in adult barnacles were analysed after long-term acclimation to different salinities. The most pronounced expression difference was seen for AQP1 with a substantial (>100-fold) decrease in the mantle tissue in low salinity (3 PSU) compared to high salinity (33 PSU). Our study provides a base for future mechanistic studies on the role of aquaporins in osmoregulation.

Problem. The signal recognition particle (SRP) is a ribonucleoprotein particle that targets proteins to the endoplasmic reticulum in eukaryotes, to the plasma membrane in Archaea and Bacteria and to the thylakoid membrane in chloroplasts of photosynthetic organisms. It has one RNA component and 1 6 proteins. The eukaryotic particle is composed of one S domain responsible for signal recognition and one Alu domain responsible for translation elongation arrest. In many phylogenetic groups the SRP is not characterized. Therefore, we aim to identify SRP component genes by computational screening of a large number of organisms where genomic information is available. Methods. For the protein gene identification, we relied on methods based on primary sequence alignments (BLAST, FASTA), profile searches (PSI-BLAST, HMMER, Profilescan), and secondary structure prediction (PSI-Pred). The main focus in this work is the identification of SRP RNA. It is highly diverse in its structure and has a low primary sequence conservation between different phylogenetic groups. As a consequence, standard sequence analysis tools, such as BLAST, are not useful. We have developed a tool for the identification of SRP RNA (SRPscan) using algorithms for pattern matching and covariance analysis of secondary structures.Results. We have carried out an extensive inventory of SRP components by screening available genomic sequences. As a result we have identified a large number of novel genes. The protein and RNA sequences are presented in the SRP database (SRPDB). We have identified full or partial SRP RNA genes in virtually all organisms where genomic sequences of nearly full genome coverage are available, and the findings have led to a proposal of a new nomenclature for SRP RNA.In an analysis of bacterial RNAs we found species with an unusual URRC tetraloop and we identified an RNA from deeply branching gram-negative bacterium Thermotoga that is of the gram-positive Bacillus type. It was previously believed that chloroplasts do not have an SRP RNA. However, we have shown that chloroplast genomes of red algae or red algal origin, as well as some green algae, encode a bacterial type SRP RNA.Eukaryotic SRP RNAs are highly divergent in their structures, mainly in the Alu domain. Based on an analysis of fungal RNAs we were able to present a novel secondary structure model of these RNAs. Analysis of eukaryotic RNAs includes a number of unexpected findings. In the fungal groups Basidiomycota and Zygomycota the SRP RNA has an Alu domain that conforms to the standard mammalian SRP RNA structure. The external loop of helix 8 is a tetraloop as a rule, but in several protists this sequence is a pentaloop. Finally, we suggest that some eukaryal species like Microsporidia might lack an SRP Alu domain.Conclusion. By computational screening of genomic sequences we have identified a large number of novel SRP RNA and proteins components. The results of these studies provide significant insights into the structure, function and phylogeny of the SRP.

BACKGROUND The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. RESULTS We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby's capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. CONCLUSIONS The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.