The Genome of the "Sea Vomit" Didemnum vexillum.

Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum, commonly known as "sea vomit", is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the D. vexillum genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the "sea vomit" genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.

Dropping the microbead: Source and sink related microplastic distribution in the Black Sea and Caspian Sea basins.

Microplastic pollution is a growing, yet poorly understood problem. Here, we assessed the relationship between microplastic concentration and distance to rivers, shorelines, cities, sediment grain size or water depth in sediments of the world's largest (semi-)enclosed aquatic basins. Microplastic was extracted from sediment using density separation, elutriation and hydrophobic adhesion. Fibers and transparent or white microplastic particles were the most abundant shape and color. The microplastic concentration in sediments of the Black Sea was about twice as high compared to that in the Caspian Sea. Fragment concentrations decreased with depth, while fiber concentrations were independent of depth. Overall, no relationship with distance to shores, rivers and cities or with grain size was observed. However, within some depth classes concentrations were related to the distance from rivers, shores and cities.

Nonprotein-Coding RNAs as Regulators of Development in Tunicates.

Tunicates, or urochordates, are a group of small marine organisms that are found widely throughout the seas of the world. As most plausible sister group of the vertebrates, they are of utmost importance for a comprehensive understanding of chordate evolution; hence, they have served as model organisms for many aspects of the developmental biology. Current genomic analysis of tunicates indicates that their genomes evolved with a fast rate not only at the level of nucleotide substitutions but also in terms of genomic organization. The latter involves genome reduction, rearrangements, as well as the loss of some important coding and noncoding RNA (ncRNAs) elements and even entire genomic regions that are otherwise well conserved. These observations are largely based on evidence from comparative genomics resulting from the analysis of well-studied gene families such as the Hox genes and their noncoding elements. In this chapter, the focus lies on the ncRNA complement of tunicates, with a particular emphasis on microRNAs, which have already been studied extensively for other animal clades. MicroRNAs are known as important regulators of key genes in animal development, and they are intimately related to the increase morphological complexity in higher metazoans. Here we review the discovery, evolution, and genome organization of the miRNA repertoire, which has been drastically reduced and restructured in tunicates compared to the chordate ancestor. Known functions of microRNAs as regulators of development in tunicates are a central topic. For instance, we consider the role of miRNAs as regulators of the muscle development and their importance in the regulation of the differential expression during the oral siphon regeneration. Beyond microRNAs, we touch upon the functions of some other ncRNAs such as yellow crescent RNA, moRNAs, RMST lncRNAs, or spliced-leader (SL) RNAs, which have diverse functions associated with the embryonic development, neurogenesis, and mediation of mRNA stability in general.

Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum.

BACKGROUND: The colonial ascidian Didemnum vexillum, sea carpet squirt, is not only a key marine organism to study morphological ancestral patterns of chordates evolution but it is also of great ecological importance due to its status as a major invasive species. Non-coding RNAs, in particular microRNAs (miRNAs), are important regulatory genes that impact development and environmental adaptation. Beyond miRNAs, not much in known about tunicate ncRNAs. RESULTS: We provide here a comprehensive homology-based annotation of non-coding RNAs in the recently sequenced genome of D. vexillum. To this end we employed a combination of several computational approaches, including blast searches with a wide range of parameters, and secondary structured centered survey with infernal. The resulting candidate set was curated extensively to produce a high-quality ncRNA annotation of the first draft of the D. vexillum genome. It comprises 57 miRNA families, 4 families of ribosomal RNAs, 22 isoacceptor classes of tRNAs (of which more than 72 % of loci are pseudogenes), 13 snRNAs, 12 snoRNAs, and 1 other RNA family. Additionally, 21 families of mitochondrial tRNAs and 2 of mitochondrial ribosomal RNAs and 1 long non-coding RNA. CONCLUSIONS: The comprehensive annotation of the D. vexillum non-coding RNAs provides a starting point towards a better understanding of the restructuring of the small RNA system in ascidians. Furthermore it provides a valuable research for efforts to establish detailed non-coding RNA annotations for other recently published and recently sequences in tunicate genomes.

Where are the polyps? Molecular identification, distribution and population differentiation of Aurelia aurita jellyfish polyps in the southern North Sea area.

For many species of metagenic jellyfish the location of the benthic polyps is unknown. To gain insight in the distribution, species composition and population structure of scyphozoan jellyfish polyps in the southern North Sea area, polyp samples were collected from natural and artificial substrates (settling plates, marina floats and wrecks) at ten inshore locations in the Netherlands, seven offshore locations in the North Sea and in the Gullmar Fjord in Sweden. Polyps were identified to species level by sequencing both a fragment of 18S rDNA and a fragment of mitochondrial COI, and comparing these sequences to reference sequences available in GenBank and to newly obtained sequences from medusae collected in the area. All polyps sequenced did belong to Aurelia aurita. For this species, molecular diversity in mitochondrial COI was high, with 50 haplotypes among 183 polyps. Population differentiation was detected between the Dogger Bank and other-more coastal-locations, indicating extremely low connectivity. No significant differences were found between coastal samples. The location of polyps of Cyanea capillata, Cyanea lamarckii, Chrysaora hysoscella and Rhizostoma octopus in the study area remains unresolved.