Genome sizes and repeatome evolution in zoantharians (Cnidaria: Hexacorallia: Zoantharia).

Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the "C-value enigma". The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson's correlation test R2 = 0.47, p = 0.0016; R2 = 0.22, p = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements' amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology.

A Draft Genome Sequence of Dorometra sesokonis (Antedonidae, Comatulida, Crinoidea, Echinodermata).

We present the complete genome sequence of Dorometra sesokonis. Genome sequencing was performed on genetic material from a single wild-collected individual. The sequence reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank.

The Complete Genome Sequences of 13 Species of Brachycnemina (Cnidaria, Hexacorallia, Anthozoa, Zoantharia).

We present the complete genome sequences of 13 species of the zoantharian suborder Brachycnemina (Haddon, and Shackleton, 1891; Poliseno et al., 2020). Genome sequencing was performed on genetic material from single wild-collected individuals. For each species the sequence reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank.

Shallow epifaunal sea cucumber densities and their relationship with the benthic community in the Okinawa Islands.

Sea cucumbers are important ecological engineers in marine ecosystems. However, the fishery demand of some species, especially large-epifaunal and commercially used (LEC) sea cucumbers, has risen drastically, resulting in serious depletion of local populations for many species. Despite this problem, basic ecological data on sea cucumbers, such as population densities and preferred habitats, are often still insufficient. Here, we report on the population densities of multiple LEC sea cucumber species, and their ambient benthic communities at eight sites around Okinawa Islands. Further, we discuss the correspondence between sea cucumber densities and the surrounding coral communities. Our results show two sites within national or quasi-national parks, Aka and Manza, where stricter rules have been placed on fisheries and land reclamation compared to other areas, had the highest and third highest sea cucumber population densities among sites, respectively. Holothuria atra was observed at all survey sites and made up the majority of sea cucumber populations at all sites except for Chatan and Sesoko, where Holothuria leucospilota and Stichopus chloronotus were most abundant, respectively. Regarding the relationships between benthic composition and LEC sea cucumber species, S. chloronotus was significantly correlated with dead corals, scleractinian corals, and coralline algae. As well, H. leucospilota had significant correlations with rubble. Although there were no significant correlations between any specific scleractinian coral genus and sea cucumber densities, S. chloronotus was marginally insignificant with Platygyra and Psammocora. Notably, medium- to highly valued species were sparse in our surveys, and most of them appeared at only one site. Additionally, at one site (Odo), only three LEC sea cucumber individuals were observed. Combining these facts with relatively low population densities around the Okinawa Islands compared to densities reported in previous research from the Indo-West Pacific Ocean region, we conclude that Okinawan LEC sea cucumber populations have been and are being impacted by high levels of direct (e.g., overexploitation, as well as coastal development) and indirect anthropogenic pressure (e.g., decreasing water quality). To address the current situation, repeated monitoring and more detailed investigations to reveal the drivers that determine LEC sea cucumber species aggregations and population densities are urgently needed, along with more robust management of remaining LEC sea cucumber populations.

Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae).

Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals.

BACKGROUND: Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. RESULTS: We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, the mtMutS, was found to undergo alternative polyadenylation, and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. CONCLUSIONS: Mt-mRNA processing in octocorals possessing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represent a first step towards understanding its functional and evolutionary implications.

Digitate and capitate soft corals (Cnidaria: Octocorallia: Alcyoniidae) from Western Australia with reports on new species and new Australian geographical records.

We report on digitate and capitate Octocorallia within the genera Parasphaerasclera McFadden & Ofwegen, 2013, Eleutherobia Pütter, 1900, Sphaerasclera McFadden & Ofwegen, 2013, and Paraminabea Williams & Alderslade, 1999 from tropical Western Australian waters. Three new species (Parasphaerasclera kimberleyensis, Eleutherobia australiensis, Eleutherobia imaharai) are described, with a discussion of their taxonomic placement in the light of a recent treatment of the genus Eleutherobia and related taxa by McFadden & Ofwegen (2013). In addition, range extensions for three species are reported, Parasphaerasclera grayi (Thomson & Dean, 1931) known from Indonesia and the Pacific Ocean, Eleutherobia somaliensis Verseveldt & Bayer, 1988 from Somalia, and Eleutherobia splendens (Thomson & Dean, 1931) recorded from Indonesia and the Philippines. Additionally, one new Australian geographical record (Sphaerasclera flammicerebra) (Williams, 2003) with a known distribution from Palau to Mauritius, has been included. We complement morphological taxonomy with molecular data (mtMutS, 28S rDNA) to analyse and clarify phylogenetic placement of these species. The mitochondrial mtMutS phylogeny supported Eleutherobia, Paraminabea, Parasphaerasclera and Sphaerasclera as distinct monophyletic genera. Phylogenetic analyses based on 28S rDNA lacked resolution and were largely unresolved. Additionally, the molecular data corroborated our proposed morphological hypothesis of the placement of the new species P. kimberleyensis sp. nov. with no anthocodial armature in the genus Parasphaerasclera, and the assignment of the new species, E. australiensis sp. nov. and E. imaharai sp. nov., with distinct polyps sclerites in the genus Eleutherobia.

Shallow-water zoantharians (Cnidaria, Hexacorallia) from the Central Indo-Pacific.

Despite the Central Indo-Pacific (CIP) and the Indonesian Archipelago being a well-known region of coral reef biodiversity, particularly in the 'Coral Triangle', little published information is available on its zoantharians (Cnidaria: Hexacorallia: Zoantharia). In order to provide a basis for future research on the Indo-Pacific zoantharian fauna and facilitate comparisons between more well-studied regions such as Japan and the Great Barrier Reef, this report deals with CIP zoantharian specimens in the Naturalis collection in Leiden, the Netherlands; 106 specimens were placed into 24 morpho-species and were supplemented with 88 in situ photographic records from Indonesia, the Philippines, and Papua New Guinea. At least nine morpho-species are likely to be undescribed species, indicating that the region needs more research in order to properly understand zoantharian diversity within the CIP. The Naturalis' zoantharian specimens are listed by species, as well as all relevant collection information, and in situ images are provided to aid in future studies on zoantharians in the CIP.