Partial Mitochondrial Genome Sequences of Two Abyssal Sponges (Porifera: Hexactinellida), Bathydorus laniger and Docosaccus maculatus.
Ontology highlight
ABSTRACT:
SUBMITTER: Kahn AS
PROVIDER: S-EPMC5908954 | biostudies-literature | 2018 Apr
REPOSITORIES: biostudies-literature
Publications
Partial Mitochondrial Genome Sequences of Two Abyssal Sponges (Porifera: Hexactinellida), Bathydorus laniger and Docosaccus maculatus.
Kahn Amanda S AS Geller Jonathan B JB
Genome announcements 20180419 16
We announce the nearly complete mitochondrial genome sequences of two hexactinellid sponges, <i>Bathydorus laniger</i> and <i>Docosaccus maculatus</i> A contiguous region of over 15,000 bp was sequenced from each genome. An uncommon structural element was identified as a series of repetitive elements with sequences matching <i>cob</i> in the genome of <i>D. maculatus</i>. ...[more]
Similar Datasets
Project description:BackgroundGlass sponges (Class Hexactinellida) are important components of deep-sea ecosystems and are of interest from geological and materials science perspectives. The reconstruction of their phylogeny with molecular data has only recently begun and shows a better agreement with morphology-based systematics than is typical for other sponge groups, likely because of a greater number of informative morphological characters. However, inconsistencies remain that have far-reaching implications for hypotheses about the evolution of their major skeletal construction types (body plans). Furthermore, less than half of all described extant genera have been sampled for molecular systematics, and several taxa important for understanding skeletal evolution are still missing. Increased taxon sampling for molecular phylogenetics of this group is therefore urgently needed. However, due to their remote habitat and often poorly preserved museum material, sequencing all 126 currently recognized extant genera will be difficult to achieve. Utilizing morphological data to incorporate unsequenced taxa into an integrative systematics framework therefore holds great promise, but it is unclear which methodological approach best suits this task.ResultsHere, we increase the taxon sampling of four previously established molecular markers (18S, 28S, and 16S ribosomal DNA, as well as cytochrome oxidase subunit I) by 12 genera, for the first time including representatives of the order Aulocalycoida and the type genus of Dactylocalycidae, taxa that are key to understanding hexactinellid body plan evolution. Phylogenetic analyses suggest that Aulocalycoida is diphyletic and provide further support for the paraphyly of order Hexactinosida; hence these orders are abolished from the Linnean classification. We further assembled morphological character matrices to integrate so far unsequenced genera into phylogenetic analyses in maximum parsimony (MP), maximum likelihood (ML), Bayesian, and morphology-based binning frameworks. We find that of these four approaches, total-evidence analysis using MP gave the most plausible results concerning congruence with existing phylogenetic and taxonomic hypotheses, whereas the other methods, especially ML and binning, performed more poorly. We use our total-evidence phylogeny of all extant glass sponge genera for ancestral state reconstruction of morphological characters in MP and ML frameworks, gaining new insights into the evolution of major hexactinellid body plans and other characters such as different spicule types.ConclusionsOur study demonstrates how a comprehensive, albeit in some parts provisional, phylogeny of a larger taxon can be achieved with an integrative approach utilizing molecular and morphological data, and how this can be used as a basis for understanding phenotypic evolution. The datasets and associated trees presented here are intended as a resource and starting point for future work on glass sponge evolution.
| S-EPMC5359874 | biostudies-literature
Project description:New Zealand's surrounding deep waters have become known as a diversity hotspot for glass sponges (Porifera: Hexactinellida) in recent years, and description and collection efforts are continuing. Here we report on eight rossellids (Hexasterophora: Lyssacinosida: Rossellidae) collected during the 2017 RV Sonne cruise SO254 by ROV Kiel 6000 as part of Project PoribacNewZ of the University of Oldenburg, Germany. The material includes six species new to science, two of which are assigned to a so far undescribed genus; we further re-describe two previously known species. The known extant rossellid diversity from the New Zealand region is thus almost doubled, from nine species in five genera to 17 species in eight genera. The specimens described here are only a small fraction of hexactinellids collected on cruise SO254. Unfortunately, the first author passed away while working on this collection, only being able to complete the nine descriptions reported here. The paper concludes with an obituary to him, the world-leading expert on glass sponge taxonomy who will be greatly missed.
| S-EPMC8463523 | biostudies-literature
Project description:With the completion of a single unified classification, the Systema Porifera (SP) and subsequent development of an online species database, the World Porifera Database (WPD), we are now equipped to provide a first comprehensive picture of the global biodiversity of the Porifera. An introductory overview of the four classes of the Porifera is followed by a description of the structure of our main source of data for this paper, the WPD. From this we extracted numbers of all 'known' sponges to date: the number of valid Recent sponges is established at 8,553, with the vast majority, 83%, belonging to the class Demospongiae. We also mapped for the first time the species richness of a comprehensive set of marine ecoregions of the world, data also extracted from the WPD. Perhaps not surprisingly, these distributions appear to show a strong bias towards collection and taxonomy efforts. Only when species richness is accumulated into large marine realms does a pattern emerge that is also recognized in many other marine animal groups: high numbers in tropical regions, lesser numbers in the colder parts of the world oceans. Preliminary similarity analysis of a matrix of species and marine ecoregions extracted from the WPD failed to yield a consistent hierarchical pattern of ecoregions into marine provinces. Global sponge diversity information is mostly generated in regional projects and resources: results obtained demonstrate that regional approaches to analytical biogeography are at present more likely to achieve insights into the biogeographic history of sponges than a global perspective, which appears currently too ambitious. We also review information on invasive sponges that might well have some influence on distribution patterns of the future.
| S-EPMC3338747 | biostudies-literature
Project description:Contiguous 14,535 and 14,536 nt near complete mitochondrial genome sequences respectively were obtained for Ostrinia nubilalis and Ostrinia furnicalis. Mitochondrial gene order was identical to that observed from Bombyx. Sequences comparatively showed 186 substitutions (1.3% sequence divergence), 170 CDS substitutions (131 at 3(rd) codon positions), and an excess of transition mutation likely resulting by purifying selection (d(N)/d(S) = omega congruent with 0.15). Overall substitution rates were significantly higher at 4-fold (5.2%) compared to 2-fold degenerate codons (2.6%). These are the 3(rd) and 4(th) lepidopteran mitochondrial genome reference sequences in GenBank and useful for comparative mitochondrial studies.
| S-EPMC1140353 | biostudies-literature
Project description:A holdfast is a root- or basal plate-like structure of principal importance that anchors aquatic sessile organisms, including sponges, to hard substrates. There is to date little information about the nature and origin of sponges' holdfasts in both marine and freshwater environments. This work, to our knowledge, demonstrates for the first time that chitin is an important structural component within holdfasts of the endemic freshwater demosponge Lubomirskia baicalensis. Using a variety of techniques (near-edge X-ray absorption fine structure, Raman, electrospray ionization mas spectrometry, Morgan-Elson assay and Calcofluor White staining), we show that chitin from the sponge holdfast is much closer to ?-chitin than to ?-chitin. Most of the three-dimensional fibrous skeleton of this sponge consists of spicule-containing proteinaceous spongin. Intriguingly, the chitinous holdfast is not spongin-based, and is ontogenetically the oldest part of the sponge body. Sequencing revealed the presence of four previously undescribed genes encoding chitin synthases in the L. baicalensis sponge. This discovery of chitin within freshwater sponge holdfasts highlights the novel and specific functions of this biopolymer within these ancient sessile invertebrates.
| S-EPMC3673046 | biostudies-literature
Project description:New hexactinellid sponges were collected from 2589 m depth on the Carlsberg Ridge in the Indian Ocean during deep-sea dredging. All fragments belong to a new genus and species, Indiellagen. n.ridgenensissp. n., a representative of the family Aulocalycidae described here. The peculiar features of this sponge, not described earlier for other Aulocalycidae, are: longitudinal strands present in several layers and epirhyses channelization.
| S-EPMC3229285 | biostudies-literature
Project description:The present synthesis focuses on the so called 'horny sponges' recorded from marine caves of the Mediterranean Sea. The main aim is to provide a list of all recorded species, diagnostic keys to their identification up to family and genus level, and exhaustive, formally uniform descriptions at the species level contributing to sharing of information on the faunistics and taxonomy of Mediterranean cave-dwelling species, including habitat preferences. The majority of species was recorded in 105 Mediterranean marine caves hosting four orders of horny sponges belonging to 9 families, 19 genera and 40 species. Species endemic to the Mediterranean Sea harboured in marine caves are 14 with an endemicity value of 35%. For each species morphological descriptions are supported by illustrations both original and from the literature, including the diagnostic traits of the skeleton by light and scanning electron microscopy giving further characterization at the specific level. A detailed map together with a list of all caves harbouring horny sponges is also provided with geographic coordinates.
| S-EPMC3677383 | biostudies-literature
Project description:This paper reports on a new species of the Baikal endemic sponge (fam. Lubomirskiidae) Swartschewskia khanaevi sp. nov. The description of this species is based on morphological and molecular data (ITS and mitochondrial IGRs). Morphologically, S. khanaevi sp. nov. differs from S. papyracea by loose tracts arranged in an irregular network as well as the presence on strongyles of compound spines looking like tubercles densely ornamented with simple spines. Moreover, specimens of S. khanaevi sp. nov. show a peculiar structure of the aquiferous system at the body surface that may be an adaptive trait for environmental conditions. Phylogenetic analysis has revealed that S. khanaevi sp. nov. forms a well-supported (0.99) monophyletic clade with S. papyracea and is allocated as its sister taxa.
| S-EPMC6989567 | biostudies-literature
Project description:Despite the large number of reports describing sponge-microbe associations, limited knowledge is available about associated fungi and their relationships with the hosts. In this work, specific fungal strains were obtained directly from in vitro sponge cell cultures (primmorphs) and single sponge cells (cytospins) and compared with those obtained from whole tissue preparations. A total of 27 fungal strains were isolated from the marine sponges Hymeniacidon heliophila and Haliclona melana. Fifteen strains, nine from H. heliophila and six from H. melana, were obtained from whole tissue and were considered as possible mesohyl associated or transient fungi. Twelve strains were isolated from in vitro sponge cell cultures (primmorphs) and were, therefore, considered as cell associated. From these, five different strains were obtained from H. heliophila isolated cells, while five were identified from cytospins and two from primmorphs of H. melana. The fungal strains obtained from cell cultures from both sponge species were different, and none of them were detected in the whole tissue preparations of the same species. Nine H. heliophila and seven H. melana strains shows low similarity with the sequences available in public databases and belong to potentially new species. This is the first report of fungi isolated directly from sponge cells, which allowed the observation and selection of specific strains that probably would not be obtained by usual culture dependent techniques.
| S-EPMC3768729 | biostudies-literature
Project description:Homoscleromorpha is the fourth major sponge lineage, recently recognized to be distinct from the Demospongiae. It contains <100 described species of exclusively marine sponges that have been traditionally subdivided into 7 genera based on morphological characters. Because some of the morphological features of the homoscleromorphs are shared with eumetazoans and are absent in other sponges, the phylogenetic position of the group has been investigated in several recent studies. However, the phylogenetic relationships within the group remain unexplored by modern methods.Here we describe the first molecular phylogeny of Homoscleromorpha based on nuclear (18S and 28S rDNA) and complete mitochondrial DNA sequence data that focuses on inter-generic relationships. Our results revealed two robust clades within this group, one containing the spiculate species (genera Plakina, Plakortis, Plakinastrella and Corticium) and the other containing aspiculate species (genera Oscarella and Pseudocorticium), thus rejecting a close relationship between Pseudocorticium and Corticium. Among the spiculate species, we found affinities between the Plakortis and Plakinastrella genera, and between the Plakina and Corticium. The validity of these clades is furthermore supported by specific morphological characters, notably the type of spicules. Furthermore, the monophyly of the Corticium genus is supported while the monophyly of Plakina is not.As the result of our study we propose to restore the pre-1995 subdivision of Homoscleromorpha into two families: Plakinidae Schulze, 1880 for spiculate species and Oscarellidae Lendenfeld, 1887 for aspiculate species that had been rejected after the description of the genus Pseudocorticium. We also note that the two families of homoscleromorphs exhibit evolutionary stable, but have drastically distinct mitochondrial genome organizations that differ in gene content and gene order.
| S-EPMC3001884 | biostudies-literature