The complete mitochondrial genome of the Antarctic stalked jellyfish, Haliclystus antarcticus Pfeffer, 1889 (Staurozoa: Stauromedusae).
ABSTRACT: In present study, the complete mitogenome sequence of the Antarctic stalked jellyfish, Haliclystus antarcticus Pfeffer (Staurozoa: Stauromedusae) has been sequenced by next-generation sequencing method. The assembled mitogenome comprises of 15,766 bp including 13 protein coding genes, 7 transfer RNAs, and 2 ribosomal RNA genes. The overall base of Antarctic stalked jellyfish constitutes of 26.5% for A, 19.6% for C, 19.8% for G, 34.1% for T and show 90% identity to Sessile Jelly, Haliclystus sanjuanensis, in the northeastern Pacific Ocean. The complete mitogenome of the Antarctic stalked jellyfish, contributes fundamental and significant DNA molecular data for further phylogeography and evolutionary analysis for seahorse phylogeny. The complete sequence was deposited in DBBJ/EMBL/GenBank under accession number KU947038.
Project description:Staurozoan classification is highly subjective, based on phylogeny-free inferences, and suborders, families, and genera are commonly defined by homoplasies. Additionally, many characters used in the taxonomy of the group have ontogenetic and intraspecific variation, and demand new and consistent assessments to establish their correct homologies. Consequently, Staurozoa is in need of a thorough systematic revision. The aim of this study is to propose a comprehensive phylogenetic hypothesis for Staurozoa, providing the first phylogenetic classification for the group. According to our working hypothesis based on a combined set of molecular data (mitochondrial markers COI and 16S, and nuclear markers ITS, 18S, and 28S), the traditional suborders Cleistocarpida (animals with claustrum) and Eleutherocarpida (animals without claustrum) are not monophyletic. Instead, our results show that staurozoans are divided into two groups, herein named Amyostaurida and Myostaurida, which can be distinguished by the absence/presence of interradial longitudinal muscles in the peduncle, respectively. We propose a taxonomic revision at the family and genus levels that preserves the monophyly of taxa. We provide a key for staurozoan genera and discuss the evolution of the main characters used in staurozoan taxonomy.
Project description:BACKGROUND:Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa-the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but there are currently no published genomes within Staurozoa and Cubozoa. FINDINGS:Here we present 3 new draft genomes of Calvadosia cruxmelitensis (Staurozoa), Alatina alata (Cubozoa), and Cassiopea xamachana (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. CONCLUSIONS:These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.
Project description:The family Eolepadidae is the only stalked barnacle in hydrothermal vent regions. Here, we determined the mitogenome of the eolepadid <i>Vulcanolepas fijiensis</i>. The mitogenome was 17,374?bp long, with 76.6% AT content. Its protein-coding gene organization was identical to that of the deep-sea scalpellid <i>Arcoscalpellum epeeum</i>. On the mitogenomic tree, two scalpellomorphan families (Eolepadidae and Scalpellidae) were monophyletic while the other scalpellomorphan family Pollicipedidae did not form the monophyletic group with them. Further mitogenomic analysis of undetermined taxa in hydrothermal vents is required to deepen our understanding of their phylogenetic relationships.
Project description:BACKGROUND:Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia?+?Octocorallia) - cnidarians with a reproductive polyp and the absence of a medusa stage - and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) - cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. RESULTS:We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia?+?Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae?+?Coronatae], Acraspeda [Cubozoa?+?Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. CONCLUSIONS:Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in these groups are plesiomorphies, originated in the branch leading to Medusozoa. The expansion of mitogenomic data along with improvements in phylogenetic inference methods and use of additional nuclear markers will further enhance our understanding of the phylogenetic relationships and character evolution within Cnidaria.
Project description:The dimorphic alphaproteobacterium Prosthecomicrobium hirschii has both short-stalked and long-stalked morphotypes. Notably, these morphologies do not arise from transitions in a cell cycle. Instead, the maternal cell morphology is typically reproduced in daughter cells, which results in microcolonies of a single cell type. In this work, we further characterized the short-stalked cells and found that these cells have a Caulobacter-like life cycle in which cell division leads to the generation of two morphologically distinct daughter cells. Using a microfluidic device and total internal reflection fluorescence (TIRF) microscopy, we observed that motile short-stalked cells attach to a surface by means of a polar adhesin. Cells attached at their poles elongate and ultimately release motile daughter cells. Robust biofilm growth occurs in the microfluidic device, enabling the collection of synchronous motile cells and downstream analysis of cell growth and attachment. Analysis of a draft P. hirschii genome sequence indicates the presence of CtrA-dependent cell cycle regulation. This characterization of P. hirschii will enable future studies on the mechanisms underlying complex morphologies and polymorphic cell cycles.Bacterial cell shape plays a critical role in regulating important behaviors, such as attachment to surfaces, motility, predation, and cellular differentiation; however, most studies on these behaviors focus on bacteria with relatively simple morphologies, such as rods and spheres. Notably, complex morphologies abound throughout the bacteria, with striking examples, such as P. hirschii, found within the stalked Alphaproteobacteria. P. hirschii is an outstanding candidate for studies of complex morphology generation and polymorphic cell cycles. Here, the cell cycle and genome of P. hirschii are characterized. This work sets the stage for future studies of the impact of complex cell shapes on bacterial behaviors.
Project description:The cnidarian jellyfishes are impressive organisms to show animal mitochondrial genomic diversities. Their mitogenome structure is linear and tRNA content has one or two in numbers, which is highly different than other metazoans. In this study, a complete mitogenome of the ghost jellyfish <i>Cyanea nozakii</i> (Cnidaria, Semaeostomeae, Cyaneidae) was sequenced and analyzed. The mitgenome is 17,381?bp long with 38.5% A, 16.0% C, 13.9% G, and 31.6% T nucleotide distributions. In addition, phylogenetic relationship of <i>C. nozakii</i> in the class Scyphozoa was investigated by using mitochondrial protein coding genes. Due to results, <i>C. nozakii</i> was positioned in the paraphyletic order Semaeostomeae. This is the first complete mitogenome from the genus <i>Cyanea.</i>
Project description:Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of specific developmental stages of C. crescentus -swarmer and stalked cells- to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis. Glucose, the only carbon source in the minimal media M2G was removed from C. crescentus exponential phase cultures, and total RNA was extracted after 30 and 60 minutes of incubation. The controls are cells growing in complete media.
Project description:During animal evolution, ancestral Cnidaria and Bilateria diverged more than 600 million years ago. The nervous systems of extant cnidarians are strongly peptidergic. Neuropeptides have been isolated and sequenced from a few model cnidarians, but a global investigation of the presence of neuropeptides in all cnidarian classes has been lacking. Here, we have used a recently developed software program to annotate neuropeptides in the publicly available genomes and transcriptomes from members of the classes Cubozoa, Scyphozoa, and Staurozoa (which all belong to the subphylum Medusozoa) and contrasted these results with neuropeptides present in the subclass Octocorallia (belonging to the class Anthozoa). We found three to six neuropeptide preprohormone genes in members of the above-mentioned cnidarian classes or subclasses, each coding for several (up to thirty-two) similar or identical neuropeptide copies. Two of these neuropeptide preprohormone genes are present in all cnidarian classes/subclasses investigated, so they are good candidates for being among the first neuropeptide genes evolved in cnidarians. One of these primordial neuropeptide genes codes for neuropeptides having the C-terminal sequence GRFamide (pQGRFamide in Octocorallia; pQWLRGRFamide in Cubozoa and Scyphozoa; pQFLRGRFamide in Staurozoa). The other primordial neuropeptide gene codes for peptides having RPRSamide or closely resembling amino acid sequences. In addition to these two primordial neuropeptide sequences, cnidarians have their own class- or subclass-specific neuropeptides, which probably evolved to serve class/subclass-specific needs. When we carried out phylogenetic tree analyses of the GRFamide or RPRSamide preprohormones from cubozoans, scyphozoans, staurozoans, and octocorallia, we found that their phylogenetic relationships perfectly agreed with current models of the phylogeny of the studied cnidarian classes and subclasses. These results support the early origins of the GRFamide and RPRSamide preprohormone genes.
Project description:For the first time, we illuminate the complete mitochondrial genome (mitogenome) sequence of the <i>Paradiplospinus antarcticus,</i> which is 16,988?bp in size and contains 13 protein-coding (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region.The base composition of the mitogenome is 26.08% A, 26.77% T, 28.46% C and 18.69% G. Here, we selected 11 genera of species from the mostly monotypic snake mackerel family, including representative Antarctic <i>Paradiplospinus antarcticus</i> that have been identified, and constructed phylogenetic trees to better study the snake mackerel family.
Project description:Identification of organisms is traditionally based on the use of "classic" identification keys, normally printed on paper. These keys have several drawbacks: they are mainly based on the systematics, requiring identification of orders, families and genera at first; they are written by experts for other experts, in a specific scientific jargon; they have a "frozen" structure (sequence of theses/antitheses); once published, they cannot be changed or updated without printing a new edition. Due to the use of computers, it is now possible to build new digital identification tools, which: 1) can be produced automatically, if the characters are stored in a database; 2) can be freed from the traditional systematics, giving priority to easy-to-observe characters, incl. those usually uncommon to the classical keys, such as ecology and distribution; 3) can be updated in real time once published on-line; 4) can be available on different media, and on mobile devices. An important feature of these new digital tools is their "collaborative" nature. They can be enriched by the contribution of several researchers, which can cooperate while maintaining rights and property of the resources and data they contribute to the system. JellyWeb, the information system on Scyphozoa, Cubozoa and Staurozoa has been developed in Trieste since 2010. The system was created with the aim of - potentially - becoming a starting point for a wide collaborative effort in developing a user-friendly worldwide digital identification system for jellyfishes.