Lytechinus variegatus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA62407 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR13350800_1.fastq.gz | Fastqsanger.gz | |||
| SRR13350800_2.fastq.gz | Fastqsanger.gz | |||
| SRR13350900_1.fastq.gz | Fastqsanger.gz | |||
| SRR13350900_2.fastq.gz | Fastqsanger.gz |
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Project description:Sea urchins (echinoids) are common model organisms for research in developmental biology and for their transition from a bilateral larva into their post-metamorphic adult with pentaradial body symmetry. The adult also has a calcareous endoskeleton with a multimetameric pattern of continuously added elements, among them the namesake of this phylum, spines. Nearly all echinoids have both large primary spines, and an associated set of smaller secondary spines.We hypothesize that the secondary spines of the tropical variegated urchin species, Lytechinus variegatus, are morphologically and molecularly distinct structures from primary spines and not just small spines. To test this premise, we examined both spine types using light microscopy, micro-CT imaging, lectin labeling, transcriptomics, and fluorescent in situ hybridization (FISH). Our findings reveal basic similarities between the two types in mineral and cellular anatomy, but with clear differences in growth patterns, genes expressed, and in the location of gene expression within the two types of spines. In particular, secondary spines have non-overlapping, longitudinally concentrated growth bands that lead to a blunt and straight profile, and a distinct transcriptome involving the upregulation in many genes in comparison to the primary spines. Neural, ciliary, and extracellular matrix interacting factors are implicated in the differentially expressed gene (DEG) dataset, including two genes - ONECUT2 and an uncharacterized discoidin- and thrombospondin-containing protein - that show spine type- specific localizations in FISH, and may be of interest to ongoing work in urchin spine patterning.These results demonstrate that primary and secondary spines have overlapping but distinct molecular and biomineralized characteristics, suggesting unique developmental and regenerative mechanisms, and devotion to this spiny dermal phylum.
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Project description:The effects of ethanol on developmental gene expression in sea urchins is compared to controls at three time points during gastrulation.
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Project description:Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken during the first 24 hours of development of Lytechinus variegatus (Lv). Developmental trajectories were constructed using Waddington-OT, a computational approach to "stitch" together developmental timepoints. Skeletogenic and primordial germ cell trajectories diverged early in cleavage. Ectodermal progenitors were distinct from other lineages by sixth cleavage, though a small percentage of ectoderm cells briefly co-expressed endoderm markers indicating an early ecto-endoderm cell state, likely in cells originating from the equatorial region of the egg. Endomesoderm cells originated at 6th cleavage also and this state persisted for more than two cleavages, then diverged into distinct endoderm and mesoderm fates asynchronously, with some cells retaining an intermediate specification status until gastrulation. 79 of 80 genes (99%) examined, and included in published developmental gene regulatory networks (dGRNs), are present in the Lv-scRNA-seq dataset, and expressed in the correct lineages in which the dGRN circuits operate.
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Project description:Ethanol-treated Lytechinus variegatus (sea urchin) embryos
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Project description:Using standard morphometric methods and gene expression profiling with a DNA microarray, we explored the impacts of high CO2 conditions on development of the sea urchin, Lytechinus pictus, a pelagic larvae that forms a calcium carbonate endoskeleton. Larvae were raised from fertilization to pluteus stage in seawater with elevated CO2 conditions based upon IPCC emissions scenarios B1 (540ppm CO2) and A1FI (970ppm CO2).
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Project description:Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo
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Project description:BACKGROUND:Matrix-regulated biomineralization involves the specific nucleation and growth of mineral phases within or upon preformed structured organic matrices. We hypothesized that there might be a general mechanism whereby anionic, phosphorylated mineral ion-binding proteins assist in specifically locating the mineral ions with respect to the mineralizing structural organic matrix. Here we extended these studies to invertebrate mineralization in Lytechinus variegatus (Lv) teeth. MATERIALS AND METHODS:The tooth proteins were extracted and the phosphoproteins occluded in the mineral were enriched by passage through a ProQ Diamond phosphoprotein enrichment column, and subjected to MS/MS analysis. A Lv RNA-seq derived transcriptome database was generated. The MS/MS data found 25 proteins previously classified as "Predicted uncharacterized proteins" and many of the spicule matrix proteins. As these 25 proteins were also identified with the transcriptome analysis, and were thus no longer "hypothetical" but real proteins in the Lv tooth. Each protein was analyzed for the presence of a signal peptide, an acidic pI?4, and the ability to be phosphorylated. RESULTS:Four new Lv tooth specific Pro-Ala-rich proteins were found, representing a new class of proteins. CONCLUSION:The tooth is different from the spicules and other urchin skeletal elements in that only the tooth contains both "high" and "very high" magnesium calcite, [Ca(1-X) Mg(X) CO3], where X is the mole fraction of Mg. We speculate that our newly discovered proline-alanine rich proteins, also containing sequences of acidic amino acids, may be involved in the formation of high magnesium and very high magnesium calcite.
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