A Transcriptomic Atlas of Adult Tissues of the Sea Urchin Lytechinus variegatus Identifies Early Transitions in Gonadogenesis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1281404 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ethanol-treated Lytechinus variegatus (sea urchin) embryos
| PRJNA853740 | ENA
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.
2021-09-24 | GSE184538 | GEO
Project description:Sea urchins have been a well-used model of fertilization and of the molecular biology of embryonic development. Our understanding of the molecular identity of adult tissues, on the other hand, has lagged significantly, a deficiency all too apparent with recent successes in mutational analyses in transgenerational studies. Here we focus on the developmental timing of gonadogenesis with particular reference to developmental features of when a juvenile reaches adulthood and begins to make eggs and sperm. We find a large variation in timing of reaching fertility in Lytechinus variegatus such that in 4.5 months, animals that have reached a mass/body ratio and making eggs or sperm. This is correlated with the external metric of opening of the gonadopore, indicative of gametogenesis. We identify a sac-like structure in juveniles that by both morphological and transcriptomic analysis appears to be an indeterminant gonad that transitions into an ovary or testis. We follow this development into adulthood and compare the transcriptomes of gonads and gametes to all 16 major tissues of the adult, revealing a broad definition of the tissue types, and displaying genes that are differentially enriched, and/or specifically expressed by each tissue. These datasets serve as a guide for gene selection in traditional CRISPR/Cas9 mutagenesis, for design of integrated transposase reporters, and for parsing out unique functions in tissues that in combination give this animal its unique attributes.
2025-09-01 | GSE300567 | GEO
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.
2024-05-15 | GSE267428 | GEO
Project description:Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo
| PRJNA765003 | ENA
Project description:Here we present LC-MS/MS proteomic datasets of Heliocidaris erythrogramma, Heliocidaris tuberculata, and Lytechinus variegatus eggs and larvae. We find dramatic proteomic differences likely associated with life history evolution and between developmental stages. This study provides a complimentary dataset to previous transcriptomic analyses of the same three sea urchin species.
2019-03-04 | PXD007065 | Pride
Project description:Genome sequencing for Lytechinus variegatus
| PRJNA62399 | ENA
Project description:Lytechinus variegatus Transcriptome or Gene expression
| PRJNA241187 | ENA