Oikopleura dioica
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA12900 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR090297_1.fastq.gz | Fastqsanger.gz | |||
| DRR090297_2.fastq.gz | Fastqsanger.gz | |||
| DRR090298_1.fastq.gz | Fastqsanger.gz | |||
| DRR090298_2.fastq.gz | Fastqsanger.gz |
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Project description:Genome-wide transcriptional responses to benzo[a]pyrene and clofibrate in the tunicate Oikopleura dioica
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Project description:Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we identified several homeobox transcription factors expressed during early OE patterning. Among these are two Pax3/7 duplicates that we named Pax37A and Pax37B. The vertebrate homologs, PAX3 and PAX7 are involved in developmental processes related to neural crest and muscles. In the ascidian tunicate Ciona intestinalis, Pax3/7 is playing a role in the development of cells deriving from the neural plate border, including trunk epidermal sensory neurons and tail nerve cord neurons, as well as in the neural tube closure. Here we have investigated the roles of Oikopleura dioica Pax37A and Pax37B in the development of the OE, using CRISPR-Cas9 mutant lines and analyzing scRNA-seq data from wild-type animals that we compared with scRNA-seq data from C. intestinalis. We revealed that Pax37B but not Pax37A is essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Trajectory analysis supports that these cells have a neuroepithelial-like transcriptional signature. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features such as “glue” secreting collocytes of ascidians. Their development seems to be controlled by a fragmented GRN that also operates in ascidian epidermal neurons.
2024-03-21 | GSE255790 | GEO
Project description:The appendicularian, Oikopleura dioica, is a marine or planktonic tunicate that has a swimming tadpole shape through its entire life. For several reasons, this animal possesses advantages as a model organisms: (1) It has a short life cycle (about 5 days at 20℃); (2) Its development is rapid and it completes organogenesis within 10 hour of post-fertilization to form functional body; (3) its morphogenesis and cell linages are well-described; (4) live imaging of embryos by introducing fluorescent protein mRNAs is feasible; (5) RNAi method is available for knockdown of zygotic mRNA as well as maternal mRNAs in the ovary and eggs. (6) It has a compact and sequenced genome of 70 Mb, the smallest ever found in chordate. The number of genes is estimated as approximately 18,000, indicating a high gene density (one gene per 5 kb in the genome). These features make O. dioica a useful organism to study development and genome plasticity in tunicate with short generation time, namely, rapidly evolving chordate lineage. Two stages: egg and larvae, two biological replicates
2015-07-23 | E-GEOD-64421 | biostudies-arrayexpress
Project description:ChIP-seq was used to generate chromatin state maps, profile binding patterns of key architectural proteins and locate putative enhancer regions in the early development (TB stage) and developing gonads of the marine chrodate Oikopleura dioica.
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Project description:The larvacean, Oikopleura dioica, is a planktonic chordate and belongs to tunicate that is the closest relative to vertebrates. Its simple and transparent body, invariant embryonic cell lineages and short life cycle of five days make it a promising model organism for research in developmental biology. The genome browser, OikoBase, has been established in 2013 using Norwegian O. dioica. However, genome information of other populations is not available, despite that many researchers have used local populations. In the present study, we sequenced genome of O. dioica of a southwestern Japanese population using RNA-Seq data. These RNA-Seq data covers expressions in 8 cell and 12 hours post fertilization (HPF) embryos of Animal(A), Vegetal(V) and whole-embryo regions, as well as whole embryo of 13 stages, including OD_STAGE01 (unfertilized egg), OD_STAGE02 (fertilized egg), OD_STAGE03 (2-cell), OD_STAGE04 (4-cell), OD_STAGE05 (8-cell), OD_STAGE06 (16-cell), OD_STAGE07 (32-cell), OD_STAGE08 (1.5 hours post fertilization), OD_STAGE09 (2.5 hours post fertilization, tadpole larvae), OD_STAGE10 (3 hours post fertilization, hatched larvae), OD_STAGE11 (5 hours post fertilization, early organogenesis), OD_STAGE12 (8 hours post fertilization, late organogenesis), OD_STAGE13 (10 hours post fertilization, juvenile), Adult male and Adult female. These genome assembly, transcript assembly, and transcript models are incorporated into the ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and blast searches. The genome and transcriptome resources will be useful datasets for developmental biology, evolutionary biology and molecular ecology using this model organism.
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