Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: Novel protein-coding genes, intra-species sequence variations, and trans-spliced RNA leaders

ABSTRACT: 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.

ORGANISM(S): Oikopleura dioica

PROVIDER: GSE64421 | GEO | 2015/07/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: Novel protein-coding genes, intra-species sequence variations, and trans-spliced RNA leaders

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

Spatio-temporal transcriptome maps in the early embryos of Oikopleura dioica

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.

2024-03-16 | GSE139330 | GEO

Genome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica

Project description:Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica and find evidence for proposed functions of SL-trans-splicing. A recent hypothesis postulates that operons facilitate recovery from growth arrested states in metazoans. We examined the expression dynamics of operons across the life-cycle of the animal and during growth arrest recovery. We show that operons do not facilitate recovery from growth arrest in O. dioica. We find that operons are enriched in the germline and that trans-spliced transcripts are predominantly maternal., Interestingly, there is a TOP-like motif in the SL sequence, and trans-splicing in TOP mRNAs, indicating that trans-spliced mRNAs are targets for nutrient-dependent translational control in O. dioica. Total RNA from a number of stages across development were pooled and used in a modified DeepCAGE protocol. A custom designed spliced-leader primer (using the SL exon) was used in the 2nd strand synthesis step.

2015-01-26 | E-GEOD-50849 | biostudies-arrayexpress

Oikopleura dioica

Project description:Oikopleura dioica genome sequencing

| PRJEA42427 | ENA

ChIP-seq in Oikopleura dioica

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.

2021-04-21 | GSE172470 | GEO

Genome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica

2015-01-26 | GSE50849 | GEO