Amphimedon queenslandica
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA316591 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3306030_1.fastq.gz | Fastqsanger.gz | |||
| SRR3306030_2.fastq.gz | Fastqsanger.gz | |||
| SRR3306040_1.fastq.gz | Fastqsanger.gz | |||
| SRR3306040_2.fastq.gz | Fastqsanger.gz | |||
| SRR3306031_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Phototransduction in a marine sponge provides insights into the origin of animal vision
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Project description:Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica
2014-01-24 | GSE54364 | GEO
Project description:Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica
2014-01-24 | E-GEOD-54364 | biostudies-arrayexpress
Project description:Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage, however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum, including a segmented worm, a flatworm, a roundworm, a water bear, a fruitfly, a sea urchin, a zebrafish, a sea anemone, a sponge, and a comb jelly. For each species, we collected the embryonic transcriptomes at ~100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly, we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation, and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes, also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility.
2016-02-18 | GSE60483 | GEO
Project description:A marine sponge native to the Great Barrier Reef off the coast of Australia
| PRJNA43557 | ENA
Project description:Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This âphylotypic stageâ has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a âzootypicâ stage, however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum, including a segmented worm, a flatworm, a roundworm, a water bear, a fruitfly, a sea urchin, a zebrafish, a sea anemone, a sponge, and a comb jelly. For each species, we collected the embryonic transcriptomes at ~100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly, we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation, and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes, also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. 124 single embryo samples.
2016-02-18 | E-GEOD-60483 | biostudies-arrayexpress
Project description:Poriferans, like the demosponge Amphimedon queenslandica, are the earliest diverging metazoans and may hold the key to understanding the evolution of metazoan pathways. A. queenslandica exhibits a biphasic lifecycle, with free-swimming larvae and sessile adult stages. To study changes in the transcriptome during this period of morphological and ecological transition, we generated poly(A) fragment libraries for A. queenslandica at four developmental stages: precompetent and competent larvae, postlarvae, and adult. These libraries were sequenced using Applied Biosystems SOLiD technology. This study provides the most comprehensive analysis to date of gene expression in the sponge. It has elucidated the genes that define the two main phases of the sponge lifestyle and identified genes that are important for competence and metamorphosis. More importantly, this study has provided insights into the expression of the genes that characterize metazoan features, such as cell adhesion and differentiation, in an early metazoan.
2012-07-10 | GSE29978 | GEO
Project description:We report a comprehensive DNA accessibility profile of the Demosponge species Amphimedon queenslandica using Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) through six embryonic developmental stages, a larval stage and adult stage. We assessed the dynamics of chromatin accessibility and identified 40,218 consensus peaks, 4,751 of them were differentially accessible in at least one developmental stage. Cis-regulatory elements were more dynamically regulated while proximal elements were more likely to be constitutively active. Furthermore, we identify a shift towards repressive chromatin in mid and late developmental stages which coincide with the increase in expression of genes of Metazoan origin. Finally, we show that cis-regulatory regions are differentially enriched in different Transcription Factor binding sites (TFBS) which demarcate three main stages of development and importantly, they are predictive of cis-regulatory regions in other animal species but not in Capsaspora owczarzaki, a close relative of animals.
2021-10-10 | E-MTAB-10203 | biostudies-arrayexpress
Project description:Poriferans, like the demosponge Amphimedon queenslandica, are the earliest diverging metazoans and may hold the key to understanding the evolution of metazoan pathways. A. queenslandica exhibits a biphasic lifecycle, with free-swimming larvae and sessile adult stages. To study changes in the transcriptome during this period of morphological and ecological transition, we generated poly(A) fragment libraries for A. queenslandica at four developmental stages: precompetent and competent larvae, postlarvae, and adult. These libraries were sequenced using Applied Biosystems SOLiD technology. This study provides the most comprehensive analysis to date of gene expression in the sponge. It has elucidated the genes that define the two main phases of the sponge lifestyle and identified genes that are important for competence and metamorphosis. More importantly, this study has provided insights into the expression of the genes that characterize metazoan features, such as cell adhesion and differentiation, in an early metazoan. 4 stages sequenced: precompetent larvae, competent larvae, postlarvae, adult
2012-07-10 | E-GEOD-29978 | biostudies-arrayexpress
Project description:Horizontal gene transfer (HGT) is common between prokaryotes and phagotrophic eukaryotes. In metazoans, the scale and significance of HGT remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. Marine sponges (Porifera), which host many microorganisms in their tissues and lack an isolated germ line, are potential carriers of genes transferred from prokaryotes. In this study, we identified a number of potential horizontally transferred genes within the genome of the sponge, Amphimedon queenslandica. We further identified homologs of some of these genes in other sponges. The transferred genes, most of which possess catalytic activity for carbohydrate or protein metabolism, have assimilated host genome characteristics and are actively expressed. The diversity of functions contributed by the horizontally transferred genes is likely an important factor in the adaptation and evolution of A. queenslandica. These findings highlight the potential importance of HGT on the success of sponges in diverse ecological niches.
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