Hypsibius dujardini
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA20345 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| LMYF01.dat.gz | Other | |||
| LMYF01.fasta.gz | Fasta.gz | |||
| LMYF01.master.dat | Other | |||
| LRSR01.dat.gz | Other |
Items per page: 5 1 - 5 of 209 |
Similar Datasets
Project description:The tardigrade, or water bear, a model Ecdysozoan
| PRJNA20353 | ENA
Project description:Limno-terrestrial tardigrades enter a state called anhydrobiosis when exposed to desiccation, and acquire tolerance against various extreme environments. The anhydrobiotic tardigrade Hypsibius dujardini, is a non-pigmented tardigrade easy to culture and RNAi method have been established, therefore making it a model tardigrade for tardigrade molecular research. Previous genome assemblies of this tardigrade had increased size due to heterozygosity. Here, we have sequenced the genome of H. dujardini using single individual Illumina DNA-Seq data and PacBio long read data, and employed a heterozygosity aware assembly method to assemble a near-complete high quality genome. In order to annotate the genome with gene predictions, we conducted RNA-Sequencing of various stages of developmental, juvenile, adult, and anhydrobiotic stage H. dujardini and Ramazzottius varieornatus, a tardigrade capable of rapid anhydrobiosis entry, and used these data for gene prediction with BRAKER v1.9 or differential gene expression analysis of the active and anhydrobiotic stages.
2017-02-28 | GSE94295 | GEO
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. 126 single embryo samples.
2016-02-18 | E-GEOD-64944 | 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 | GSE64944 | GEO
Project description:Comparative transcriptomics in an anhydrobiotic tardigrade, Hypsibius dujardini, during desiccation treatment
| PRJDB5599 | ENA
Project description:Genome and transcriptome sequencing from a single animal of Hypsibius dujardini
| PRJDB4575 | ENA
Project description:Tardigrades can survive remarkable doses of ionizing radiation, up to about 1000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but damage is repaired. We show that this tardigrade has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme, making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important for tardigrade radiation tolerance. We hypothesize that tardigrades’ ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.
2024-04-12 | GSE240501 | GEO
Project description:Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molecular studies of tardigrades are prone to contamination. To minimize the possibility of microbial contaminations and to obtain high-quality genomic information, we have developed an ultra-low input library sequencing protocol to enable the genome sequencing of a single tardigrade Hypsibius dujardini individual. Here, we describe the details of our sequencing data and the ultra-low input library preparation methodologies.
| S-EPMC4986543 | biostudies-literature
Project description:Hypsibius dujardini Genome sequencing and assembly
| PRJNA298443 | ENA