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RNA-Seq analysis of developmental, juvenile, and anhydrobiotic stages of Hypsibius dujardini and Ramazzottius varieornatus

ABSTRACT: RNA-Seq analysis of developmental, juvenile, and anhydrobiotic stages of Hypsibius dujardini and Ramazzottius varieornatus

OTHER RELATED OMICS DATASETS IN: GSE94295

PROVIDER: PRJNA369262 | ENA |

REPOSITORIES: ENA

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RNA-Seq analysis of developmental, juvenile, and anhydrobiotic stages of Hypsibius dujardini and Ramazzottius varieornatus

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

RNA-Seq analysis of juvenile stages of Ramazzottius varieornatus

Project description:Tardigrades are microscopic organisms, famous for their tolerance against extreme environments. The establishment of rearing systems of multiple species has allowed for comparison of tardigrade physiology, in particular in embryogenesis. Interestingly, in-lab cultures of limnic species showed smaller variation in hatching timing than terrestrial species, suggesting a hatching regulation mechanism acquired by adaptation to their habitat. To this end, we screened for coordinated gene expression during the development of two species of tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, and observed induction of the arthropod molting pathway. Exposure of ecdysteroids and juvenile hormone analog affected egg hatching but not embryonic development in only the limnic H. exemplaris. These observations suggest a hatching regulation mechanism by the molting pathway in H. exemplaris.

2019-10-31 | GSE130111 | GEO

Ramazzottius varieornatus

Project description:Ramazzottius varieornatus genome

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Project description:Ramazzottius varieornatus overview

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Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus.

Project description:Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.

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Time-course RNA-Seq analysis of UVC exposed Ramazzottius varieornatus.

Project description:Time-course RNA-Seq analysis of Ramazzottius varieornatus exposed to UVC for up to 72 hours

2022-03-25 | GSE152753 | GEO

Transcriptome analysis of the extremotolerant Ramazzottius varieornatus exposed to 60Co gamma ray

Project description:Transcriptome sequencing of Ramazzottius varieornatus exposed to 500Gy gamma ray.

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Project description:Hypsibius dujardini Genome sequencing and assembly