Comparative genomics of bdelloid rotifers: evaluating the effects of asexuality and desiccation tolerance on genome evolution
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ABSTRACT:
PROVIDER: PRJEB22744 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2135450_1.fastq.gz | Fastqsanger.gz | |||
| ERR2135451_1.fastq.gz | Fastqsanger.gz | |||
| ERR2135451_2.fastq.gz | Fastqsanger.gz | |||
| ERR2135452_1.fastq.gz | Fastqsanger.gz | |||
| ERR2135452_2.fastq.gz | Fastqsanger.gz |
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Project description:Population genomics of bdelloid rotifers
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Project description:Genome sequencing of desiccating bdelloid rotifers
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Project description:Evolutionary dynamics of transposable elements in bdelloid rotifers
| PRJEB39843 | ENA
Project description:Desiccation tolerance has been implicated as an important characteristic that potentiates the spread of the bacterial pathogen Acinetobacter baumannii through hospitals on dry surfaces. Despite the potential importance of this stress response, scarce information is available describing the underlying mechanisms of A. baumannii desiccation tolerance. Here we characterize the factors influencing desiccation survival of A. baumannii. At the macroscale level, we find that desiccation tolerance is influenced by cell density, growth phase, and desiccation medium. Our transcriptome analysis indicates that desiccation represents a unique state for A. baumannii compared to commonly studied growth conditions and strongly influences pathways responsible for proteostasis. Remarkably, we find that an increase in total cellular protein aggregates, which is often considered deleterious, correlates positively with the ability of A. baumannii to survive desiccation. We show that artificially inducing protein aggregate formation increases desiccation survival, and more importantly, that proteins incorporated into cellular aggregates can retain activity. Our results suggest that protein aggregates may promote desiccation tolerance in A. baumannii through preserving and protecting proteins from damage during desiccation until rehydration occurs.
2018-10-27 | GSE111383 | GEO
Project description:BackgroundBdelloid rotifers are micro-invertebrates distributed worldwide, from temperate latitudes to the most extreme areas of the planet like Antarctica or the Atacama Desert. They have colonized any habitat where liquid water is temporarily available, including terrestrial environments such as soils, mosses, and lichens, tolerating desiccation and other types of stress such as high doses of ionizing radiation (IR). It was hypothesized that bdelloid desiccation and radiation resistance may be attributed to their potential ability to repair DNA double-strand breaks (DSBs). Here, these properties are investigated and compared among nine bdelloid species collected from both mild and harsh habitats, addressing the correlation between the ability of bdelloid rotifers to survive desiccation and their capacity to repair massive DNA breakage in a phylogenetically explicit context. Our research includes both specimens isolated from habitats that experience frequent desiccation (at least 1 time per generation), and individuals sampled from habitats that rarely or never experienced desiccation.ResultsOur analysis reveals that DNA repair prevails in somatic cells of both desiccation-tolerant and desiccation-sensitive bdelloid species after exposure to X-ray radiation. Species belonging to both categories are able to withstand high doses of ionizing radiation, up to 1000 Gy, without experiencing any negative effects on their survival. However, the fertility of two desiccation-sensitive species, Rotaria macrura and Rotaria rotatoria, was more severely impacted by low doses of radiation than that of desiccation-resistant species. Surprisingly, the radioresistance of desiccation-resistant species is not related to features of their original habitat. Indeed, bdelloids isolated from Atacama Desert or Antarctica were not characterized by a higher radioresistance than species found in more temperate environments.ConclusionsTolerance to desiccation and radiation are supported as ancestral features of bdelloid rotifers, with a group of species of the genus Rotaria having lost this trait after colonizing permanent water habitats. Together, our results provide a comprehensive overview of the evolution of desiccation and radiation resistance among bdelloid rotifers.
| S-EPMC10080820 | biostudies-literature
Project description:Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga was used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis showed that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis revealed its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improved their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.
2024-01-24 | PXD043051 | Pride
Project description:Desiccation tolerance (DT) allowed seed plants to conquer ecosystems with long periods of limited water availability. This adaptive features allows seeds to remain dried for very long times without losing their ability to germinate. There is little information about all the signaling components required to achieve DT and on how transcription factors (TFs) modulate global DT processes. We performed RNA-seq experiment and carbohydrates profiles of lec1, lec2, fus3 and abi3, as well as their corresponding wild types, at three stages of seed development 15, 17 and 21 DAF (day after open flower) belonging to the seed desiccation period. A complex experimental design approach and regulatory networks prediction were used to identify differentially expressed genes specifically involved in DT process. In order to identify mechanisms involved in the acquisition of DT during seed development, we designed a comparative transcriptomic analysis between the seed desiccation intolerant (DI) mutants lec1-1, abi3-5 and fus3-3, the desiccation tolerant mutant lec2-1 and the desiccation tolerant weak allele of abi3 (abi3-1) with their respective wild type controls. This analysis should allow to identify genes that are differentially expressed in the desiccation intolerant mutants respect to tolerant mutants and WT controls.
2016-09-06 | E-GEOD-76015 | biostudies-arrayexpress
Project description:Characterizing Acinetobacter baumannii desiccation tolerance.
| PRJNA436809 | ENA
Project description:Rotifers of class Bdelloidea have evolved for millions of years apparently without sexual reproduction. We have sequenced 45- to 70-kb regions surrounding the four copies of the hsp82 gene of the bdelloid rotifer Philodina roseola, each of which is on a separate chromosome. The four regions comprise two colinear gene-rich pairs with gene content, order, and orientation conserved within each pair. Only a minority of genes are common to both pairs, also in the same orientation and order, but separated by gene-rich segments present in only one or the other pair. The pattern is consistent with degenerate tetraploidy with numerous segmental deletions, some in one pair of colinear chromosomes and some in the other. Divergence in 1,000-bp windows varies along an alignment of a colinear pair, from zero to as much as 20% in a pattern consistent with gene conversion associated with recombinational repair of DNA double-strand breaks. Although pairs of colinear chromosomes are a characteristic of sexually reproducing diploids and polyploids, a quite different explanation for their presence in bdelloids is suggested by the recent finding that bdelloid rotifers can recover and resume reproduction after suffering hundreds of radiation-induced DNA double-strand breaks per oocyte nucleus. Because bdelloid primary oocytes are in G(1) and therefore lack sister chromatids, we propose that bdelloid colinear chromosome pairs are maintained as templates for the repair of DNA double-strand breaks caused by the frequent desiccation and rehydration characteristic of bdelloid habitats.
| S-EPMC2278229 | biostudies-literature