Global patterns and rates of habitat transitions across the eukaryotic tree of life
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB45931 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6454470.fastq.gz | Fastqsanger.gz | |||
| ERR6454461.fastq.gz | Fastqsanger.gz | |||
| ERR6454471.fastq.gz | Fastqsanger.gz | |||
| ERR6454462.fastq.gz | Fastqsanger.gz | |||
| ERR6454472.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.
| S-EPMC9525238 | biostudies-literature
Project description:Habitat preference and diversification rates in a speciose lineage of diving beetles
| PRJEB36931 | ENA
Project description:Changes in protein synthesis and degradation rates, transcript, protein and phytohormone abundance of 99 targets using qPCR and LC-MS parallel reaction monitoring (PRM) were measured in the transitions between optimal growth conditions (homeostasis), fully induced pattern triggered immunity (PTI) and back in Arabidopsis thaliana, chronologically. Protein turnover rates play an important role in the tryptophan and glucosinolate biosynthesis and photosynthesis associated (PAP) proteins. Most transcripts returned to normal levels 3 to 16 hours post elicitation, while protein levels remained at fully induced PTI levels up to 16 hours into the transitory phase back to optimal growth. Same measurements in the myc234 background revealed an important role of these transcription factors in the immune response including effects on protein turnover rates.
2023-10-13 | PXD041215 | Pride
Project description:Cryoconite habitat bacteria Metagenome
| PRJNA819567 | ENA
Project description:Open-habitat chat phylogenomics
| PRJEB58431 | ENA
Project description:The first analyses of gene sequence data indicated that the eukaryotic tree of life consisted of a long stem of microbial groups "topped" by a crown-containing plants, animals, and fungi and their microbial relatives. Although more recent multigene concatenated analyses have refined the relationships among the many branches of eukaryotes, the root of the eukaryotic tree of life has remained elusive. Inferring the root of extant eukaryotes is challenging because of the age of the group (?1.7-2.1 billion years old), tremendous heterogeneity in rates of evolution among lineages, and lack of obvious outgroups for many genes. Here, we reconstruct a rooted phylogeny of extant eukaryotes based on minimizing the number of duplications and losses among a collection of gene trees. This approach does not require outgroup sequences or assumptions of orthology among sequences. We also explore the impact of taxon and gene sampling and assess support for alternative hypotheses for the root. Using 20 gene trees from 84 diverse eukaryotic lineages, this approach recovers robust eukaryotic clades and reveals evidence for a eukaryotic root that lies between the Opisthokonta (animals, fungi and their microbial relatives) and all remaining eukaryotes.
| S-EPMC3376375 | biostudies-literature
Project description:An unexpectedly large fraction of genes in metazoans (human, mouse, zebrafish, worm, fruit fly) express high levels of circularized RNAs containing canonical exons. Here we report that circular RNA isoforms are found in diverse species whose most recent common ancestor existed more than one billion years ago: fungi (Schizosaccharomyces pombe and Saccharomyces cerevisiae), a plant (Arabidopsis thaliana), and protists (Plasmodium falciparum and Dictyostelium discoideum). For all species studied to date, including those in this report, only a small fraction of the theoretically possible circular RNA isoforms from a given gene are actually observed. Unlike metazoans, Arabidopsis, D. discoideum, P. falciparum, S. cerevisiae, and S. pombe have very short introns (∼ 100 nucleotides or shorter), yet they still produce circular RNAs. A minority of genes in S. pombe and P. falciparum have documented examples of canonical alternative splicing, making it unlikely that all circular RNAs are by-products of alternative splicing or 'piggyback' on signals used in alternative RNA processing. In S. pombe, the relative abundance of circular to linear transcript isoforms changed in a gene-specific pattern during nitrogen starvation. Circular RNA may be an ancient, conserved feature of eukaryotic gene expression programs.
| S-EPMC3946582 | biostudies-literature
Project description:The switch between biological states during key life-history transitions requires major reprogramming at the behavioural level that is under the control of the brain. In this study we focused on major life-history transitions in bumblebee queens (Bombus terrestris) that involve switching from virgin to mated and reproductively mature. To reveal the molecular processes underpinning the behavioural changes that accompany these transitions, we characterised the neurogenomic state of queens that succeeded or failed in making these transitions. Analyses of shared transcription patterns suggested that failures are associated with larger molecular signatures than successes. This was observed at the level of total numbers of differentially expressed genes (DEGs) and proportions of these genes that were up-regulated, and applies to both mating and reproductive maturation. ‘Failed Reproductive’ queens were the most distinct phenotype, associated with the highest number of DEGs (1,578) and two networks of co-expressed genes. Mating status influenced gene expression the least, followed by the transition between the two successful phenotypes (mating to reproductive maturation) and reproductive maturation. However, this pattern was not mirrored in terms of functional specialisations, for Gene Ontology (GO) terms, KEGG pathways and co-expression networks associated with DEGs. Out of the 21 highly connected (hub) genes associated with co-expression networks, 9 are involved in neural processes and 4 are regulators of gene expression. This study shows that different life-history transitions trigger distinct molecular profiles, within a single caste of a eusocial insect. Failure to surmount key life-history transitions has the largest effect on a queen’s neurogenomic state, and it triggers a massive overall up-regulation of gene expression. Hence, failure is an important outcome that must be taken into account when analysing the molecular regulation of important life-history transitions.
2017-10-27 | GSE92730 | GEO
Project description:High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes--generically known as restriction site associated DNA sequencing (RAD-seq)--is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for nonmodel species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting "neutral" elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced representation data are available (including transcriptomes and neutral RAD-seq data sets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods.
| S-EPMC4700943 | biostudies-literature
Project description: Not available
| S-EPMC3979859 | biostudies-literature