Capsaspora owczarzaki
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD002342
PROVIDER: PRJNA290432 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Recent evidence that the unicellular ancestor of animals had a complex repertoire of genes linked to multicellular processes suggests that changes in the regulatory genome, rather than gene innovation, were key to the origin of animals. Here, we carry out multiple functional genomic assays in Capsaspora owczarzaki, the unicellular relative of animals with the largest known gene repertoire for transcriptional regulation. We show that changing chromatin states, differential lincRNA expression and dynamic cis-regulatory sites are associated with life cycle transitions in Capsaspora. Moreover, we demonstrate conservation of animal developmental transcription factor networks and extensive network interconnection in this premetazoan organism. In contrast, however, Capsaspora lacks animal promoter types and its regulatory sites are small, proximal and lack signatures of animal enhancers. Overall, our results indicate that the emergence of animal multicellularity was linked to a major shift in genome regulatory complexity, most notably the appearance of distal enhancer regulation.
2018-10-24 | PXD002342 | Pride
Project description:Cell-specific regulation of protein levels and activity is essential for the distribution of functions among multiple cell types in animals. The finding that many genes involved in these regulatory processes have a premetazoan origin raises the intriguing possibility that the mechanisms required for spatially regulated cell differentiation evolved prior to the appearance of animals. Here, we use high-throughput proteomics in Capsaspora owczarzaki, a close unicellular relative of animals, to characterize the dynamic proteome and phosphoproteome profiles of three temporally distinct cell types in this premetazoan species. We show that life-cycle transitions are linked to extensive proteome and phosphoproteome remodeling and that they affect key genes involved in animal multicellularity, such as transcription factors and tyrosine kinases. The observation of shared features between Capsaspora and metazoans indicates that elaborate and conserved phosphosignaling and proteome regulation supported temporal cell-type differentiation in the unicellular ancestor of animals.
2016-11-30 | PXD004567 | Pride
Project description:The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants was a major evolutionary event that has transformed our planet. So far lack of genome information on unicellular charophyte algae hinders our understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
2019-11-21 | GSE123850 | GEO
Project description:The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants was a major evolutionary event that has transformed our planet. So far lack of genome information on unicellular charophyte algae hinders our understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
2019-11-21 | GSE123851 | GEO
Project description:The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants was a major evolutionary event that has transformed our planet. So far lack of genome information on unicellular charophyte algae hinders our understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
2019-11-21 | GSE123849 | GEO
Project description:The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants was a major evolutionary event that has transformed our planet. So far lack of genome information on unicellular charophyte algae hinders our understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
2019-11-21 | GSE123848 | GEO
Project description:Vertebrates have highly methylated genomes at CpG positions while most invertebrates have sparsely methylated genomes. Therefore, hypermethylation is considered a major innovation that shaped the genome and the regulatory roles of DNA methylation in vertebrates. However, here we report that the marine sponge Amphimedon queenslandica, belonging to one of the earliest branching animal lineages, has evolved a hypermethylated genome with remarkable similarities to that of a vertebrate. Despite major differences in genome size and architecture, independent acquisition of hypermethylation reveal common distribution patterns and repercussions for genome regulation between both lineages. Genome wide depletion of CpGs is counterbalanced by CpG enrichment at unmethylated promoters, mirroring CpG islands. Furthermore, a subset of CpG-bearing transcription factor motifs are enriched at Amphimedon unmethylated promoters. We find that the animal-specific transcription factor NRF has conserved methyl-sensitivity over 700 million years, indicating an ancient cross-talk between transcription factors and DNA methylation. Finally, the sponge shows vertebrate-like levels of 5-hydroxymethylcytosine, the oxidative derivative of cytosine methylation involved in active demethylation. Hydroxymethylation is concentrated in regions that are enriched for transcription factor motifs and show developmentally dynamic demethylation. Together, these findings push back the links between DNA methylation and its regulatory roles to the early steps of animal evolution. Thus, the Amphimedon methylome challenges the prior hypotheses about the origins of vertebrate genome hypermethylation and its implications for regulatory complexity.
2019-08-02 | GSE124016 | GEO
Project description:What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. To shed light into the origin and evolution of the vertebrate regulatory genome, we have generated an unprecedented transcriptomic and epigenomic resource for the non-duplicated genome of the European amphioxus, a closely related invertebrate chordate. These data include RNA-seq for more than 35 developmental stages and adult tissues, CAGE-seq, ChIP-seq, bisulphite-seq and ATAC-seq for several developmental stages and adult tissues. By comparing these data sets with equivalent novel and previously available data for various vertebrate species, especially zebrafish, we uncovered multiple conserved and vertebrate-specific regulatory landmarks. We first identify a conserved chordate phylotypic stage, a developmental period in which different chordate species show the highest gene expression similarity. We also shed light on the origin of enhancer demethylation in vertebrates, by identifying, for the first time in an invertebrate species, differentially methylated enhancers. Furthermore, we show that conserved clusters of co-expressed and tissue-specific genes display similar enrichments for cis-regulatory motifs between amphioxus and vertebrates. Finally, we study the impact of vertebrate WGDs on the evolution of gene regulation, providing the first genome-wide quantitative assessment of sub-functionalization and neo-functionalization processes after the vertebrate WGDs; changing the way in which these evolutionary mechanisms have been traditionally understood.
2018-08-15 | GSE106372 | GEO