Ontology highlight
ABSTRACT:
PROVIDER: PRJNA885464 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Kunzea spp. endemic to New Zealand Raw sequence reads
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Project description:The Xenopus genus is well known for the high degree of polyploidy observed in its constituent species, but there is minimal information about transcriptional changes observed in these highly polyploid vertebrates. Xenopus andrei, an octoploid species within the Xenopus genus, presents a novel system for assessing a polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through late tailbud stages. Additionally, using Trinity, RNA-seq data from all nine stages was pooled to create a draft de novo assembly of the transcriptome. This represents the first published assembly of an octoploid vertebrate transcriptome. This RNA-Seq and transcriptome data will be useful in comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication in vertebrates.
2018-03-10 | GSE111639 | GEO
Project description:<p>The biogeography of tropical Andean plants and the effects of altitudinal barriers as evolutionary constraints have been the focus of great debate. Although genetic markers have provided evidence for the geographic isolation of Andean-endemic groups, even highly variable molecular markers commonly used to assess biogeography do not have the resolving power needed for a fine geographic discrimination in some Andean taxa. We present a metabolomics approach based on ultrahigh-performance liquid chromatography-mass spectrometry combined with multivariate statistical methods and machine learning algorithms of multiple species and populations of Espeletiinae (Asteraceae) to provide metabolomic evidence for biogeographic segregation in this Andean-endemic subtribe. Our approach allows the discrimination of Espeletiinae taxa at different geographic scales with characteristic metabolic fingerprints related to their country of origin on a global scale, to their páramo massifs on a regional scale and to their páramo complexes on a local scale, revealing inter- and intraspecific metabolic variations. Our results, together with previous studies, suggest that Andean geography and Pleistocene glacial cycles not only shaped the evolutionary history of Espeletiinae but also its metabolic fingerprints, demonstrating the potential of metabolomics for understanding biogeographic patterns in recently diversified plant groups where genetic divergence is still at an early stage.</p><p><br></p><p><strong>Interspecific chemical variability assay</strong> protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS944' rel='noopener noreferrer' target='_blank'><strong>MTBLS944</strong></a>.</p><p><strong>Intraspecific chemical variability assay</strong> protocols and data are reported in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS943' rel='noopener noreferrer' target='_blank'><strong>MTBLS943</strong></a>.</p>
2020-03-24 | MTBLS944 | MetaboLights
Project description:<p>The biogeography of tropical Andean plants and the effects of altitudinal barriers as evolutionary constraints have been the focus of great debate. Although genetic markers have provided evidence for the geographic isolation of Andean-endemic groups, even highly variable molecular markers commonly used to assess biogeography do not have the resolving power needed for a fine geographic discrimination in some Andean taxa. We present a metabolomics approach based on ultrahigh-performance liquid chromatography-mass spectrometry combined with multivariate statistical methods and machine learning algorithms of multiple species and populations of Espeletiinae (Asteraceae) to provide metabolomic evidence for biogeographic segregation in this Andean-endemic subtribe. Our approach allows the discrimination of Espeletiinae taxa at different geographic scales with characteristic metabolic fingerprints related to their country of origin on a global scale, to their páramo massifs on a regional scale and to their páramo complexes on a local scale, revealing inter- and intraspecific metabolic variations. Our results, together with previous studies, suggest that Andean geography and Pleistocene glacial cycles not only shaped the evolutionary history of Espeletiinae but also its metabolic fingerprints, demonstrating the potential of metabolomics for understanding biogeographic patterns in recently diversified plant groups where genetic divergence is still at an early stage.</p><p><br></p><p><strong>Intraspecific chemical variability assay</strong> protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS943' rel='noopener noreferrer' target='_blank'><strong>MTBLS943</strong></a>.</p><p>I<strong>nterspecific chemical variability assay</strong> protocols and data are reported in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS944' rel='noopener noreferrer' target='_blank'><strong>MTBLS944</strong></a>.</p>
2020-03-24 | MTBLS943 | MetaboLights
Project description:The brushtail possum, Trichosurus vulpecula, is threatened in parts of its native range in Australia, but has also become a devastating mammalian pest following introduction into New Zealand from the mid 1800s. We have completed the first chromosome-level assembly of the possum genome and, using nuclear and mitochondrial analyses, traced southern New Zealand possums to distinct Tasmanian and mainland Australian subspecies, which have subsequently hybridised. This admixture is reflected in high levels of genetic diversity within New Zealand populations despite a founding bottleneck. Functional genomics revealed unique adaptations to altricial birth and extending weaning, including novel chemo-sensory genes, and at least four genes with imprinted, parent-specific expression not yet detected in other species (MLH1, EPM2AIP1, UBP1 and GPX7). We found that reprogramming of possum germline imprints and the wider epigenome was similar to eutherian mammals, except onset occurs after birth. Together, our data and analysis is useful for genetic-based control and conservation of possums, and contributes to understanding of the evolution of novel mammalian epigenetic traits such as germline methylation erasure and genomic imprinting.
2022-11-29 | GSE218734 | GEO
Project description:The brushtail possum, Trichosurus vulpecula, is threatened in parts of its native range in Australia, but has also become a devastating mammalian pest following introduction into New Zealand from the mid 1800s. We have completed the first chromosome-level assembly of the possum genome and, using nuclear and mitochondrial analyses, traced southern New Zealand possums to distinct Tasmanian and mainland Australian subspecies, which have subsequently hybridised. This admixture is reflected in high levels of genetic diversity within New Zealand populations despite a founding bottleneck. Functional genomics revealed unique adaptations to altricial birth and extending weaning, including novel chemo-sensory genes, and at least four genes with imprinted, parent-specific expression not yet detected in other species (MLH1, EPM2AIP1, UBP1 and GPX7). We found that reprogramming of possum germline imprints and the wider epigenome was similar to eutherian mammals, except onset occurs after birth. Together, our data and analysis is useful for genetic-based control and conservation of possums, and contributes to understanding of the evolution of novel mammalian epigenetic traits such as germline methylation erasure and genomic imprinting.
2022-11-29 | GSE218695 | GEO