Ontology highlight
ABSTRACT:
PROVIDER: PRJNA749176 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67X coverage, Sample GSM1551550). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that virtually all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, accurate, and can be applied to many species.
2017-03-24 | GSE95797 | GEO
Project description:Three Draft Single-Cell Genomes Sequences of Novel SAR324 Strains Isolated from the Abyssopelagic Southern Ocean
| PRJEB47084 | ENA
Project description:Bathymodiolin mussels are a group of bivalves associated with deep-sea reducing habitats, such as hydrothermal vents and cold seeps. These mussels usually engage in an obligatory symbiosis with sulfur and/or methane oxidizing Gammaproteobacteria. In addition to these bacteria, Bathymodiolus heckerae that inhabit gas and oil seeps in Campeche Bay, the southern Gulf of Mexico, host bacteria phylogenetically with the Cycloclasticus genus. We recently discovered the capability for short-chain alkane degradation in draft genomes of symbiotic Cycloclasticus. With proteomics, we investigated whether the genes required for this process are expressed by the symbionts.
2016-12-05 | PXD005351 | Pride
Project description:The Antarctic krill provides central ecosystems services to the Southern Ocean grazing on autotroph and heterotoph diet and constituting the dominant food source for higher trophic levels. Moreover, E. superba's extensive equipment with biomacromolecule hydrolysing enzymes represents a largely untapped resource for applied purposes. The proteome compendium of krill provides a valuable basis for future studies on krill biology (e.g., metabolism, development, migration behaviour), for krill's contribution to organic matter turnover in the Southern Ocean, as well as for multilevel biotechnological prospecting.
2022-09-28 | PXD033602 | Pride
Project description:The Antarctic krill provides central ecosystems services to the Southern Ocean grazing on autotroph and heterotoph diet and constituting the dominant food source for higher trophic levels. Moreover, E. superba's extensive equipment with biomacromolecule hydrolysing enzymes represents a largely untapped resource for applied purposes. The proteome compendium of krill provides a valuable basis for future studies on krill biology (e.g., metabolism, development, migration behaviour), for krill's contribution to organic matter turnover in the Southern Ocean, as well as for multilevel biotechnological prospecting.
2022-09-28 | PXD033775 | Pride
Project description:The Antarctic krill provides central ecosystems services to the Southern Ocean grazing on autotroph and heterotoph diet and constituting the dominant food source for higher trophic levels. Moreover, E. superba's extensive equipment with biomacromolecule hydrolysing enzymes represents a largely untapped resource for applied purposes. The proteome compendium of krill provides a valuable basis for future studies on krill biology (e.g., metabolism, development, migration behaviour), for krill's contribution to organic matter turnover in the Southern Ocean, as well as for multilevel biotechnological prospecting
2022-09-28 | PXD033594 | Pride
Project description:The Antarctic krill provides central ecosystems services to the Southern Ocean grazing on autotroph and heterotoph diet and constituting the dominant food source for higher trophic levels. Moreover, E. superba's extensive equipment with biomacromolecule hydrolysing enzymes represents a largely untapped resource for applied purposes. The proteome compendium of krill provides a valuable basis for future studies on krill biology (e.g., metabolism, development, migration behaviour), for krill's contribution to organic matter turnover in the Southern Ocean, as well as for multilevel biotechnological prospecting.
2022-09-28 | PXD033597 | Pride
Project description:The Antarctic krill provides central ecosystems services to the Southern Ocean grazing on autotroph and heterotoph diet and constituting the dominant food source for higher trophic levels. Moreover, E. superba's extensive equipment with biomacromolecule hydrolysing enzymes represents a largely untapped resource for applied purposes. The proteome compendium of krill provides a valuable basis for future studies on krill biology (e.g., metabolism, development, migration behaviour), for krill's contribution to organic matter turnover in the Southern Ocean, as well as for multilevel biotechnological prospecting.
2022-09-28 | PXD033601 | Pride
Project description:Nicotiana benthamiana is an important model organism and representative of the Solanaceae (Nightshade) family. N. benthamiana has a complex ancient allopolyploid genome with 19 chromosomes, and an estimated genome size of 3.1Gb. Several draft assemblies of the N. benthamiana genome have been generated, however, many of the gene-models in these draft assemblies appear incorrect. Here we present a nearly non-redundant database of improved N. benthamiana gene-models based on gene annotations from well-annotated genomes in the Nicotiana genus. We show that the new predicted proteome is more complete than the previous proteomes and more sensitive and accurate in proteomics applications, while maintaining a reasonable low gene number (~43,000). As a proof-of-concept we use this proteome to compare the leaf extracellular (apoplastic) proteome to a total extract of leaves. Several gene families are more abundant in the apoplast. For one of these apoplastic protein families, the subtilases, we present a phylogenetic analysis illustrating the utility of this database. Besides proteome annotation, this database will aid the research community with improved target gene selection for genome editing and off-target prediction for gene silencing.
2019-10-09 | PXD010435 | Pride
Project description:Iron and light are typically recognized as major limiting factors controlling phytoplankton growth in the Southern Ocean. Recent field-based evidence suggests, however, that manganese concentrations in this region can be low enough to impact phytoplankton physiology and primary productivity. Our study examined the interactive influence of combined iron and manganese deprivation on protein expression and photophysiology in Phaeocystis antarctica, a key Antarctic phytoplankter, and provide taxon-specific proteomic evidence that natural Southern Ocean Phaeocystis populations regularly experience stress due to combined low manganese and iron availability. In culture, combined low iron and manganese induced large scale changes in the Phaeocystis proteome and resulted in reorganization of key components of the photosynthetic apparatus; these differences were largely distinct from those arising from changes in irradiance. These results implicate manganese availability as an important driver of Southern Ocean productivity and demonstrate the utility of peptide mass spectrometry as a tool for mapping of manganese contributions to HNLC conditions in this region.
2019-06-25 | PXD010974 | Pride