Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Improved High-Quality Draft Genome Sequence of the Eurypsychrophile Rhodotorula sp. JG1b, Isolated from Permafrost in the Hyperarid Upper-Elevation McMurdo Dry Valleys, Antarctica.

ABSTRACT: Here, we report the draft genome sequence of Rhodotorula sp. strain JG1b, a yeast that was isolated from ice-cemented permafrost in the upper-elevation McMurdo Dry Valleys, Antarctica. The sequenced genome size is 19.39 Mb, consisting of 156 scaffolds and containing a total of 5,625 predicted genes. This is the first known cold-adapted Rhodotorula sp. sequenced to date.

SUBMITTER: Goordial J

PROVIDER: S-EPMC4796114 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Improved High-Quality Draft Genome Sequence of the Eurypsychrophile Rhodotorula sp. JG1b, Isolated from Permafrost in the Hyperarid Upper-Elevation McMurdo Dry Valleys, Antarctica.

Goordial Jacqueline J Raymond-Bouchard Isabelle I Riley Robert R Ronholm Jennifer J Shapiro Nicole N Woyke Tanja T LaButti Kurt M KM Tice Hope H Amirebrahimi Mojgan M Grigoriev Igor V IV Greer Charles C Bakermans Corien C Whyte Lyle L

Genome announcements 20160317 2

Here, we report the draft genome sequence of Rhodotorula sp. strain JG1b, a yeast that was isolated from ice-cemented permafrost in the upper-elevation McMurdo Dry Valleys, Antarctica. The sequenced genome size is 19.39 Mb, consisting of 156 scaffolds and containing a total of 5,625 predicted genes. This is the first known cold-adapted Rhodotorula sp. sequenced to date. ...[more]

PMID: 26988035

Similar Datasets

Draft Genome Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica.

Project description:A draft genome sequence was assembled and annotated of the basidiomycetous yeast Rhodotorula sp. strain CCFEE 5036, isolated from Antarctic soil communities. The genome assembly is 19.07 megabases and encodes 6,434 protein-coding genes. The sequence will contribute to understanding the diversity of fungi inhabiting polar regions.

| S-EPMC7118180 | biostudies-literature

Accelerated thermokarst formation in the McMurdo Dry Valleys, Antarctica.

Project description:Thermokarst is a land surface lowered and disrupted by melting ground ice. Thermokarst is a major driver of landscape change in the Arctic, but has been considered to be a minor process in Antarctica. Here, we use ground-based and airborne LiDAR coupled with timelapse imaging and meteorological data to show that 1) thermokarst formation has accelerated in Garwood Valley, Antarctica; 2) the rate of thermokarst erosion is presently ~ 10 times the average Holocene rate; and 3) the increased rate of thermokarst formation is driven most strongly by increasing insolation and sediment/albedo feedbacks. This suggests that sediment enhancement of insolation-driven melting may act similarly to expected increases in Antarctic air temperature (presently occurring along the Antarctic Peninsula), and may serve as a leading indicator of imminent landscape change in Antarctica that will generate thermokarst landforms similar to those in Arctic periglacial terrains.

| S-EPMC3721085 | biostudies-other

Cryostratigraphy and the sublimation unconformity in permafrost from an ultraxerous environment, University Valley, McMurdo Dry Valleys of Antarctica.

Project description:The cryostratigraphy of permafrost in ultraxerous environments is poorly known. In this study, icy permafrost cores from University Valley (McMurdo Dry Valleys, Antarctica) were analyzed for sediment properties, ground-ice content, types and distribution of cryostructures and presence of unconformities. No active layer exists in the valley, but the ice table, a sublimation unconformity, ranges from 0 to 60 cm depth. The sediments are characterized as a medium sand, which classifies them as low to non-frost susceptible. CT scan images of the icy permafrost cores revealed composite cryostructures that included the structureless, porous visible, suspended and crustal types. These cryostructures were observed irrespective of ground-ice origin (vapour deposited and freezing of snow meltwater), suggesting that the type and distribution of cryostructures could not be used as a proxy to infer the mode of emplacement of ground ice. Volumetric ice content derived from the CT scan images underestimated measured volumetric ice content, but approached measured excess ice content. A paleo-sublimation unconformity could not be detected from a change in cryostructures, but could be inferred from an increase in ice content at the maximum predicted ice table depth. This study highlights some of the unique ground ice processes and cryostructures in ultraxerous environments.

| S-EPMC7380095 | biostudies-literature

Drivers of solar radiation variability in the McMurdo Dry Valleys, Antarctica.

Project description:Annually averaged solar radiation in the McMurdo Dry Valleys, Antarctica has varied by over 20?W?m-2 during the past three decades; however, the drivers of this variability are unknown. Because small differences in radiation are important to water availability and ecosystem functioning in polar deserts, determining the causes are important to predictions of future desert processes. We examine the potential drivers of solar variability and systematically eliminate all but stratospheric sulfur dioxide. We argue that increases in stratospheric sulfur dioxide increase stratospheric aerosol optical depth and decrease solar intensity. Because of the polar location of the McMurdo Dry Valleys (77-78°S) and relatively long solar ray path through the stratosphere, terrestrial solar intensity is sensitive to small differences in stratospheric transmissivity. Important sources of sulfur dioxide include natural (wildfires and volcanic eruptions) and anthropogenic emission.

| S-EPMC5864877 | biostudies-other

Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica.

Project description:In the McMurdo Dry Valleys of Antarctica, microorganisms colonize the pore spaces of exposed rocks and are thereby protected from the desiccating environmental conditions on the surface. These cryptoendolithic communities have received attention in microscopy and culture-based studies but have not been examined by molecular approaches. We surveyed the microbial biodiversity of selected cryptoendolithic communities by analyzing clone libraries of rRNA genes amplified from environmental DNA. Over 1,100 individual clones from two types of cryptoendolithic communities, cyanobacterium dominated and lichen dominated, were analyzed. Clones fell into 51 relatedness groups (phylotypes) with > or =98% rRNA sequence identity (46 bacterial and 5 eucaryal). No representatives of Archaea were detected. No phylotypes were shared between the two classes of endolithic communities studied. Clone libraries based on both types of communities were dominated by a relatively small number of phylotypes that, because of their relative abundance, presumably represent the main primary producers in these communities. In the lichen-dominated community, three rRNA sequences, from a fungus, a green alga, and a chloroplast, of the types known to be associated with lichens, accounted for over 70% of the clones. This high abundance confirms the dominance of lichens in this community. In contrast, analysis of the supposedly cyanobacterium-dominated community indicated, in addition to cyanobacteria, at least two unsuspected organisms that, because of their abundance, may play important roles in the community. These included a member of the alpha subdivision of the Proteobacteria that potentially is capable of aerobic anoxygenic photosynthesis and a distant relative of Deinococcus that defines, along with other Deinococcus-related sequences from Antarctica, a new clade within the Thermus-Deinococcus bacterial phylogenetic division.

| S-EPMC165166 | biostudies-literature

McMurdo Dry Valleys

Project description:McMurdo Dry Valleys Raw sequence reads

| PRJNA527658 | ENA

McMurdo dry valleys

Project description:McMurdo dry valleys | Raw sequence reads

| PRJNA788986 | ENA

Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica.

Project description:Bacteria are assumed to disperse widely via aerosolized transport due to their small size and resilience. The question of microbial endemicity in isolated populations is directly related to the level of airborne exogenous inputs, yet this has proven hard to identify. The ice-free terrestrial ecosystem of Antarctica, a geographically and climatically isolated continent, was used to interrogate microbial bio-aerosols in relation to the surrounding ecology and climate. High-throughput sequencing of bacterial ribosomal RNA (rRNA) genes was combined with analyses of climate patterns during an austral summer. In general terms, the aerosols were dominated by Firmicutes, whereas surrounding soils supported Actinobacteria-dominated communities. The most abundant taxa were also common to aerosols from other continents, suggesting that a distinct bio-aerosol community is widely dispersed. No evidence for significant marine input to bioaerosols was found at this maritime valley site, instead local influence was largely from nearby volcanic sources. Back trajectory analysis revealed transport of incoming regional air masses across the Antarctic Plateau, and this is envisaged as a strong selective force. It is postulated that local soil microbial dispersal occurs largely via stochastic mobilization of mineral soil particulates.

| S-EPMC3907674 | biostudies-literature

Endolithic Fungal Species Markers for Harshest Conditions in the McMurdo Dry Valleys, Antarctica.

Project description:The microbial communities that inhabit lithic niches inside sandstone in the Antarctic McMurdo Dry Valleys of life's limits on Earth. The cryptoendolithic communities survive in these ice-free areas that have the lowest temperatures on Earth coupled with strong thermal fluctuations, extreme aridity, oligotrophy and high levels of solar and UV radiation. In this study, based on DNA metabarcoding, targeting the fungal Internal Transcribed Spacer region 1 (ITS1) and multivariate statistical analyses, we supply the first comprehensive overview onto the fungal diversity and composition of these communities sampled over a broad geographic area of the Antarctic hyper-arid cold desert. Six locations with surfaces that experience variable sun exposure were sampled to compare communities from a common area across a gradient of environmental pressure. The Operational Taxonomic Units (OTUs) identified were primarily members of the Ascomycota phylum, comprised mostly of the Lecanoromycetes and Dothideomycetes classes. The fungal species Friedmanniomyces endolithicus, endemic to Antarctica, was found to be a marker species to the harshest conditions occurring in the shady, south exposed rock surfaces. Analysis of community composition showed that sun exposure was an environmental property that explained community diversity and structured endolithic colonization.

| S-EPMC7175349 | biostudies-literature

Further characterization of glycine-containing microcystins from the McMurdo dry Valleys of Antarctica.

Project description:Microcystins are hepatotoxic cyclic peptides produced by several cyanobacterial genera worldwide. In 2008, our research group identified eight new glycine-containing microcystin congeners in two hydro-terrestrial mat samples from the McMurdo Dry Valleys of Eastern Antarctica. During the present study, high-resolution mass spectrometry, amino acid analysis and micro-scale thiol derivatization were used to further elucidate their structures. The Antarctic microcystin congeners contained the rare substitution of the position-1 ᴅ-alanine for glycine, as well as the acetyl desmethyl modification of the position-5 Adda moiety (3S-amino-9S-methoxy-2S,6,8S-trimethyl-10-phenyldeca-4E,6E-dienoic acid). Amino acid analysis was used to determine the stereochemistry of several of the amino acids and conclusively demonstrated the presence of glycine in the microcystins. A recently developed thiol derivatization technique showed that each microcystin contained dehydrobutyrine in position-7 instead of the commonly observed N-methyl dehydroalanine.

| S-EPMC4344637 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data