Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna.

ABSTRACT: Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from homogenized guts of 4 days starved zooplankton Daphnia magna. Here we report the draft genome of this bacterium, which comprises 7,677,812 bp and 7505 predicted protein-coding genes.

SUBMITTER: Poehlein A

PROVIDER: S-EPMC4748535 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna.

Poehlein Anja A Freese Heike H Daniel Rolf R Simeonova Diliana D DD

Standards in genomic sciences 20160209

Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from homogenized guts of 4 days starved zooplankton Daphnia magna. Here we report the draft genome of this bacterium, which comprises 7,677,812 bp and 7505 predicted protein-coding genes. ...[more]

PMID: 26865909

Similar Datasets

Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna.

Project description:The phosphite assimilating bacterium, P. glucosidilyticus DD6b, was isolated from the gut of the zooplankton Daphnia magna. Its 3,872,381 bp high-quality draft genome is arranged into 93 contigs containing 3311 predicted protein-coding and 41 RNA-encoding genes. This genome report presents the specific properties and common features of P. glucosidilyticus DD6b genome in comparison with the genomes of P. glucosidilyticus type strain DSM 23,534, and another five Pedobacter type strains with publicly available completely sequenced genomes. Here, we present the first journal report on P. glucosidilyticus genome sequence and provide information on a new specific physiological determinant of P. glucosidilyticus species.

| S-EPMC4642753 | biostudies-literature

Biodegradation mechanism of 1H-1,2,4-triazole by a newly isolated strain Shinella sp. NJUST26.

Project description:The highly recalcitrant 1H-1,2,4-triazole (TZ) is widely used in the synthesis of agricultural pesticide and considered to be an environmental pollutant. In this study, a novel strain NJUST26 capable of utilizing TZ as the sole carbon and nitrogen source, was isolated from TZ-contaminated soil, and identified as Shinella sp. The biodegradation assays suggested that optimal temperature and pH for TZ degradation by NJUST26 were 30 °C and 6-7, respectively. With the increase of initial TZ concentration from 100 to 320 mg L(-1), the maximum volumetric degradation rate increased from 29.06 to 82.96 mg L(-1) d(-1), indicating high tolerance of NJUST26 towards TZ. TZ biodegradation could be accelerated through the addition of glucose, sucrose and yeast extract at relatively low dosage. The main metabolites, including 1,2-dihydro-3H-1,2,4-triazol-3-one (DHTO), semicarbazide and urea were identified. Based on these results, biodegradation pathway of TZ by NJUST26 was proposed, i.e., TZ was firstly oxidized to DHTO, and then the cleavage of DHTO ring occurred to generate N-hydrazonomethyl-formamide, which could be further degraded to biodegradable semicarbazide and urea.

| S-EPMC4951651 | biostudies-literature

Draft genome sequence data and analysis of Shinella sp. strain JR1-6 isolated from nitrate- and radionuclide-contaminated groundwater in Russia.

Project description:Shinella sp. strain JR1-6 is a Gram-negative, facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium isolated from radionuclide- and nitrate-contaminated groundwater. This bacterium reduces nitrate to N2. Strain JR1-6 has potential for removal of nitrate contamination, which is the main reason for the interest in sequencing its genome. Here, we present a set of features of Shinella sp. strain JR1-6, together with the description of its genomic sequencing and annotation. The draft genome of strain JR1-6 has a size of ?7.09 Mb and contains 6,945 genes, including 62 RNA genes. In the genome of strain JR1-6, the genes were revealed encoding nitrate reduction to N2, as well as the genes associated with metal resistance, showing its adaptation to the conditions of the environment and possible role in nitrate removal from contaminated groundwater. The draft genome sequence of Shinella sp. strain JR1-6 is available at DDBJ/EMBL/GenBank under the accession no. SHMI00000000.

| S-EPMC6695273 | biostudies-literature

DNMT3.1 controls trade-offs between growth, reproduction, and life span under starved conditions in Daphnia magna.

Project description:The cladoceran crustacean Daphnia has long been a model of energy allocation studies due to its important position in the trophic cascade of freshwater ecosystems. However, the loci for controlling energy allocation between life history traits still remain unknown. Here, we report CRISPR/Cas-mediated target mutagenesis of DNA methyltransferase 3.1 (DNMT3.1) that is upregulated in response to caloric restriction in Daphnia magna. The resulting biallelic mutant is viable and did not show any change in growth rate, reproduction, and longevity under nutrient rich conditions. In contrast, under starved conditions, the growth rate of this DNMT3.1 mutant was increased but its reproduction was reciprocally reduced compared to the wild type when the growth and reproduction activities competed during a period from instar 4 to 8. The life span of this mutant was significantly shorter than that of the wild type. We also compared transcriptomes between DNMT3.1 mutant and wild type under nutrient-rich and starved conditions. Consistent with the DNMT3.1 mutant phenotypes, the starved condition led to changes in the transcriptomes of the mutant including differential expression of vitellogenin genes. In addition, we found upregulation of the I am not dead yet (INDY) ortholog, which has been known to shorten the life span in Drosophila, explaining the shorter life span of the DNMT3.1 mutant. These results establish DNMT3.1 as a key regulator for life span and energy allocation between growth and reproduction during caloric restriction. Our findings reveal how energy allocation is implemented by selective expression of a DNMT3 ortholog that is widely distributed among animals. We also infer a previously unidentified adaptation of Daphnia that invests more energy for reproduction than growth under starved conditions.

| S-EPMC8016896 | biostudies-literature

Complete Genome Sequences of Kinneretia sp. Strain XES5, Shinella sp. Strain XGS7, and Vogesella sp. Strain XCS3, Isolated from Xenopus laevis Skin.

Project description:Here, we report the genome sequences of three bacterial isolates, Kinneretia sp. strain XES5, Shinella sp. strain XGS7, and Vogesella sp. strain XCS3, which were cultured from skin of adult female laboratory-bred Xenopus laevis.

| S-EPMC8675264 | biostudies-literature

A novel (S)-6-hydroxynicotine oxidase gene from Shinella sp. strain HZN7.

Project description:Nicotine is an important environmental toxicant in tobacco waste. Shinella sp. strain HZN7 can metabolize nicotine into nontoxic compounds via variations of the pyridine and pyrrolidine pathways. However, the catabolic mechanism of this variant pathway at the gene or enzyme level is still unknown. In this study, two 6-hydroxynicotine degradation-deficient mutants, N7-M9 and N7-W3, were generated by transposon mutagenesis. The corresponding mutant genes, designated nctB and tnp2, were cloned and analyzed. The nctB gene encodes a novel flavin adenine dinucleotide-containing (S)-6-hydroxynicotine oxidase that converts (S)-6-hydroxynicotine into 6-hydroxy-N-methylmyosmine and then spontaneously hydrolyzes into 6-hydroxypseudooxynicotine. The deletion and complementation of the nctB gene showed that this enzyme is essential for nicotine or (S)-6-hydroxynicotine degradation. Purified NctB could also convert (S)-nicotine into N-methylmyosmine, which spontaneously hydrolyzed into pseudooxynicotine. The kinetic constants of NctB toward (S)-6-hydroxynicotine (Km = 0.019 mM, kcat = 7.3 s(-1)) and nicotine (Km = 2.03 mM, kcat = 0.396 s(-1)) indicated that (S)-6-hydroxynicotine is the preferred substrate in vivo. NctB showed no activities toward the R enantiomer of nicotine or 6-hydroxynicotine. Strain HZN7 could degrade (R)-nicotine into (R)-6-hydroxynicotine without any further degradation. The tnp2 gene from mutant N7-W3 encodes a putative transposase, and its deletion did not abolish the nicotine degradation activity. This study advances the understanding of the microbial diversity of nicotine biodegradation.

| S-EPMC4178596 | biostudies-literature

Assembly of Olivibacter sp. Strain UJ_SKK_5.1 Genome Sequence, Isolated from Metagenomes of Macrotermes bellicosus Guts Collected from Hot, Arid Nigeria.

Project description:The metagenome-assembled genome sequence of Olivibacter sp. strain UJ_SKK_5.1 was generated from the metagenome of a Macrotermes bellicosus (termites) gut collected from Nigeria's hot, arid environment. The assembled genome (6,135,249 bp) contains 432 contigs, with an N50 value of 22,779 bp, GC content of 41.1%, 5,043 protein-coding sequences, 5,034 proteins with functional assignments, and 9 pseudogenes and 48 RNA genes.

| S-EPMC9670977 | biostudies-literature

Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna.

Project description:BACKGROUND:Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, climate change, and antagonistic interactions with predators and parasites, which have all been demonstrated to induce micro-evolutionary and adaptive responses. Although its ecology and evolutionary biology is intensively studied, little is known on the functional genomics underpinning of phenotypic responses to environmental stressors. The aim of the present study was to find genes expressed in presence of environmental stressors, and target such genes for single nucleotide polymorphic (SNP) marker development. RESULTS:We developed three expressed sequence tag (EST) libraries using clonal lineages of D. magna exposed to ecological stressors, namely fish predation, parasite infection and pesticide exposure. We used these newly developed ESTs and other Daphnia ESTs retrieved from NCBI GeneBank to mine for SNP markers targeting synonymous as well as non synonymous genetic variation. We validate the developed SNPs in six natural populations of D. magna distributed at regional scale. CONCLUSIONS:A large proportion (47%) of the produced ESTs are Daphnia lineage specific genes, which are potentially involved in responses to environmental stress rather than to general cellular functions and metabolic activities, or reflect the arthropod's aquatic lifestyle. The characterization of genes expressed under stress and the validation of their SNPs for population genetic study is important for identifying ecologically responsive genes in D. magna.

| S-EPMC3146954 | biostudies-literature

Annotation of the Daphnia magna nuclear receptors: comparison to Daphnia pulex.

Project description:Most nuclear receptors (NRs) are ligand-dependent transcription factors crucial in homeostatic physiological responses or environmental responses. We annotated the Daphnia magna NRs and compared them to Daphnia pulex and other species, primarily through phylogenetic analysis. Daphnia species contain 26 NRs spanning all seven gene subfamilies. Thirteen of the 26 receptors found in Daphnia species phylogenetically segregate into the NR1 subfamily, primarily involved in energy metabolism and resource allocation. Some of the Daphnia NRs, such as RXR, HR96, and E75 show strong conservation between D. magna and D. pulex. Other receptors, such as EcRb, THRL-11 and RARL-10 have diverged considerably and therefore may show different functions in the two species. Curiously, there is an inverse association between the number of NR splice variants and conservation of the LBD. Overall, D. pulex and D. magna possess the same NRs; however not all of the NRs demonstrate high conservation indicating the potential for a divergence of function.

| S-EPMC4186893 | biostudies-literature

Hierarchical Assessment of Mutation Properties in Daphnia magna.

Project description:Understanding the context-dependence of spontaneous mutations is crucial to predicting evolutionary trajectories. In this experiment, the impact of genetic background and trait-type on mutational susceptibility was investigated. Mutant and non-mutant lines of six unique genotypes from two populations of Daphnia magna were phenotypically assayed using a common-garden experiment. Morphological, life-history, and behavioral traits were measured and estimates of the mutation parameters were generated. The mutation parameters varied between the populations and among genotypes, suggesting differential susceptibility to mutation depending upon genomic background. Traits also varied in their susceptibility to mutation with behavioral traits evolving more rapidly than life-history and morphological traits. These results may reflect the unique selection histories of these populations.

| S-EPMC6222573 | biostudies-other

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