Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft Genome Sequence of the Freshwater Diatom Fragilaria crotonensis SAG 28.96.

ABSTRACT: Here, we report the assembled and annotated genome of the freshwater diatom Fragilaria crotonensis SAG 28.96. The 61.85-Mb nuclear genome was assembled into 879 contigs, has a GC content of 47.40%, contains 26,015 predicted genes, and shows completeness of 81%.

SUBMITTER: Zepernick BN

PROVIDER: S-EPMC9476933 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Draft Genome Sequence of the Freshwater Diatom Fragilaria crotonensis SAG 28.96.

Zepernick Brittany N BN Truchon Alexander R AR Gann Eric R ER Wilhelm Steven W SW

Microbiology resource announcements 20220817 9

Here, we report the assembled and annotated genome of the freshwater diatom Fragilaria crotonensis SAG 28.96. The 61.85-Mb nuclear genome was assembled into 879 contigs, has a GC content of 47.40%, contains 26,015 predicted genes, and shows completeness of 81%. ...[more]

PMID: 35976009

Similar Datasets

Draft Genome Sequence of the Green Alga Scenedesmus acuminatus SAG 38.81.

Project description:Scenedesmus acuminatus, also known as Tetradesmus acuminatus, is a promising green microalga for sustainable production of microalga products, including valuable compounds such as astaxanthin, β-carotene, and lutein, polysaccharides such as β-glucan, and polyunsaturated fatty acids. Here, we report the draft whole-genome sequence of Scenedesmus acuminatus SAG 38.81.

| S-EPMC7291106 | biostudies-literature

De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal.

Project description:Diatoms are a group of eukaryotic microalgae populating almost all aquatic and wet environments. Their abundance and species diversity make these organisms significant contributors to biogeochemical cycles and important components of aquatic ecosystems. Although significant progress has been made in studies of Diatoms (Bacillariophyta) over the last two decades, since the spread of "omics" technologies, our current knowledge of the molecular processes and gene regulatory networks that facilitate environmental adaptation remain incomplete. Here, we present a transcriptome analysis of Fragilaria radians isolated from Lake Baikal. The resulting assembly contains 27,446 transcripts encoding 21,996 putative proteins. The transcriptome assembly and annotation were coupled with quantitative experiments to search for differentially expressed transcripts between (i) exponential growth phase and dark-acclimated cell cultures, and (ii) those changing expression level during the early response to light treatment in dark-acclimated cells. The availability of F. radians genome and transcriptome data provides the basis for future targeted studies of this species. Furthermore, our results extend taxonomic and environmental sampling of Bacillariophyta, opening new opportunities for comparative omics-driven surveys.

| S-EPMC6765018 | biostudies-literature

Growth at the limits: comparing trace metal limitation of a freshwater cyanobacterium (Dolichospermum lemmermannii) and a freshwater diatom (Fragilaria crotonensis).

Project description:Freshwater phytoplankton blooms are increasing in prevalence and there are conflicting views on whether trace metals limit growth of key species and thus bloom formation. The Taupō Volcanic Zone (TVZ), New Zealand, was formed by multiple eruptions of a super-volcano which emitted rhyolitic tephra leaving lakes depleted in trace metals. This provides an opportunity to test the potential of trace metal limitation on freshwater phytoplankton growth under nanomolar concentrations. Growth responses of two algal species isolated from Lake Taupō, Dolichospermum lemmermannii (cyanobacteria) and Fragilaria crotonensis (diatom), to six biologically important trace metals (manganese, iron, zinc, cobalt, copper and molybdenum) were examined in culture experiments. These were conducted at three trace metal concentrations: (1) ambient, (2) two-times ambient, and (3) ten-times ambient concentrations in Lake Taupō. Elevated concentrations of iron significantly increased growth rates and maximum cell densities in D. lemmermannii, whereas no significant concentration dependence was observed for other trace metals. Fragilaria crotonensis showed no significant growth response to elevated concentrations of trace metals. These results highlight the importance of iron as a growth limiting nutrient for cyanobacteria and indicate that even small (twofold) increases in Fe concentrations could enhance cyanobacteria growth rates in Lake Taupō, potentially causing cyanobacterial blooms.

| S-EPMC8748459 | biostudies-literature

Morphological, physiological, and transcriptional responses of the freshwater diatom <i>Fragilaria crotonensis</i> to elevated pH conditions.

Project description:Harmful algal blooms (HABs) caused by the toxin-producing cyanobacteria Microcystis spp., can increase water column pH. While the effect(s) of these basified conditions on the bloom formers are a high research priority, how these pH shifts affect other biota remains understudied. Recently, it was shown these high pH levels decrease growth and Si deposition rates in the freshwater diatom Fragilaria crotonensis and natural Lake Erie (Canada-US) diatom populations. However, the physiological mechanisms and transcriptional responses of diatoms associated with these observations remain to be documented. Here, we examined F. crotonensis with a set of morphological, physiological, and transcriptomic tools to identify cellular responses to high pH. We suggest 2 potential mechanisms that may contribute to morphological and physiological pH effects observed in F. crotonensis. Moreover, we identified a significant upregulation of mobile genetic elements in the F. crotonensis genome which appear to be an extreme transcriptional response to this abiotic stress to enhance cellular evolution rates-a process we have termed "genomic roulette." We discuss the ecological and biogeochemical effects high pH conditions impose on fresh waters and suggest a means by which freshwater diatoms such as F. crotonensis may evade high pH stress to survive in a "basified" future.

| S-EPMC9732472 | biostudies-literature

Complete mitochondrial genome sequence of the freshwater diatom <i>Asterionella formosa</i>.

Project description:We report the complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa. The large 61.9 kb circular sequence encodes 34 proteins and 25 tRNAs that are universally conserved in other sequenced diatoms. We fully resolved a unique 24 kb region containing highly conserved repeated sequence units, possibly collocating with an origin of replication.

| S-EPMC7800273 | biostudies-literature

Draft genome sequence of diatom Synedra acus

Project description:Draft genome sequence of the freshwater araphid pennate diatom Synedra acus from Lake Baikal

| PRJEB30567 | ENA

Draft Genome Sequence of Deinococcus indicus DR1, a Novel Strain Isolated from a Freshwater Wetland.

Project description:Deinococcus indicus strain DR1, a red-pigmented, arsenic- and radiation-resistant bacterium, was isolated from a water sample of the Dadri wetland, Uttar Pradesh, India. Here, we report a draft genome sequence of this strain, which may provide useful information regarding the genes and pathways involved in heavy-metal bioremediation.

| S-EPMC5543649 | biostudies-other

Draft Genome Sequence of the Toxic Freshwater Microcystis aeruginosa Strain PMC 728.11 (Cyanobacteria, Chroococcales).

Project description:Microcystis aeruginosa is one of the major species that cause toxic cyanobacterial blooms in freshwater systems worldwide. Here, we report the draft genome sequence of M. aeruginosa PMC 728.11, a microcystin-producing cyanobacterium isolated from the freshwater reservoir of Juanon in Valence, France. The genome sequence contains 276 contigs, consisting of 5,536,025 bp and 5,594 putative protein-coding genes, among which are several biosynthetic gene clusters encoding enzyme complexes involved in the production of various bioactive and toxic metabolites.

| S-EPMC7686424 | biostudies-literature

Fragilaria crotonensis strain:SAG 28.96

Project description:Genome of the freshwater diatom Fragilaria crotonensis SAG 28.96

| PRJNA807324 | ENA

Draft Genome Sequence of the Psychrotolerant Bacterium Methylobacterium sp. Strain BTF04, Isolated from Freshwater in Antarctica.

Project description:Methylobacterium sp. strain BTF04, a pink-pigmented psychrotolerant bacterium, was isolated from freshwater on Barton Peninsula, King George Island, Antarctica. Here, we report the assembled draft genome sequence of Methylobacterium sp. strain BTF04.

| S-EPMC7242663 | 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