Comparative genomic hybridization of Emiliania huxleyi infected with coccolithovirus to investigate EhV-99B1 strain diversity
Ontology highlight
ABSTRACT:
ORGANISM(S): Emiliania huxleyi
SUBMITTER: Michael Allen
PROVIDER: E-MAXD-23 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Use of microarrays to assess viral diversity: from genotype to phenotype.
Allen Michael J MJ Martinez-Martinez Joaquin J Schroeder Declan C DC Somerfield Paul J PJ Wilson William H WH
Environmental microbiology 20070401 4
The diversity among the coccolithovirus strains held in the Plymouth Virus Collection (PVC) was assessed using three complementary techniques: phylogeny based on DNA polymerase and major capsid protein gene sequence; host range; and a new, microarray-based genome-wide approach. The PVC is composed of three groups of strains that are geographically and temporally distinct. Virus strains clustered according to these groups in all three diversity assessments. Furthermore, the microarray approach ba ...[more]
Similar Datasets
Project description:The coccolithoviruses contained within the Plymouth Virus Collection (PVC) were screened for genomic content using a microarray. The diversity in genomic content was assessed for twelve strains: EhV-86, on which the microarray is based; EhV-84, EhV-88, EhV-163, EhV-V2, EhV-201, EhV-202, EhV-205, EhV-206, EhV-207, EhV-208 and EhV-209. A direct labelling method was employed to label each virus' genomic DNA which was hybridised onto a separate microarray slides.
2013-01-30 | E-MAXD-11 | biostudies-arrayexpress
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2013-01-30 | E-MAXD-8 | biostudies-arrayexpress
Project description:Transcription profiling of haploid and diploid Emiliania huxleyi growing into N limitation
2014-10-01 | E-MTAB-2274 | biostudies-arrayexpress
Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling. Transcriptomes were collected for diatom cultures harvested at the onset of stationary phase in low nitrate media (55 M-NM-<M NaNO3, 212 M-NM-<M Na2SiO3, 72.4 M-NM-<M NaH2PO4) or during mid-exponential growth in nutrient-replete media (882 M-NM-<M NaNO3, 106 M-NM-<M Na2SiO3, 36.2 M-NM-<M NaH2PO4) in artificial seawater, maintaining three biological replicates per condition and per diatom (N=18). The SOLiD sequencer (version 4) was used to generate the transcriptomes and the SEAStAR software package was used to process the SOLiD reads and to calculate gene counts. Pooled counts for the nitrate-limited treatment were normalized to pooled counts for the nutrient-replete M-bM-^@M-^\controlM-bM-^@M-^] treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor.
2014-03-25 | E-GEOD-56132 | biostudies-arrayexpress
Project description:Animal and plant genomes produce numerous small RNAs (smRNAs) regulating gene expression affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 53 plant-like target sites in 51,917 genes. We assembled a transcriptome of 58,649 genes and determined differentially expressed genes (DEGs) between treatments. Heat stress was found to produce a much larger number of DEGs than other treatments. Analysis of DEGs also revealed that minicircle-encoded photosynthesis proteins seem to be common targets of transcriptional regulation. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally. Symbiodinium cultures were treated with nine different conditions: cold shock, cold stress, heat stress, heat shock, hyposalinity, hypersalinity, dark stress, dark cycle and control.
2013-12-31 | E-GEOD-47373 | biostudies-arrayexpress
Project description:Animal and plant genomes produce numerous small RNAs (smRNAs) regulating gene expression affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 53 plant-like target sites in 51,917 genes. We assembled a transcriptome of 58,649 genes and determined differentially expressed genes (DEGs) between treatments. Heat stress was found to produce a much larger number of DEGs than other treatments. Analysis of DEGs also revealed that minicircle-encoded photosynthesis proteins seem to be common targets of transcriptional regulation. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally. Symbiodinium cultures were treated with nine different conditions: cold shock, cold stress, heat stress, heat shock, hyposalinity, hypersalinity, dark stress, dark cycle and control.
2013-12-31 | E-GEOD-47372 | biostudies-arrayexpress
Project description:Haploid (1N) and diploid (2N) cells of Emiliania huxley (RCC 1217/1216) were grown under 50 and 300 µmol photons m-2 s-1. Differential gene expression was assessed between the ploidy stages at same irradiance and between the light treatments of same strains.
2010-10-01 | E-MEXP-2896 | biostudies-arrayexpress
Project description:Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and Analysis of Sequence Counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. K-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability < 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes. Axenic T. pseudonana CCMP 1335 was grown at 14°C under 24 hour light (120 µmol photons m-2 s-1) after Dyhrman et al. (2012) in f/2 plus silica chelated media made from surface Sargasso Sea water. Nitrate, silica, vitamins, and trace metals were at f/2 concentrations (Guillard and Ryther 1962), while iron and phosphate were modified across treatments. In brief, triplicate cultures of replete (36 µM PO4, 400 nM Fe), P-limited (0.4 µM PO4, 400 nM Fe), Fe-limited (36 µM PO4, 40 nM Fe), and Co-limited (0.4 µM PO4, 40 nM Fe) treatments were harvested when growth deviated from the replete control. Growth was monitored by cell counts. Biomass was harvested onto 0.2 µm filters and flash frozen in liquid nitrogen and total RNA was extracted as described in Dyhrman et al. (2012). Tag-seq sequencing of the transcriptome was performed by Illumina with a polyA selection and NlaIII digestion, resulting in 21 bp sequence reads or tags (Dyhrman et al., 2012). Libraries were of varied sizes as follows: replete (~12 million), P-limited (~13 million), Fe-limited (~23 million), and Co-limited (~26 million). Tags were mapped to gene models (predicted protein coding regions) with a pipeline designed by Genesifter Inc., requiring 100% identity and covering 9759 genes. Tag counts within a gene were pooled and normalized to the size of the library, with resulting data expressed in tags per million (tpm). Genes with normalized tag counts less than 2.5 tpm for each of the four treatments were excluded (Figure S1) , leaving 7380 genes in the analysis.
2013-01-01 | E-GEOD-40509 | biostudies-arrayexpress
Project description:Diatoms are important primary producers in the world’s oceans, yet their growth is constrained in large regions by low bioavailable iron (Fe). Low Fe-induced limitation of primary production is due to requirements for Fe in components of essential metabolic pathways including photosynthesis and other chloroplast plastid functions. Studies have shown that under Fe-limited stress, diatoms alter plastid-specific processes, including components of electron transport. These physiological changes suggest changes of protein content and their abundance within the diatom plastid. While in-silico predictions provide putative information on plastid-localized proteins, knowledge of diatom plastid proteins remains limited in comparison to model photosynthetic organisms. To characterize proteins enriched in diatom plastids we have used shotgun proteomics to assess the proteome of subcellular plastid-enriched fractions from Thalassiosira pseudonana. To improve our understanding of how the plastid proteome is remodeled in response to Fe limitation, proteome sequencing has been performed on T. pseudonana grown under Fe replete and limited conditions. These analyses have shown that Fe limitation regulates major metabolic pathways in the plastid, including the Calvin cycle, as well as changes in light harvesting protein expression. In-silico localization predictions of proteins identified in this plastid-enriched proteome allowed for an in-depth comparison of theoretical vs observed plastid-localization, providing evidence for the potential of additional protein import pathways into the diatom plastid.
2023-08-04 | PXD040824 | Pride
Project description:Investigation of the genetic diversity of Emiliania huxleyi, genomic DNA from 15 different strains were compared with the genomic DNA of the sequenced E. huxleyi strain CCMP1516. Gephyrocapsa oceanica and Isochrysis galbana as phylogenetic closely related taxa were used as out-groups.
2010-03-01 | E-MEXP-2388 | biostudies-arrayexpress