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Dissolved lipidomes of three Chaetoceros diatom host virus systems

ABSTRACT: Dissolved lipidomes from three diatom host-virus pairs. At each time point (T=0, 1, 3, 4, and 21 days), ~20 mL of 0.2 um filtered sample was extracted using Waters HLB SPE cartridges. In 2016, the samples were run on a Q Exactive mass spec with all ion fragmentation. This data was used for quantification. In 2021, the samples were rerun on an Orbitrap ID-X with targeted ms2 for further annotation of putative oxylipins. Methods and interpretation of the oxylipin and free fatty acid data are presented in: Edwards, B.R.; Thamatrakoln, K.; Fredricks, H.F.; Bidle, K.D.; Van Mooy, B.A.S. Viral Infection Leads to a Unique Suite of Allelopathic Chemical Signals in Three Diatom Host Virus Pairs. Mar. Drugs 2024, 22, x. https://doi.org/10.3390/xxxxx

INSTRUMENT(S): Orbitrap ID-X, Exactive

ORGANISM(S): Chaetoceros Tenuissimus Rna Virus Type-ii (ncbitaxon:1516128) Chaetoceros Socialis Forma Radians Rna Virus 1 (ncbitaxon:2169725) Chaetoceros Socialis (ncbitaxon:163503) Chaetoceros Tenuissimus Dna Virus Type-ii (ncbitaxon:1516127) Chaetoceros Tenuissimus (ncbitaxon:426638)

SUBMITTER: Bethanie R Edwards

PROVIDER: MSV000094770 | MassIVE | Wed May 15 13:36:00 BST 2024

REPOSITORIES: MassIVE

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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.

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Dissolved lipidomes of three Chaetoceros diatom host virus systems

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