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Aureococcus anophagefferens (Pelagophyceae) genomes improve evaluation of nutrient acquisition strategies involved in brown tide dynamics

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms)
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Construction and comparative analysis of mitochondrial genome in the brown tide forming alga Aureococcus anophagefferens (Pelagophyceae, Ochrophyta)
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The state of algal genome quality and diversity
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Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
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Suspension feeding by the Atlantic slipper limpet (Crepidula fornicata) and the northern quahog (Mercenaria mercenaria) in the presence of cultured and wild populations of the harmful brown tide alga, Aureococcus anophagefferens
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Ecosystem disruptive algal blooms of the brown tide species, Aureococcus anophagefferens and Aureoumbra lagunensis
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Emergence of brown tides caused by Aureococcus anophagefferens Hargraves et Sieburth in China
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Resolving the intra-specific succession within Cochlodinium polykrikoides populations in southern Korean coastal waters via use of quantitative PCR assays
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Utilization of various forms of nitrogen and expression regulation of transporters in the harmful alga Heterosigma akashiwo (Raphidophyceae)
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Transcriptome responses of the dinoflagellate Karenia mikimotoi driven by nitrogen deficiency
inferredcites →https://doi.org/10.1016/j.isci.2018.12.035openalex-snapshot
Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae
inferredcites →https://doi.org/10.1016/j.virol.2014.06.031openalex-snapshot
Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host–virus coevolution
inferredcites →https://doi.org/10.1016/j.virol.2014.07.023openalex-snapshot
Attenuation of virus production at high multiplicities of infection in Aureococcus anophagefferens
inferredcites →https://doi.org/10.1016/s0025-326x(00)00170-3openalex-snapshot
Brown Tides and Mariculture in Saldanha Bay, South Africa
inferredcites →https://doi.org/10.1029/ce035p0229openalex-snapshot
Role of environmental variables, specifically organic compounds and micronutrients, in the growth of the chrysophyte Aureococcus anophagefferens
inferredcites →https://doi.org/10.1038/ismej.2014.146openalex-snapshot
Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages
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Pan genome of the phytoplankton Emiliania underpins its global distribution
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KBase: The United States Department of Energy Systems Biology Knowledgebase
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Fast gapped-read alignment with Bowtie 2
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Comparative genomics reveals new functional insights in uncultured MAST species
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Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis
inferredcites →https://doi.org/10.1038/s41598-020-63326-8openalex-snapshot
Species specific gene expression dynamics during harmful algal blooms
inferredcites →https://doi.org/10.1073/pnas.1016106108openalex-snapshot
Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
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Prokka: rapid prokaryotic genome annotation
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NanoPack: visualizing and processing long-read sequencing data
inferredcites →https://doi.org/10.1093/gbe/evab018openalex-snapshot
Mitochondrial Genome Evolution in Pelagophyte Algae
inferredcites →https://doi.org/10.1093/gbe/evz171openalex-snapshot
Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msx148openalex-snapshot
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
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VISTA: computational tools for comparative genomics
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Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
inferredcites →https://doi.org/10.1093/nar/gks1193openalex-snapshot
NCBI GEO: archive for functional genomics data sets—update
inferredcites →https://doi.org/10.1093/nar/gkw1092openalex-snapshot
KEGG: new perspectives on genomes, pathways, diseases and drugs
inferredcites →https://doi.org/10.1093/nar/gkw294openalex-snapshot
Redundans: an assembly pipeline for highly heterozygous genomes
inferredcites →https://doi.org/10.1093/plankt/23.12.1339openalex-snapshot
Elevated organic nutrient ratios associated with brown tide algal blooms of Aureococcus anophagefferens (Pelagophyceae)
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1099/mgen.0.000132openalex-snapshot
Completing bacterial genome assemblies with multiplex MinION sequencing
inferredcites →https://doi.org/10.1101/076331openalex-snapshot
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1101/gr.6743907openalex-snapshot
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
inferredcites →https://doi.org/10.1111/1462-2920.12374openalex-snapshot
Expression of a xanthine permease and phosphate transporter in cultures and field populations of the harmful alga A ureococcus anophagefferens : tracking nutritional deficiency during brown tides
inferredcites →https://doi.org/10.1111/gcb.15667openalex-snapshot
Distinct interaction effects of warming and anthropogenic input on diatoms and dinoflagellates in an urbanized estuarine ecosystem
inferredcites →https://doi.org/10.1111/j.1529-8817.1988.tb04485.xopenalex-snapshot
ULTRASTRUCTURE AND ECOLOGY OF AUREOCOCCUS ANOPHAGEFERENS GEN. ET SP. NOV. (CHRYSOPHYCEAE): THE DOMINANT PICOPLANKTER DURING A BLOOM IN NARRAGANSETT BAY, RHODE ISLAND, SUMMER 19851
inferredcites →https://doi.org/10.1111/j.1529-8817.2006.00303.xopenalex-snapshot
PHYSIOLOGICAL RESPONSES DURING DARK SURVIVAL AND RECOVERY INAUREOCOCCUS ANOPHAGEFFERENS(PELAGOPHYCEAE)1
inferredcites →https://doi.org/10.1111/j.1529-8817.2008.00571.xopenalex-snapshot
UNDERSTANDING NITROGEN LIMITATION IN AUREOCOCCUS ANOPHAGEFFERENS (PELAGOPHYCEAE) THROUGH cDNA AND qRT‐PCR ANALYSIS1
inferredcites →https://doi.org/10.1111/j.1529-8817.2010.00841.xopenalex-snapshot
ANALYSES OF THE COMPLETE CHLOROPLAST GENOME SEQUENCES OF TWO MEMBERS OF THE PELAGOPHYCEAE: AUREOCOCCUS ANOPHAGEFFERENS CCMP1984 AND AUREOUMBRA LAGUNENSIS CCMP15071
inferredcites →https://doi.org/10.1111/j.1574-6941.2012.01349.xopenalex-snapshot
Dynamics and genotypic composition of Emiliania huxleyi and their co-occurring viruses during a coccolithophore bloom in the North Sea
inferredcites →https://doi.org/10.1111/mec.15198openalex-snapshot
Genome evolution and host‐microbiome shifts correspond with intraspecific niche divergence within harmful algal bloom‐forming Microcystis aeruginosa
inferredcites →https://doi.org/10.1111/tpj.14508openalex-snapshot
Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions
inferredcites →https://doi.org/10.1128/aem.66.11.4916-4920.2000openalex-snapshot
Viral Impacts on Total Abundance and Clonal Composition of the Harmful Bloom-Forming Phytoplankton Heterosigma akashiwo
inferredcites →https://doi.org/10.1128/aem.68.1.401-404.2002openalex-snapshot
Dissolved Organic Nitrogen Hydrolysis Rates in Axenic Cultures of Aureococcus anophagefferens (Pelagophyceae): Comparison with Heterotrophic Bacteria
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/s12864-018-5144-5openalex-snapshot
Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom
inferredcites →https://doi.org/10.1186/s13059-016-1103-0openalex-snapshot
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
inferredcites →https://doi.org/10.1186/s13059-019-1727-yopenalex-snapshot
Performance of neural network basecalling tools for Oxford Nanopore sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0111069openalex-snapshot
Understanding Strategy of Nitrate and Urea Assimilation in a Chinese Strain of Aureococcus anophagefferens through RNA-Seq Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.1534/g3.120.401411openalex-snapshot
A Reference Genome from the Symbiotic Hydrozoan, Hydra viridissima
inferredcites →https://doi.org/10.17504/protocols.io.f3ybqpwopenalex-snapshot
ASP12A Recipe for culturing Aureococcus anophagefferens v2
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3354/ame035031openalex-snapshot
Nutrient limitation, organic matter cycling, and plankton dynamics during an Aureococcus anophagefferens bloom
inferredcites →https://doi.org/10.3354/ame047025openalex-snapshot
Ecological aspects of viral infection and lysis in the harmful brown tide alga Aureococcus anophagefferens
inferredcites →https://doi.org/10.3354/meps153067openalex-snapshot
Growth and photosynthesis of the 'brown tide' microalga Aureococcus anophagefferens in subsaturating constant and fluctuating irradiance
inferredcites →https://doi.org/10.3354/meps282101openalex-snapshot
Concentration-dependent effects of toxic and non-toxic isolates of the brown tide alga Aureococcus anophagefferens on growth of juvenile bivalves
inferredcites →https://doi.org/10.3389/fmicb.2014.00375openalex-snapshot
De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms
inferredcites →https://doi.org/10.3389/fmicb.2018.00752openalex-snapshot
Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae
inferredcites →https://doi.org/10.3389/fmicb.2019.00136openalex-snapshot
Transcriptional Shifts Highlight the Role of Nutrients in Harmful Brown Tide Dynamics
inferredcites →https://doi.org/10.3389/fmicb.2019.01064openalex-snapshot
Urea Is Both a Carbon and Nitrogen Source for Microcystis aeruginosa: Tracking 13C Incorporation at Bloom pH Conditions
inferredcites →https://doi.org/10.3389/fmicb.2021.664189openalex-snapshot
Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom
inferredcites →https://doi.org/10.3390/ijms21155393openalex-snapshot
Differences in the Formation Mechanism of Giant Colonies in Two Phaeocystis globosa Strains
inferredcites →https://doi.org/10.3390/jmse8121027openalex-snapshot
Laboratory Culture-Based Characterization of the Resting Stage Cells of the Brown-Tide-Causing Pelagophyte, Aureococcus anophagefferens
inferredcites →https://doi.org/10.3390/metabo10070273openalex-snapshot
Surviving Starvation: Proteomic and Lipidomic Profiling of Nutrient Deprivation in the Smallest Known Free-Living Eukaryote
inferredcites →https://doi.org/10.4319/lo.2002.47.4.1094openalex-snapshot
Peptide hydrolysis, amino acid oxidation, and nitrogen uptake in communities seasonally dominated by Aureococcus anophagefferens

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes
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Genetic diversity of Aureococcus anophagefferens in the coastal waters of China and implications for intraspecific differentiation of environmental adaptability
inferred← citeshttps://doi.org/10.1016/j.hal.2025.102987openalex-snapshot
Unique distribution pattern of Aureococcus anophagefferens in the Yellow Sea during late summer influenced by complex hydrodynamics and green tide decomposition
inferred← citeshttps://doi.org/10.1016/j.hal.2025.102997openalex-snapshot
From human-driven eutrophication to effective management: Controlling brown tides in the coastal waters of Qinhuangdao, China
inferred← citeshttps://doi.org/10.1093/femsec/fiae123openalex-snapshot
Time of day of infection shapes development of a eukaryotic algal-Nucleocytoviricota virocell
inferred← citeshttps://doi.org/10.1093/ismeco/ycae004openalex-snapshot
High amino acid osmotrophic incorporation by marine eukaryotic phytoplankton revealed by click chemistry
inferred← citeshttps://doi.org/10.1093/ismejo/wraf244openalex-snapshot
Contrasting viral infection strategies for single cell and colonial Microcystis populations consistent with Black Queen dynamics
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Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales
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“Quasigenus” among Phycodnaviridae : A diversity of chlorophyte-infecting viruses in response to a dense algal culture in a high-rate algal pond
inferred← citeshttps://doi.org/10.1101/2024.02.19.580968openalex-snapshot
Nitrogen metabolism in the picoalga Pelagomonas calceolata: disentangling cyanate lyase function under different nutrient conditions.
inferred← citeshttps://doi.org/10.1101/2024.10.30.620910openalex-snapshot
Pangenome biology and evolution in harmful algal-bloom-forming pelagophyte algae
inferred← citeshttps://doi.org/10.1101/2025.02.11.637735openalex-snapshot
Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales
inferred← citeshttps://doi.org/10.1101/2025.02.12.637950openalex-snapshot
Lysogen formation governs colonies while lytic infection is more prevalent in single cells of the bloom-forming cyanobacterium, Microcystis
inferred← citeshttps://doi.org/10.1128/mbio.02803-24openalex-snapshot
Viral dynamics in a high-rate algal pond reveals a burst of Phycodnaviridae diversity correlated with episodic algal mortality
inferred← citeshttps://doi.org/10.1128/mra.00289-22openalex-snapshot
Draft Genome Sequence of the Freshwater Diatom Fragilaria crotonensis SAG 28.96
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Aureococcus anophagefferens strain CCMP1851: draft genome of a second Kratosvirus quantuckense- susceptible host strain for an emerging host–giant virus model system
inferred← citeshttps://doi.org/10.1128/spectrum.02654-24openalex-snapshot
Transcriptomic response of the picoalga Pelagomonas calceolata to nitrogen availability: new insights into cyanate lyase function
inferred← citeshttps://doi.org/10.3389/fmars.2023.1156490openalex-snapshot
Genome-wide identification of the GT7 and GH16 genes and their correlations with agar metabolism in the agarophyte Gracilariopsis lemaneiformis
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Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1295160openalex-snapshot
Transcription of biochemical defenses by the harmful brown tide pelagophyte, Aureococcus anophagefferens, in response to the protozoan grazer, Oxyrrhis marina
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The diel disconnect between cell growth and division in Aureococcus is interrupted by giant virus infection
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