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Genetic variability in microbial eukaryotes reshapes marine biodiversity assessment in the age of amplicon sequencing

https://doi.org/10.1371/journal.pone.0326053

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What this work says

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

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Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

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Planktonic equatorial diversity troughs: fact or artifact? Latitudinal diversity gradients in Radiolaria

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Radiolaria

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ggplot2

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Biology and Ecology of Radiolaria

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Plankton stratigraphy

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Diversity and ecology of protists revealed by metabarcoding

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DNA metabarcoding reveals organisms contributing to particulate matter flux to abyssal depths in the North East Pacific ocean

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Concepts in protistology: Species definitions and boundaries

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Ultrastructural morphology of the reproductive swarmers of Sphaerozoum punctatum (Huxley) from the East China Sea

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Light and electron microscopic observations of the reproductive swarmer cells of nassellarian and spumellarian polycystines (Radiolaria)

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The high molecular diversity in Noctiluca scintillans is dominated by intra-genomic variations revealed by single cell high-throughput sequencing of 18S rDNA V4

inferredcites →https://doi.org/10.1016/j.isci.2023.107291openalex-snapshot

Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding

inferredcites →https://doi.org/10.1016/j.marpolbul.2024.116198openalex-snapshot

Extensive intragenomic variations of the 18S rDNA V4 region in the toxigenic diatom species Pseudo-nitzschia multistriata revealed through high-throughput sequencing

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Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

inferredcites →https://doi.org/10.1016/j.protis.2014.07.006openalex-snapshot

Wide Occurrence of SSU rDNA Intragenomic Polymorphism in Foraminifera and its Implications for Molecular Species Identification

inferredcites →https://doi.org/10.1016/j.protis.2015.05.002openalex-snapshot

Towards an Integrative Morpho-molecular Classification of the Collodaria (Polycystinea, Radiolaria)

inferredcites →https://doi.org/10.1016/j.protis.2019.02.002openalex-snapshot

Time Calibrated Morpho-molecular Classification of Nassellaria (Radiolaria)

inferredcites →https://doi.org/10.1016/j.protis.2021.125806openalex-snapshot

A Morpho-molecular Perspective on the Diversity and Evolution of Spumellaria (Radiolaria)

inferredcites →https://doi.org/10.1016/j.tim.2018.10.009openalex-snapshot

Are We Overestimating Protistan Diversity in Nature?

inferredcites →https://doi.org/10.1016/j.ympev.2014.05.021openalex-snapshot

Uncovering sibling species in Radiolaria: Evidence for ecological partitioning in a marine planktonic protist

inferredcites →https://doi.org/10.1016/s0040-8166(16)30336-6openalex-snapshot

Light and Electron Microscopic Observations of Feeding Behavior, Nutrition, and Reproduction in Laboratory Cultures of Thalassicolla Nucleata

inferredcites →https://doi.org/10.1016/s0377-8398(98)00028-0openalex-snapshot

Towards a molecular phylogeny of colonial spumellarian radiolaria

inferredcites →https://doi.org/10.1029/2008gb003221openalex-snapshot

Radiolaria: Major exporters of organic carbon to the deep ocean

inferredcites →https://doi.org/10.1029/2019gb006286openalex-snapshot

Estimating Biogenic Silica Production of Rhizaria in the Global Ocean

inferredcites →https://doi.org/10.1038/ismej.2015.224openalex-snapshot

Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

inferredcites →https://doi.org/10.1038/ismej.2017.12openalex-snapshot

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

inferredcites →https://doi.org/10.1038/nature16942openalex-snapshot

Plankton networks driving carbon export in the oligotrophic ocean

inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot

DADA2: High-resolution sample inference from Illumina amplicon data

inferredcites →https://doi.org/10.1038/s41396-018-0322-7openalex-snapshot

High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding

inferredcites →https://doi.org/10.1038/s41467-020-18879-7openalex-snapshot

Marine plankton show threshold extinction response to Neogene climate change

inferredcites →https://doi.org/10.1038/s41467-022-34989-wopenalex-snapshot

Varying strength of selection contributes to the intragenomic diversity of rRNA genes

inferredcites →https://doi.org/10.1038/s41467-024-47651-4openalex-snapshot

Global census of the significance of giant mesopelagic protists to the marine carbon and silicon cycles

inferredcites →https://doi.org/10.1038/s41587-019-0209-9openalex-snapshot

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

inferredcites →https://doi.org/10.1038/s41598-019-45146-7openalex-snapshot

Eukaryotic and cyanobacterial communities associated with marine snow particles in the oligotrophic Sargasso Sea

inferredcites →https://doi.org/10.1038/s43705-023-00274-0openalex-snapshot

Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms

inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btu531openalex-snapshot

AliView: a fast and lightweight alignment viewer and editor for large datasets

inferredcites →https://doi.org/10.1093/bioinformatics/btz305openalex-snapshot

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

inferredcites →https://doi.org/10.1093/molbev/msae263openalex-snapshot

MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing

inferredcites →https://doi.org/10.1093/molbev/msn032openalex-snapshot

The Dynamic Nature of Eukaryotic Genomes

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/nar/gks1160openalex-snapshot

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

inferredcites →https://doi.org/10.1093/nar/gkz569openalex-snapshot

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

inferredcites →https://doi.org/10.1093/plankt/17.1.131openalex-snapshot

Planktonic sarcodines (Acantharia, Radiolaria, Foraminifera) in surface waters near Bermuda: abundance, biomass and vertical flux

inferredcites →https://doi.org/10.1111/1462-2920.14764openalex-snapshot

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

inferredcites →https://doi.org/10.1111/1462-2920.16081openalex-snapshot

Intra‐genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing

inferredcites →https://doi.org/10.1111/1755-0998.13117openalex-snapshot

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

inferredcites →https://doi.org/10.1111/1755-6724.14249openalex-snapshot

Mikrotax: Developing a Genuinely Effective Platform for Palaeontological Geoinformatics

inferredcites →https://doi.org/10.1111/brv.13065openalex-snapshot

The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton

inferredcites →https://doi.org/10.1111/j.1365-294x.2009.04478.xopenalex-snapshot

Diversity in a hidden world: potential and limitation of next‐generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

inferredcites →https://doi.org/10.1111/j.1365-294x.2009.04480.xopenalex-snapshot

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

inferredcites →https://doi.org/10.1111/j.1550-7408.1998.tb05105.xopenalex-snapshot

Insights on the Diversity within a “Species” of Thalassicolla (Spumellarida) Based on 16S‐like Ribosomal RNA Gene Sequencing

inferredcites →https://doi.org/10.1111/jeu.12813openalex-snapshot

Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

inferredcites →https://doi.org/10.1111/maec.12427openalex-snapshot

Using species distribution modelling to predict future distributions of phytoplankton: Case study using species important for the biological pump

inferredcites →https://doi.org/10.1126/science.1203060openalex-snapshot

Interplay Between Changing Climate and Species’ Ecology Drives Macroevolutionary Dynamics

inferredcites →https://doi.org/10.1126/science.1261605openalex-snapshot

Eukaryotic plankton diversity in the sunlit ocean

inferredcites →https://doi.org/10.1128/mr.58.2.233-267.1994openalex-snapshot

The DNA of ciliated protozoa

inferredcites →https://doi.org/10.1371/journal.pbio.1001473openalex-snapshot

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

inferredcites →https://doi.org/10.1371/journal.pone.0023526openalex-snapshot

Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny

inferredcites →https://doi.org/10.1371/journal.pone.0035775openalex-snapshot

Phylogenetic Relationships and Evolutionary Patterns of the Order Collodaria (Radiolaria)

inferredcites →https://doi.org/10.1371/journal.pone.0084857openalex-snapshot

Cenozoic Planktonic Marine Diatom Diversity and Correlation to Climate Change

inferredcites →https://doi.org/10.1371/journal.pone.0104297openalex-snapshot

Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing

inferredcites →https://doi.org/10.2307/1485665openalex-snapshot

Variability in Skeletal Morphology of Colonial Radiolaria (Actinopoda: Polycystinea: Collosphaeridae)

inferredcites →https://doi.org/10.32614/cran.package.dplyropenalex-snapshot

dplyr: A Grammar of Data Manipulation

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.3389/fmars.2019.00219openalex-snapshot

Estimation of 18S Gene Copy Number in Marine Eukaryotic Plankton Using a Next-Generation Sequencing Approach

inferredcites →https://doi.org/10.3800/pbr.6.69openalex-snapshot

Radiolaria: achievements and unresolved issues: taxonomy and cytology

inferredcites →https://doi.org/10.7717/peerj.15255openalex-snapshot

Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera

What points at this work

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

inferred← backgroundhttps://doi.org/10.5281/zenodo.15550382zenodo-depositor-declared

inferred← citeshttps://doi.org/10.1002/bies.70148openalex-snapshot

Unifying Retaria Research: A Common Framework for Studying Foraminifera and Radiolaria

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.