Protist diversity and phylogeny

A Small Genome Amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba

This study analyzes the genome of Echinamoeba silvestris, revealing its reduced genome size and unique gene contraction patterns compared to other amoebae.

The macronuclear genomic landscape within Tetrahymena thermophila

This study sequenced the macronuclear genomes of 22 Tetrahymena thermophila strains to explore intraspecific genomic variation, revealing gene diversification in micronuclear centromeres and a genomic barcode for population dynamics.

Targeted metagenomics reveals pangenomic diversity of the nitroplast (UCYN-A) and its algal host plastid

The paper uses targeted metagenomics to analyze UCYN-A and its algal host in coastal Northwest Atlantic waters, revealing pangenomic diversity and co-occurring microbes.

Transportome remodeling of a symbiotic microalga inside a planktonic host

This study identifies sugar transporter remodeling in a symbiotic microalga, revealing how metabolic exchange is reprogrammed during photosymbiosis with a planktonic host.

Massive genome reduction occurred prior to the origin of coral algal symbionts

The paper presents genome and transcriptome data from Effrenium voratum, showing genome reduction predates symbiosis in Symbiodiniaceae and highlights differences between free-living and symbiotic lineages.

Newly obtained genome of fungi-related amoeba is enriched with genes shared with animals-related protists

The paper reports the genome of Nuclearia thermophila, showing it shares more protein domains with Holozoa than other Holomycota groups.

Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate

The paper presents a multi-omics analysis of Prorocentrum cordatum under heat stress, revealing RNA editing and exon usage regulation of biomolecules.

On the relationship between protist metabarcoding and protist metagenome-assembled genomes

This study investigates the relationship between protist metabarcoding OTUs and metagenome-assembled genomes by analyzing their abundance correlations across environmental samples.

THE RHODOEXPLORER PLATFORM FOR RED ALGAL GENOMICS AND WHOLE GENOME ASSEMBLIES FOR SEVERAL GRACILARIA SPECIES

Intraspecies genomic divergence of coral algal symbionts shaped by gene duplication

The paper examines intraspecies genomic divergence in Symbiodiniaceae and Polarella glacialis, revealing greater sequence divergence and the role of gene duplication in functional innovation.

Single-cell genomics reveals the divergent mitochondrial genomes of Retaria (Foraminifera and Radiolaria)

The paper presents mitochondrial genomes of Foraminifera and Radiolaria, revealing reduced gene content and a non-canonical genetic code in retarian mitogenomes.

Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of marine parasites

The paper develops a computational workflow to analyze unassigned protist genetic barcodes across marine surveys, identifying spatio-temporal patterns in Syndiniales parasites.

High quality genome and transcriptome data for two new species of Mantamonas, a deep-branching eukaryote clade

The paper describes two new mantamonad species and provides transcriptomic and genomic data for one, offering insights into the CRuMs supergroup's evolutionary history.

Complete mitochondrial genome and draft chloroplastic genome of Northern Atlantic Haslea ostrearia (Gaillon/Bory) Simonsen, 1974 (Naviculaceae, Bacillariophyceae)

The paper describes the first completed mitochondrial genome and draft chloroplast genome of Haslea ostrearia, providing genetic insights into its structure and phylogenetic relationships.

Resolving Complexities in Taxonomic Lineages of the Organellar and Nuclear Genomes of Galdieria through Comparative Phylogenomic Analysis

This study resolves the complex phylogenetic relationships within Galdieria by analyzing genome-scale data from multiple strains, revealing divergent lineages and incongruent interlineage relationships across organellar and nuclear genomes.

Comparisons between Complete Genomes of the Eukaryotic Extremophile Galdieria sulphuraria Reveals Complex Nuclear Chromosomal Structures

The paper compares whole-genome sequences of three Galdieria sulphuraria strains, revealing structural rearrangements and a high number of nuclear chromosomes associated with adaptability in extreme environments.

Plastomes of Hyalomonas oviformis and Hyalogonium fusiforme evolved dissimilar architecture after loss of photosynthesis

The plastid genomes of two free-living chlamydomonadalean algae show different evolutionary trajectories after losing photosynthesis.

Genomic adaptation of the picoeukaryote Pelagomonas calceolata to temperate iron-poor oceans revealed by a chromosome-scale genome sequence.

The paper reports the chromosome-scale genome of Pelagomonas calceolata, revealing adaptations to iron-poor environments and its potential expansion under climate change.

Mitochondrial genomes in Perkinsus decode conserved frameshifts in all genes

The paper sequences four Perkinsus mitochondrial genomes, identifies conserved frameshifts in all genes, and proposes a decoding mechanism involving unused codons.

Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genes

The paper presents an improved genome assembly of Cladocopium goreaui using long-read data, revealing structural features and a complex evolutionary history involving horizontal gene transfer.

Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex

The paper uses transcriptome and morphometric analyses to resolve the evolutionary relationships within the Nitzschia palea species complex, revealing reticulate patterns and hybridization.

Ten Ostreobium (Ulvophyceae) strains from Great Barrier Reef corals as a resource for algal endolith biology and genomics

The paper reports on 10 Ostreobium strains isolated from Great Barrier Reef corals, describing their phenotypic diversity, phylogenetic placement, and chloroplast genome structure.

Genome evolution of a non-parasitic secondary heterotroph, the diatom Nitzschia putrida

This study reports the diploid genome of the free-living diatom Nitzschia putrida and identifies genetic changes associated with its transition from a photosynthetic to a non-parasitic secondary heterotrophic lifestyle.

Omics of an enigmatic marine amoeba uncovers unprecedented giant viruses gene trafficking and provides insights into its complex life cycle

The paper uses integrated omics to study Trichosphaerium, revealing its complete meiosis toolkit, sexual-like processes, and high gene trafficking from giant viruses.

Draft Genome of Cochliopodium minus (Amoebozoa): Insights into Its Complex Sexual Behavior, Across Domain Gene Acquisitions and Metazoan Type Signaling

This paper presents a draft genome of Cochliopodium minus, revealing lateral gene transfers and meiosis-related genes, and insights into its sexual behavior.

Coupling between ribotypic and phenotypic traits of protists across life-cycle stages and temperatures

The paper examines relationships between ribotypic and phenotypic traits in protists across life-cycle stages and temperatures, finding allometric relationships and proposing a framework to estimate resting cysts.

A database and comprehensive analysis of the algae genomes

The paper compiles and analyzes 191 algae genomes to study genome features and evolutionary relationships, revealing the phylogenetic path from Glaucophyte to terrestrial plants.

The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis

The paper sequenced the genome of a nonphotosynthetic diatom to understand metabolic changes after losing photosynthesis and found key genetic constraints and alternative pathways for energy acquisition.

Marine gregarine genomes reveal the breadth of apicomplexan diversity and provide new insights on gliding motility

The paper characterizes the genome of Porospora gigantea, a marine gregarine, revealing its divergence from other apicomplexans and insights into gliding motility mechanisms.

Complete Mitochondrial and Plastid DNA Sequences of the Freshwater Green Microalga Medakamo hakoo

The paper reports the complete mitochondrial and plastid DNA sequences of Medakamo hakoo, identifying it as having the smallest known organellar genomes in core Trebouxiophyceae.