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Paramecium Genetics, Genomics, and Evolution

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Editorial Material Genetics & Heredity

Small RNA-mediated genome rearrangement pathways in ciliates

Yunyi Gao et al.

Summary: Most eukaryotes use both transcriptional and post-transcriptional silencing mechanisms to suppress transposons, while ciliates take a more extreme approach by separating germline and somatic functions into distinct nuclei, allowing the elimination of transposons from the somatic genome through various small RNA-mediated genome rearrangement pathways during sexual reproduction.

TRENDS IN GENETICS (2023)

Article Biochemistry & Molecular Biology

Dynamics of Gene Loss following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex

Jean-Francois Gout et al.

Summary: Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages, but the maintenance of WGD-derived paralogs is still debated. The analysis of 13 Paramecium species revealed that gene retention biases and strong selective pressures against post-WGD gene loss play a major role in maintaining duplicate genes. Paramecium is an exceptional model organism in evolutionary cell biology, and this dataset of 13 species sharing an ancestral WGD will be useful for future studies.

MOLECULAR BIOLOGY AND EVOLUTION (2023)

Review Microbiology

Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution

Caitlin M. Timmons et al.

Summary: Mobile genetic elements play important roles in evolution by influencing genome structure and molecular evolution, providing adaptive advantages and genetic diversity, as well as altering host cell defense mechanisms against viral pathogens.

JOURNAL OF EUKARYOTIC MICROBIOLOGY (2022)

Article Cell Biology

Paramecium Polycomb repressive complex 2 physically interacts with the small RNA-binding PIWI protein to repress transposable elements

Caridad Miro-Pina et al.

Summary: Polycomb repressive complex 2 (PRC2) is involved in maintaining transcriptional silence and silencing transposable elements (TEs) through deposition of specific histone marks. This study identified the core complex and cofactors of PRC2 in Paramecium, and revealed the importance of RNA interference (RNAi) pathway in targeting histone marks to TEs.

DEVELOPMENTAL CELL (2022)

Review Microbiology

Paramecium epigenetics in development and proliferation

Franziska Drews et al.

Summary: The translation introduces the concept of epigenetics and its role in different organisms. Mammalian research focuses on cytosine methylation and histone modification, while ciliate research focuses on small RNA-mediated effects. Ciliates control the DNA content of sexual progeny through transgenerational RNA effects, suggesting that epigenetics plays an important role in controlling the genetic process of sexual macronuclei.

JOURNAL OF EUKARYOTIC MICROBIOLOGY (2022)

Article Multidisciplinary Sciences

Somatic mutation rates scale with lifespan across mammals

Alex Cagan et al.

Summary: Through whole-genome sequencing of 208 intestinal crypts from 56 individuals, this study reveals that somatic mutation in mammals is dominated by endogenous mutational processes, and mutational signatures in different species show similarities to those in humans, though with variations in relative contribution. The study also finds a strong inverse relationship between somatic mutation rate and species lifespan, suggesting that somatic mutation rates are evolutionarily constrained and may contribute to aging.

NATURE (2022)

Article Genetics & Heredity

Convergent evolution of polyploid genomes from across the eukaryotic tree of life

Yue Hao et al.

Summary: The study finds that the evolutionary forces acting on polyploids are remarkably similar regardless of the species they occur in. The rate of duplicate gene loss is relatively high in the early stages of polyploid evolution, suggesting that most selectively neutral duplicate gene losses occur during this period. There is strong evidence of biases in the duplicate losses, indicating that allopolyploidies with distinct progenitors are common. Additionally, reciprocal gene losses are ongoing and extensive between these polyploid genomes, making the formation of viable diploid hybrid species highly unlikely. The ability of new polyploidies to bypass reciprocal gene loss barriers may explain the relatively high frequency of recurrent polyploidy in certain lineages.

G3-GENES GENOMES GENETICS (2022)

Review Microbiology

Evolutionary bioenergetics of ciliates

Michael Lynch et al.

Summary: Understanding the evolution of alternative lifestyles requires knowledge of both the advantages and costs associated with phenotypic modifications and cellular features. This study uses observations on various ciliate species and insights from evolutionary bioenergetics to estimate the total cost of a cell per cell cycle and investigate how different investments scale with cell size. The study focuses on the costs of large macronuclear genomes, ribosomes, internal membranes, osmoregulation, cilia, and swimming activities in ciliates.

JOURNAL OF EUKARYOTIC MICROBIOLOGY (2022)

Article Biochemistry & Molecular Biology

A Population-Genetic Lens into the Process of Gene Loss Following Whole-Genome Duplication

Parul Johri et al.

Summary: This study investigates the selective forces and ongoing loss of gene duplicates created by whole-genome duplications (WGDs) in multiple species of Paramecium. The results show that one of the WGD paralogs undergoes relaxation of purifying selection, leading to degeneration in functional efficiency and expression. Additionally, highly expressed duplicate genes experience more deleterious effects from new mutations compared to their lower-expressed paralogs.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

Article Biochemistry & Molecular Biology

Recommendations for improving statistical inference in population genomics

Parul Johri et al.

Summary: The field of population genomics has grown rapidly, but there is a tendency to focus on specific models at the expense of exploring underlying evolutionary processes. We need to pay more attention to statistical inference and theory and establish relevant baseline models for each analysis.

PLOS BIOLOGY (2022)

Article Multidisciplinary Sciences

Morphological diversity and molecular phylogeny of five Paramecium bursaria (Alveolata, Ciliophora, Oligohymenophorea) syngens and the identification of their green algal endosymbionts

Christian Spanner et al.

Summary: This study investigated the diversity of Paramecium bursaria isolates from around the world and revealed five distinct lineages based on phylogenetic analyses. Morphological and genetic features were used to assign the existing GenBank entries to specific lineages. Additionally, synapomorphies were discovered to identify different lineages.

SCIENTIFIC REPORTS (2022)

Article Microbiology

Intronization Signatures in Coding Exons Reveal the Evolutionary Fluidity of Eukaryotic Gene Architecture

Judith Ryll et al.

Summary: The conventional distinction between exons and introns in eukaryotic genes is actually blurred. This article provides evidence, through studies on Paramecium, that resolves the disconnect between traditional views on introns and the role of RNA splicing.

MICROORGANISMS (2022)

Article Evolutionary Biology

Evolutionary Plasticity of Mating-Type Determination Mechanisms in Paramecium aurelia Sibling Species

Natalia Sawka-Gadek et al.

Summary: Studies on the Paramecium aurelia complex have shown diversity in the mating-type systems among different species, with various genetic determinations and inheritance modes, all specifying mating type through mtA gene expression. These findings highlight the diverse molecular solutions explored among sibling species to maintain essential mating-type polymorphism in cell populations.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Microbiology

Clarification of the Taxonomic Position of Paramecium caudatum Micronucleus Symbionts

N. D. Wackerow-Kouzova et al.

Summary: Holospora bacteria are obligate intranuclear symbionts of Paramecium ciliates with strict host and nuclear specificity. Among the studied species, Holospora undulata, Holospora elegans, and 'Holospora recta' occupy the same ecological niche in the micronucleus of Paramecium caudatum, showing some differences in infectious form morphology. Genetic diversity analysis suggests that Holospora elegans and 'Holospora recta' should be considered subspecies of Holospora undulata.

CURRENT MICROBIOLOGY (2021)

Article Evolutionary Biology

One Cell, Two Gears: Extensive Somatic Genome Plasticity Accompanies High Germline Genome Stability in Paramecium

Francesco Catania et al.

Summary: MA experiments reveal extraordinary germline genome stability in Paramecium tetraurelia, but the polyploid somatic genome of isogenic P. tetraurelia lines propagated for >40 sexual cycles in nutrient-rich medium accumulated numerous intervening DNA segments (IESs) that exhibit diversity and are epigenetically controlled.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Biodiversity Conservation

Paramecium bursaria-A Complex of Five Cryptic Species: Mitochondrial DNA COI Haplotype Variation and Biogeographic Distribution

Magdalena Greczek-Stachura et al.

Summary: Ciliates are a diverse protistan group with many cryptic species complexes. Mitochondrial genes have been utilized to identify new species and distinguish closely related morphospecies. Analysis of COI mtDNA fragments in P. bursaria species revealed five reproductively isolated haplogroups.

DIVERSITY-BASEL (2021)

Article Biochemistry & Molecular Biology

Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Diamantis Sellis et al.

Summary: Ciliates are unicellular eukaryotes with a complex genomic architecture including internal eliminated sequences (IESs) that have undergone multiple waves of gains, some of which are under strong purifying selection. The evolution of IESs in Paramecium highlights the important role of selfish genetic elements in shaping genome complexity and gene expression, similar to the evolution of introns in eukaryotes.

PLOS BIOLOGY (2021)

Article Evolutionary Biology

One Cell, Two Gears: Extensive Somatic Genome Plasticity Accompanies High Germline Genome Stability in Paramecium

Francesco Catania et al.

Summary: The study examines somatic genome plasticity in Paramecium tetraurelia through Mutation Accumulation (MA) experiments. Results show that the polyploid somatic genome of P. tetraurelia accrues hundreds of intervening DNA segments (IESs), affecting somatic DNA copies and producing IES excision/retention polymorphisms. These findings suggest a relationship between the organism's high germline DNA replication fidelity and pervasive somatic genome plasticity, highlighting the importance of MA regimes in studying developmental plasticity, somatic mutations, and epimutations in ecology and evolution.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Parasitology

The first case of microsporidiosis inParamecium

Yulia Yakovleva et al.

PARASITOLOGY (2020)

Article Biodiversity Conservation

Paramecium Diversity and a New Member of the Paramecium aurelia Species Complex Described from Mexico

Alexey Potekhin et al.

DIVERSITY-BASEL (2020)

Article Multidisciplinary Sciences

One thousand plant transcriptomes and the phylogenomics of green plants

James H. Leebens-Mack et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium

Amy L. Dapper et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Genetics & Heredity

Limited Mutation-Rate Variation Within the Paramecium aurelia Species Complex

Hongan Long et al.

G3-GENES GENOMES GENETICS (2018)

Article Ecology

Evolutionary determinants of genome-wide nucleotide composition

Hongan Long et al.

NATURE ECOLOGY & EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Population Genomics of Paramecium Species

Parul Johri et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Review Biology

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

Jessica Stapley et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Article Biotechnology & Applied Microbiology

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Baptiste Saudemont et al.

GENOME BIOLOGY (2017)

Article Biotechnology & Applied Microbiology

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

Olivier Arnaiz et al.

BMC GENOMICS (2017)

Article Evolutionary Biology

Similar Mutation Rates but Highly Diverse Mutation Spectra in Ascomycete and Basidiomycete Yeasts

Hongan Long et al.

GENOME BIOLOGY AND EVOLUTION (2016)

Review Genetics & Heredity

Genetic drift, selection and the evolution of the mutation rate

Michael Lynch et al.

NATURE REVIEWS GENETICS (2016)

Article Biochemistry & Molecular Biology

Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans

Hongan Long et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

Jean-Francois Gout et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biotechnology & Applied Microbiology

Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts

Yuuki Kodama et al.

BMC GENOMICS (2014)

Article Biochemistry & Molecular Biology

Differential retention and divergent resolution of duplicate genes following whole-genome duplication

Casey L. McGrath et al.

GENOME RESEARCH (2014)

Article Multidisciplinary Sciences

Genome-defence small RNAs exapted for epigenetic mating-type inheritance

Deepankar Pratap Singh et al.

NATURE (2014)

Article Genetics & Heredity

Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena thermophila

Hong-An Long et al.

GENETICS (2013)

Article Genetics & Heredity

Robust Demographic Inference from Genomic and SNP Data

Laurent Excoffier et al.

PLOS GENETICS (2013)

Article Multidisciplinary Sciences

Extraordinary genome stability in the ciliate Paramecium tetraurelia

Way Sung et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

James A. Birchler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Evolutionary Biology

The Lower Bound to the Evolution of Mutation Rates

Michael Lynch

GENOME BIOLOGY AND EVOLUTION (2011)

Article Multidisciplinary Sciences

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

Laura Wegener Parfrey et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biotechnology & Applied Microbiology

The collapse of gene complement following whole genome duplication

David Sankoff et al.

BMC GENOMICS (2010)

Article Evolutionary Biology

Alternative Processing of Scrambled Genes Generates Protein Diversity in the Ciliate Chilodonella uncinata

Laura A. Katz et al.

JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION (2010)

Review Genetics & Heredity

Evolution of the mutation rate

Michael Lynch

TRENDS IN GENETICS (2010)

Article Biochemistry & Molecular Biology

Genetic Diversity in the Paramecium aurelia Species Complex

Francesco Catania et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Biochemistry & Molecular Biology

Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia

Gersende Lepere et al.

NUCLEIC ACIDS RESEARCH (2009)

Review Biology

The causes of mutation accumulation in mitochondrial genomes

Maurine Neiman et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2009)

Article Multidisciplinary Sciences

Translational control of intron splicing in eukaryotes

Olivier Jaillon et al.

NATURE (2008)

Article Cell Biology

Consequences of genome duplication

Marie Semon et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2007)

Review Biochemistry & Molecular Biology

The evolutionary consequences of polyploidy

Sarah P. Otto

Review Genetics & Heredity

The distribution of fitness effects of new mutations

Adam Eyre-Walker et al.

NATURE REVIEWS GENETICS (2007)

Article Microbiology

The particle inflow gun can be used to co-transform Paramecium using tungsten particles

D Fraga et al.

JOURNAL OF EUKARYOTIC MICROBIOLOGY (2006)

Article Biochemistry & Molecular Biology

Two rounds of whole genome duplication in the ancestral vertebrate

P Dehal et al.

PLOS BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Detection and evaluation of intron retention events in the human transcriptome

PAF Galante et al.

Article Biochemistry & Molecular Biology

High coding density on the largest Paramecium tetraurlia somatic chromosome

M Zagulski et al.

CURRENT BIOLOGY (2004)

Article Genetics & Heredity

RNA interference by feeding in Paramecium

A Galvani et al.

TRENDS IN GENETICS (2002)

Review Biology

Effects of metapopulation processes on measures of genetic diversity

JR Pannell et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2000)

Article Multidisciplinary Sciences

The evolutionary fate and consequences of duplicate genes

M Lynch et al.

SCIENCE (2000)

Article Cell Biology

Expression of the green fluorescent protein in Paramecium tetraurelia

K Hauser et al.

EUROPEAN JOURNAL OF CELL BIOLOGY (2000)