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Universal trends of post-duplication evolution revealed by the genomes of 13 Paramecium species sharing an ancestral whole-genome duplication

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What this work says

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

inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot

Evolution by Gene Duplication

inferredcites →https://doi.org/10.1007/s00438-014-0889-2openalex-snapshot

Whole-genome duplication in teleost fishes and its evolutionary consequences

inferredcites →https://doi.org/10.1007/s10577-009-9055-9openalex-snapshot

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

inferredcites →https://doi.org/10.1007/s10709-008-9311-5openalex-snapshot

Preservation of duplicate genes by originalization

inferredcites →https://doi.org/10.1016/0031-9422(80)85004-7openalex-snapshot

Deviations from michaelis-menten behaviour of plant glutamate dehydrogenase with ammonium as variable substrate

inferredcites →https://doi.org/10.1016/j.cub.2011.01.026openalex-snapshot

High Spontaneous Rate of Gene Duplication in Caenorhabditis elegans

inferredcites →https://doi.org/10.1016/j.molp.2018.01.002openalex-snapshot

Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

inferredcites →https://doi.org/10.1016/j.tplants.2018.07.006openalex-snapshot

Whole-Genome Duplication and Plant Macroevolution

inferredcites →https://doi.org/10.1016/j.tree.2005.07.008openalex-snapshot

Genome duplication and the origin of angiosperms

inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot

Basic Local Alignment Search Tool

inferredcites →https://doi.org/10.1016/s0169-5347(03)00033-8openalex-snapshot

Evolution by gene duplication: an update

inferredcites →https://doi.org/10.1016/s0955-0674(99)00039-3openalex-snapshot

Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions

inferredcites →https://doi.org/10.1016/s1369-5274(99)00015-6openalex-snapshot

Yeast genome evolution in the post-genome era

inferredcites →https://doi.org/10.1023/a:1022661917301openalex-snapshot

The 2R hypothesis and the human genome sequence

inferredcites →https://doi.org/10.1038/nature02424openalex-snapshot

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

inferredcites →https://doi.org/10.1038/nature03025openalex-snapshot

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

inferredcites →https://doi.org/10.1038/nature04562openalex-snapshot

Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts

inferredcites →https://doi.org/10.1038/nature05230openalex-snapshot

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

inferredcites →https://doi.org/10.1038/nature12111openalex-snapshot

The zebrafish reference genome sequence and its relationship to the human genome

inferredcites →https://doi.org/10.1038/nature19840openalex-snapshot

Genome evolution in the allotetraploid frog Xenopus laevis

inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

inferredcites →https://doi.org/10.1038/ncomms4657openalex-snapshot

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

inferredcites →https://doi.org/10.1038/nrg2600openalex-snapshot

The evolutionary significance of ancient genome duplications

inferredcites →https://doi.org/10.1073/pnas.0501102102openalex-snapshot

Modeling gene and genome duplications in eukaryotes

inferredcites →https://doi.org/10.1073/pnas.0608218104openalex-snapshot

Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication

inferredcites →https://doi.org/10.1073/pnas.0608796103openalex-snapshot

Almost all human genes resulted from ancient duplication

inferredcites →https://doi.org/10.1073/pnas.1207726109openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1503926112openalex-snapshot

The butterfly plant arms-race escalated by gene and genome duplications

inferredcites →https://doi.org/10.1073/pnas.1507669112openalex-snapshot

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

inferredcites →https://doi.org/10.1073/pnas.1607237113openalex-snapshot

Little evidence for enhanced phenotypic evolution in early teleosts relative to their living fossil sister group

inferredcites →https://doi.org/10.1073/pnas.1710791115openalex-snapshot

Multiple large-scale gene and genome duplications during the evolution of hexapods

inferredcites →https://doi.org/10.1073/pnas.23.7.378openalex-snapshot

Sex, Sex Inheritance and Sex Determination in Paramecium Aurelia

inferredcites →https://doi.org/10.1089/cmb.2013.0084openalex-snapshot

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

inferredcites →https://doi.org/10.1091/mbc.e16-06-0361openalex-snapshot

Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies inParameciumspecies

inferredcites →https://doi.org/10.1093/genetics/151.4.1531openalex-snapshot

Preservation of Duplicate Genes by Complementary, Degenerative Mutations

inferredcites →https://doi.org/10.1093/genetics/154.1.459openalex-snapshot

The Probability of Duplicate Gene Preservation by Subfunctionalization

inferredcites →https://doi.org/10.1093/molbev/msp259openalex-snapshot

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

inferredcites →https://doi.org/10.1093/molbev/msv095openalex-snapshot

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

inferredcites →https://doi.org/10.1093/nar/gks1118openalex-snapshot

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

inferredcites →https://doi.org/10.1101/cshperspect.a016592openalex-snapshot

Mechanisms of Gene Duplication and Amplification

inferredcites →https://doi.org/10.1101/gr.173740.114openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.3672305openalex-snapshot

The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species

inferredcites →https://doi.org/10.1155/2012/292068openalex-snapshot

Polyploidy and the Evolution of Complex Traits

inferredcites →https://doi.org/10.1186/1471-2105-5-113openalex-snapshot

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.1186/s12864-016-3423-6openalex-snapshot

Both mechanism and age of duplications contribute to biased gene retention patterns in plants

inferredcites →https://doi.org/10.1186/s12864-017-3887-zopenalex-snapshot

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

inferredcites →https://doi.org/10.1186/s13059-018-1592-0openalex-snapshot

A new look at an old question: when did the second whole genome duplication occur in vertebrate evolution?

inferredcites →https://doi.org/10.1371/journal.pbio.0030314openalex-snapshot

Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate

inferredcites →https://doi.org/10.1371/journal.pgen.1000944openalex-snapshot

The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

inferredcites →https://doi.org/10.1371/journal.pone.0105015openalex-snapshot

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

inferredcites →https://doi.org/10.1371/journal.pone.0176384openalex-snapshot

No evidence for the radiation time lag model after whole genome duplications in Teleostei

inferredcites →https://doi.org/10.1371/journal.pone.0180936openalex-snapshot

Expansion by whole genome duplication and evolution of the sox gene family in teleost fish

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.1534/genetics.113.151670openalex-snapshot

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

inferredcites →https://doi.org/10.1534/genetics.114.163287openalex-snapshot

Insights into Three Whole-Genome Duplications Gleaned from theParamecium caudatumGenome Sequence

inferredcites →https://doi.org/10.2174/157489308784340702openalex-snapshot

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

What points at this work

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

inferred← citeshttps://doi.org/10.1002/admt.202000152openalex-snapshot

Characterization, Manipulation, and Isolation ofParamecium aureliaUsing a Micro‐Electromigration Chip and Computer Vision

inferred← citeshttps://doi.org/10.1093/gbe/evaa258openalex-snapshot

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

inferred← citeshttps://doi.org/10.1093/molbev/msac118openalex-snapshot

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

inferred← citeshttps://doi.org/10.1093/nar/gkac106openalex-snapshot

The transient Spt4-Spt5 complex as an upstream regulator of non-coding RNAs during development

inferred← citeshttps://doi.org/10.1098/rsos.210140openalex-snapshot

Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, Paramecium bursaria

inferred← citeshttps://doi.org/10.1101/2020.12.16.423098openalex-snapshot

Characterisation of the RNA-interference pathway as a Tool for Genetics in the Nascent Phototrophic Endosymbiosis, Paramecium bursaria

inferred← citeshttps://doi.org/10.1128/mmbr.00184-22openalex-snapshot

Programmed chromosome fragmentation in ciliated protozoa: multiple means to chromosome ends

inferred← citeshttps://doi.org/10.1146/annurev-arplant-050718-100344openalex-snapshot

Patterns and Processes of Diploidization in Land Plants

inferred← citeshttps://doi.org/10.1371/journal.pbio.3001309openalex-snapshot

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

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008723openalex-snapshot

Functional diversification of Paramecium Ku80 paralogs safeguards genome integrity during precise programmed DNA elimination

inferred← citeshttps://doi.org/10.3389/fpls.2019.00534openalex-snapshot

Fine-Tuning the Expression of Duplicate Genes by Translational Regulation in Arabidopsis and Maize

inferred← citeshttps://doi.org/10.70675/60e0aaadz31f3z4873z8fafz9d3e86686fccopenalex-snapshot

Spécialisation de Ku80c dans le couplage entre coupure et réparation de l’ADN lors des réarrangements programmés du génome chez Paramecium tetraurelia

inferred← citeshttps://doi.org/10.70675/cef4bacezab19z4a37za5e5z90809f6d6f7eopenalex-snapshot

Annotation des génomes de paramécies

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