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Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote

https://doi.org/10.1101/809541
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What this work says

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

inferredcites →https://doi.org/10.1016/bs.aivir.2018.09.002openalex-snapshot
Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism
inferredcites →https://doi.org/10.1016/j.bbabio.2015.08.011openalex-snapshot
Cyanobacterial high-light-inducible proteins — Protectors of chlorophyll–protein synthesis and assembly
inferredcites →https://doi.org/10.1016/j.cub.2008.02.051openalex-snapshot
Chromatophore Genome Sequence of Paulinella Sheds Light on Acquisition of Photosynthesis by Eukaryotes
inferredcites →https://doi.org/10.1016/j.cub.2009.02.043openalex-snapshot
Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophora
inferredcites →https://doi.org/10.1016/j.cub.2013.12.025openalex-snapshot
Rhizaria
inferredcites →https://doi.org/10.1016/j.protis.2017.01.003openalex-snapshot
Diversity of the Photosynthetic Paulinella Species, with the Description of Paulinella micropora sp. nov. and the Chromatophore Genome Sequence for strain KR01
inferredcites →https://doi.org/10.1016/j.tig.2005.07.007openalex-snapshot
Non-mammalian c-integrases are encoded by giant transposable elements
inferredcites →https://doi.org/10.1038/nature07218openalex-snapshot
The virophage as a unique parasite of the giant mimivirus
inferredcites →https://doi.org/10.1038/nature20593openalex-snapshot
Host genome integration and giant virus-induced reactivation of the virophage mavirus
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/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
inferredcites →https://doi.org/10.1038/srep00356openalex-snapshot
Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis
inferredcites →https://doi.org/10.1071/pp01213openalex-snapshot
Evolution and diversity of CO 2 concentrating mechanisms in cyanobacteria
inferredcites →https://doi.org/10.1073/pnas.0600833103openalex-snapshot
Self-synthesizing DNA transposons in eukaryotes
inferredcites →https://doi.org/10.1073/pnas.0700531104openalex-snapshot
Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals
inferredcites →https://doi.org/10.1073/pnas.0911354106openalex-snapshot
Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms
inferredcites →https://doi.org/10.1073/pnas.1506469112openalex-snapshot
Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses
inferredcites →https://doi.org/10.1073/pnas.1608016113openalex-snapshot
Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora
inferredcites →https://doi.org/10.1073/pnas.1620089114openalex-snapshot
Early photosynthetic eukaryotes inhabited low-salinity habitats
inferredcites →https://doi.org/10.1073/pnas.182432999openalex-snapshot
Evolutionary analysis of Arabidopsis , cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
inferredcites →https://doi.org/10.1093/bioinformatics/bth088openalex-snapshot
GOstat: find statistically overrepresented Gene Ontologies within a group of genes
inferredcites →https://doi.org/10.1093/bioinformatics/btn013openalex-snapshot
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot
TopHat: discovering splice junctions with RNA-Seq
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/btr011openalex-snapshot
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
inferredcites →https://doi.org/10.1093/bioinformatics/bts507openalex-snapshot
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btu031openalex-snapshot
InterProScan 5: genome-scale protein function classification
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/gbe/evr001openalex-snapshot
Correlation between Nuclear Plastid DNA Abundance and Plastid Number Supports the Limited Transfer Window Hypothesis
inferredcites →https://doi.org/10.1093/molbev/msh075openalex-snapshot
A Molecular Timeline for the Origin of Photosynthetic Eukaryotes
inferredcites →https://doi.org/10.1093/molbev/msq032openalex-snapshot
Differential Gene Retention in Plastids of Common Recent Origin
inferredcites →https://doi.org/10.1093/molbev/msq209openalex-snapshot
Endosymbiotic Gene Transfer and Transcriptional Regulation of Transferred Genes in Paulinella chromatophora
inferredcites →https://doi.org/10.1093/molbev/mst197openalex-snapshot
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msw054openalex-snapshot
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
inferredcites →https://doi.org/10.1093/molbev/msy044openalex-snapshot
Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates
inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
inferredcites →https://doi.org/10.1093/nar/gkg033openalex-snapshot
Database resources of the National Center for Biotechnology
inferredcites →https://doi.org/10.1093/nar/gkg770openalex-snapshot
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkm321openalex-snapshot
KAAS: an automatic genome annotation and pathway reconstruction server
inferredcites →https://doi.org/10.1093/nar/gkw1129openalex-snapshot
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
inferredcites →https://doi.org/10.1101/cshperspect.a016105openalex-snapshot
Origin and Evolution of Plastids and Photosynthesis in Eukaryotes
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1105/tpc.104.027706openalex-snapshot
The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast–Nuclear DNA Flux
inferredcites →https://doi.org/10.1111/jeu.12102openalex-snapshot
Detailed Process of Shell Construction in the Photosynthetic Testate Amoeba Paulinella chromatophora (Euglyphid, Rhizaria)
inferredcites →https://doi.org/10.1126/science.1199412openalex-snapshot
A Virophage at the Origin of Large DNA Transposons
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-6-31openalex-snapshot
Automated generation of heuristics for biological sequence comparison
inferredcites →https://doi.org/10.1186/1471-2148-10-210openalex-snapshot
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
inferredcites →https://doi.org/10.1186/1471-2148-7-85openalex-snapshot
The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like γ-proteobacterium
inferredcites →https://doi.org/10.1186/1471-2148-9-98openalex-snapshot
A single origin of the photosynthetic organelle in different Paulinella lineages
inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot
Repbase Update, a database of repetitive elements in eukaryotic genomes
inferredcites →https://doi.org/10.12688/f1000research.16248.1openalex-snapshot
Multiple evolutionary origins of giant viruses
inferredcites →https://doi.org/10.1371/currents.tol.e68a099364bb1a1e129a17b4e06b0c6bopenalex-snapshot
How Really Ancient Is Paulinella Chromatophora?
inferredcites →https://doi.org/10.1371/journal.pone.0200961openalex-snapshot
Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer

What points at this work

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

inferred← citeshttps://doi.org/10.1002/bies.202200165openalex-snapshot
Endosymbiotic ratchet accelerates divergence after organelle origin
inferred← citeshttps://doi.org/10.1007/978-3-031-57446-7_1openalex-snapshot
The Evolutionary Origin of Primary Plastids
inferred← citeshttps://doi.org/10.1007/978-3-031-57446-7_12openalex-snapshot
What Has Paulinella Taught us About Endosymbiont Metabolic Integration?
inferred← citeshttps://doi.org/10.1073/pnas.2121241119openalex-snapshot
Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella
inferred← citeshttps://doi.org/10.1073/pnas.2300465120openalex-snapshot
Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses
inferred← citeshttps://doi.org/10.1101/2023.01.27.525846openalex-snapshot
Eukaryote-to-eukaryote gene transfer pervades the genome evolution of Rhizaria
inferred← citeshttps://doi.org/10.1111/jpy.13003openalex-snapshot
Paulinella , a model for understanding plastid primary endosymbiosis
inferred← citeshttps://doi.org/10.1111/jpy.13247openalex-snapshot
Hypothesis: Trans‐splicing Generates Evolutionary Novelty in the Photosynthetic Amoeba Paulinella
inferred← citeshttps://doi.org/10.1111/jpy.13321openalex-snapshot
Algae obscura: The potential of rare species as model systems
inferred← citeshttps://doi.org/10.1111/nph.17478openalex-snapshot
Why is primary endosymbiosis so rare?
inferred← citeshttps://doi.org/10.1111/nph.18220openalex-snapshot
Chromosome‐level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment
inferred← citeshttps://doi.org/10.3389/fcell.2023.1232685openalex-snapshot
Three-dimensional architecture and assembly mechanism of the egg-shaped shell in testate amoeba Paulinella micropora
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