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Hidden diversity and macroevolutionary mode of Caulimoviridae uncovered by euphyllophyte paleoviruses

https://doi.org/10.1101/170415
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What this work says

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

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Endogenous viruses: Connecting recent and ancient viral evolution
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Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution
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Broad-scale phylogenomics provides insights into retrovirus–host evolution
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Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants
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Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
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Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
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An Exploration into Fern Genome Space
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Transposable Element Targeting by piRNAs in Laurasiatherians with Distinct Transposable Element Histories
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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CDD: NCBI's conserved domain database
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Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences
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Reverse transcription in the eukaryotic genome: retroviruses, pararetroviruses, retrotransposons, and retrotranscripts.
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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes
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Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus
inferredcites →https://doi.org/10.1111/j.1463-6409.1997.tb00421.xopenalex-snapshot
Phylogenetic approaches in coevolution and biogeography
inferredcites →https://doi.org/10.1126/science.aad5497openalex-snapshot
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
inferredcites →https://doi.org/10.1128/jvi.00212-08openalex-snapshot
A Single Banana Streak Virus Integration Event in the Banana Genome as the Origin of Infectious Endogenous Pararetrovirus
inferredcites →https://doi.org/10.1128/jvi.00401-10openalex-snapshot
Evolution of Endogenous Sequences of Banana Streak Virus : What Can We Learn from Banana ( Musa sp.) Evolution?
inferredcites →https://doi.org/10.1128/jvi.00832-16openalex-snapshot
Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses
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The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes
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LINE-1 Elements in Structural Variation and Disease
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Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution
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Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees
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Jane: a new tool for the cophylogeny reconstruction problem
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Draft genome of the living fossil Ginkgo biloba
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Paleovirology—Modern Consequences of Ancient Viruses
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Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
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Endogenous Viral Elements in Animal Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1003400openalex-snapshot
Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene, the EnvV Syncytin, Captured for a Function in Placentation
inferredcites →https://doi.org/10.1371/journal.pgen.1004559openalex-snapshot
Early Mesozoic Coexistence of Amniotes and Hepadnaviridae
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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1128/jvi.02043-17openalex-snapshot
Euphyllophyte Paleoviruses Illuminate Hidden Diversity and Macroevolutionary Mode of Caulimoviridae
inferred← citeshttps://doi.org/10.3389/fsufs.2020.00021openalex-snapshot
Cauliflower mosaic virus (CaMV) Biology, Management, and Relevance to GM Plant Detection for Sustainable Organic Agriculture
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