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Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method

https://doi.org/10.1101/692798
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What this work says

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

inferredcites →https://doi.org/10.1002/ece3.2051openalex-snapshot
phylosignal: an R package to measure, test, and explore the phylogenetic signal
inferredcites →https://doi.org/10.1007/bf00021486openalex-snapshot
Chloroplast genome organisation in sugar beet and maize
inferredcites →https://doi.org/10.1007/bf00418530openalex-snapshot
Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda
inferredcites →https://doi.org/10.1007/bf00420317openalex-snapshot
Recombination within the inverted repeat sequences of the Chlamydomonas reinhardii chloroplast genome produces two orientation isomers
inferredcites →https://doi.org/10.1007/s001220100741openalex-snapshot
PCR-mediated recombination in amplification products derived from polyploid cotton
inferredcites →https://doi.org/10.1007/s11103-011-9762-4openalex-snapshot
The evolution of the plastid chromosome in land plants: gene content, gene order, gene function
inferredcites →https://doi.org/10.1007/s11105-015-0853-2openalex-snapshot
Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution
inferredcites →https://doi.org/10.1016/0014-5793(82)80777-1openalex-snapshot
Cyanelle DNA from Cyanophora paradoxa exists in two forms due to intramolecular recombination
inferredcites →https://doi.org/10.1016/0305-1978(92)90067-nopenalex-snapshot
A rare chloroplast-DNA structural mutation is shared by all conifers
inferredcites →https://doi.org/10.1016/j.gene.2014.07.041openalex-snapshot
Complete chloroplast genome sequences of Praxelis (Eupatorium catarium Veldkamp), an important invasive species
inferredcites →https://doi.org/10.1016/j.molp.2018.05.003openalex-snapshot
Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance
inferredcites →https://doi.org/10.1038/301092a0openalex-snapshot
Chloroplast DNA exists in two orientations
inferredcites →https://doi.org/10.1038/44766openalex-snapshot
Inferring the historical patterns of biological evolution
inferredcites →https://doi.org/10.1038/s41467-018-07271-1openalex-snapshot
A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping
inferredcites →https://doi.org/10.1038/s41477-018-0289-4openalex-snapshot
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps
inferredcites →https://doi.org/10.1038/s41598-017-01518-5openalex-snapshot
Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants
inferredcites →https://doi.org/10.1093/bioinformatics/btw152openalex-snapshot
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
inferredcites →https://doi.org/10.1093/biomet/37.1-2.17openalex-snapshot
NOTES ON CONTINUOUS STOCHASTIC PHENOMENA
inferredcites →https://doi.org/10.1093/gbe/evr026openalex-snapshot
Comparative Chloroplast Genomes of Pinaceae: Insights into the Mechanism of Diversified Genomic Organizations
inferredcites →https://doi.org/10.1093/gbe/evr095openalex-snapshot
Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny
inferredcites →https://doi.org/10.1093/gbe/evt042openalex-snapshot
The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms
inferredcites →https://doi.org/10.1093/gbe/evu046openalex-snapshot
Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution
inferredcites →https://doi.org/10.1093/gbe/evw278openalex-snapshot
Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes)
inferredcites →https://doi.org/10.1093/gbe/evx071openalex-snapshot
Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae)
inferredcites →https://doi.org/10.1111/j.0014-3820.2003.tb00285.xopenalex-snapshot
TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
inferredcites →https://doi.org/10.1186/s12864-018-5348-8openalex-snapshot
Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case
inferredcites →https://doi.org/10.1186/s13059-016-1004-2openalex-snapshot
Chloroplast genomes: diversity, evolution, and applications in genetic engineering
inferredcites →https://doi.org/10.1266/ggs.81.311openalex-snapshot
Complete Nucleotide Sequence of the Cotton (Gossypium barbadense L.) Chloroplast Genome with a Comparative Analysis of Sequences among 9 Dicot Plants
inferredcites →https://doi.org/10.1371/journal.pone.0012762openalex-snapshot
The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)
inferredcites →https://doi.org/10.1371/journal.pone.0057533openalex-snapshot
Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other Plants
inferredcites →https://doi.org/10.1371/journal.pone.0067350openalex-snapshot
The Complete Chloroplast Genome of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution
inferredcites →https://doi.org/10.1554/0014-3820(2003)057[0717:tfpsic]2.0.co;2openalex-snapshot
TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
inferredcites →https://doi.org/10.2144/000113219openalex-snapshot
Reducing the Impact of PCR-Mediated Recombination in Molecular Evolution and Environmental Studies Using a New-Generation High-Fidelity DNA Polymerase
inferredcites →https://doi.org/10.3389/fpls.2016.00057openalex-snapshot
Chloroplast DNA Copy Number Changes during Plant Development in Organelle DNA Polymerase Mutants
inferredcites →https://doi.org/10.3732/ajb.1500299openalex-snapshot
Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s10681-025-03664-8openalex-snapshot
Plastome phylogenomics of egyptian barley: evolution, mutational landscapes, and DNA barcoding
inferred← citeshttps://doi.org/10.11110/kjpt.2023.53.1.47openalex-snapshot
The complete chloroplast genome of Erigeron canadensis isolated in Korea (Asteraceae): Insight into the genetic diversity of the invasive species
inferred← citeshttps://doi.org/10.1186/s12870-021-03053-yopenalex-snapshot
The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions
inferred← citeshttps://doi.org/10.1186/s12870-025-07739-5openalex-snapshot
Plastome diversity and phylogenetic insights among modern Egyptian wheat cultivars: Genome-Wide and Gene-Level perspectives
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