ArticleGenome biology and evolution2019
Long-Reads Reveal That the Chloroplast Genome Exists in Two Distinct Versions in Most Plants.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed.
- Complete chloroplast-based analysis reveals the emergence of candidate new species and revised divergence time in Vincetoxicum.Genes & genomics · 2026Article
- Towards whole plastome phylogeography: resolving small genetic distances among European Arnica montana L. with the PlastidPipeline.Scientific reports · 2026Article
- Phylogenomic insights into the genus Tulipa (Liliaceae): Taxonomy, evolution, and biogeography.American journal of botany · 2026Article
- Ongoing structural changes highlight the dynamic nature of chloroplast genomes.Nucleic acids research · 2026Article
- The pan-plastome of Strobilanthes cusia provided new information about the genetic diversity and cultivation history of an important medicinal and natural dye plant.BMC genomics · 2026Article
- Structural and phylogenetic insights from complete chloroplast genomes of seven Vicia species.PloS one · 2026Article
- Complex plastome structural variation caused by intermolecular and intramolecular recombination accounts for leaf variegation inPlant diversity · 2026Article
- Comparative and phylogenetic analysis of chloroplast genomes in the subtribe Leptoboeinae (Gesneriaceae).Frontiers in plant science · 2026Article
- Plastome diversity and phylogenetic insights among modern Egyptian wheat cultivars: Genome-Wide and Gene-Level perspectives.BMC plant biology · 2025Article
- The genome of Chenopodium ficifolium: developing genetic resources and a diploid model system for allotetraploid quinoa.G3 (Bethesda, Md.) · 2025Article
- Oatk: a de novo assembly tool for complex plant organelle genomes.Genome biology · 2025Article
- Phylogenetic reconstruction and species delimitation in Stipeae with special reference to Stipa (Poaceae, Pooideae) using mitochondrial genomes.Cladistics : the international journal of the Willi Hennig Society · 2025Article
- Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction.Current biology : CB · 2025Article
- TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data.Molecular biology and evolution · 2025Article
- Comparative analysis of chloroplast genomes in three Araceae species: genomic difference, genetic distance and species morphology association.Frontiers in genetics · 2025Article
- Article
- Comparative Analysis of Plastome Sequences of SevenInternational journal of molecular sciences · 2024Article
- The complete chloroplast genome of Marupa (Ecology and evolution · 2024Article
- The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species.Scientific reports · 2024Article
- Plastid genome of Chenopodium petiolare from Trujillo, Peru.BMC research notes · 2024Article
1 more citing papers are in PubMed but not listed here.
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Abstract
The chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labor-intensive, and this phenomenon remains understudied. Here, we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms, and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.
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