ArticleGenome biology and evolution2016
Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Long-Read Assembly and a Within-Genus Structural Survey Reveal an Exceptionally Long Inverted Repeat in theGenes · 2026Article
- Phylogenomic discordance among plastid genes in endangered Maltese Limonium.Scientific reports · 2026Article
- The Complete Chloroplast Genome of Tree Fern Cyathea delgadii and Its Comparison to Other Cyatheales.Biochemical genetics · 2026Article
- Losing genes, gaining edits: how relaxed selection and inverted repeat expansion shape RNA editing in Schizaeaceae plastomes.The Plant journal : for cell and molecular biology · 2026Article
- Pan-Plastome Evolution and Metabolite Variation Provide Insights to Conservation of the Tibetan Medicinal PlantPlants (Basel, Switzerland) · 2026Article
- Complete chloroplast genome of Crotalaria juncea, a bast fibre crop with late-acting self-incompatibility, reveals evolutionary insights and phylogenetic relationships within Fabaceae.BMC plant biology · 2026Article
- The evolutionary path of widespread IR heteroplasmy of chloroplast genomes in the context of Rhodophyta phylogeny.Journal of molecular evolution · 2026Article
- Evolutionary mobility and genetic dynamics of MORFFO genes: shuttling among ancient plant lineages.The New phytologist · 2026Article
- Comparative analysis of morphology and chloroplast genomes in endangered plantFrontiers in plant science · 2026Article
- Comparative plastid genomics reveals phylogenetic relationships and candidate molecular markers inFrontiers in plant science · 2026Article
- Plastome variation and phylogenetic relationships ofFrontiers in plant science · 2026Article
- A record-setting mitogenome in the holoparasitic plant Balanophora yakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes.BMC biology · 2025Article
- Comparative and phylogenetic analyses of Stipa L. (Poaceae) species based on the complete chloroplast genome sequences.BMC plant biology · 2025Article
- Pan-Plastome Analysis Reveals the Genetic Diversity and Genetic Divergence ofInternational journal of molecular sciences · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Article
- A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum.Scientific reports · 2025Article
- A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples.Scientific data · 2024Article
- Assessing the phylogenetic relationship among varieties ofEcology and evolution · 2023Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution. Here we examine four loci (psbA, ycf2, rps7, and rps12 exon 2-3) that were translocated from the SC into the IR during fern evolution. We use a model-based method, within a phylogenetic context, to test for substitution rate shifts. All four loci show a significant, 2- to 3-fold deceleration in their substitution rate following translocation into the IR, a phenomenon not observed in any other, nontranslocated plastid genes. Also, we show that after translocation, the GC content of the third codon position and of the noncoding regions is significantly increased, implying that gene conversion within the IR is GC-biased. Taken together, our results suggest that the IR region not only reduces substitution rates, but also impacts nucleotide composition. This finding highlights a potential vulnerability of correlating substitution rate heterogeneity with organismal life history traits without knowledge of the underlying genome structure.
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