ArticleGenome biology and evolution2023
The Evolutionary Constraints on Angiosperm Chloroplast Adaptation.
Article in Genome biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 33 citations in OpenAlex.
- Evolutionary dynamics of the chloroplast genome in Abutilon (Malvoideae, Malvaceae).BMC plant biology · 2026Article
- Comparative Chloroplast Genomics, Codon Usage Bias, and Phylogenetic Placement ofCurrent issues in molecular biology · 2026Article
- Comparative analysis of six new chloroplast genomes in Platanthera (Orchidaceae) enhances understanding of its diversification.Scientific reports · 2026Article
- Comprehensive analysis of the pan-plastome in Panax: implications for interspecies divergence and shade tolerance.BMC plant biology · 2026Article
- RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments.Molecular biology and evolution · 2026Article
- Chloroplast genome comparison of Valeriana species with sequence variation, selective pressure, and divergence analysis.PloS one · 2026Article
- Characterization of the complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2026Article
- Comparative genomics and phylogenetic analysis of three Malvaceae species on the basis of chloroplast genomes.Frontiers in plant science · 2026Article
- Sequence dynamics and plastome evolution: decoding the complete chloroplast genome of Oenothera drummondii and comparative analysis within Oenothera (Onagraceae).Functional & integrative genomics · 2025Article
- Pan-Plastome Analysis Reveals the Genetic Diversity and Genetic Divergence ofInternational journal of molecular sciences · 2025Article
- Comparative plastome analysis reveals evolutionary dynamics and codon usage patterns in Bidens (Asteraceae).Functional & integrative genomics · 2025Article
- Exploring the Complete Chloroplast Genome ofCurrent issues in molecular biology · 2025Article
- Decoding the Chloroplast Genome of Bitterwood (Ecology and evolution · 2025Article
- Widespread adaptive evolution in angiosperm photosystems provides insight into the evolution of photosystem II repair.The Plant cell · 2024Article
- From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation.BMC plant biology · 2024Article
- Chloroplast Genome Variation and Phylogenetic Relationships of Autochthonous Varieties ofInternational journal of molecular sciences · 2024Article
- Comparative Analysis of Plastome Sequences of SevenInternational journal of molecular sciences · 2024Article
- Rubisco is evolving for improved catalytic efficiency and COProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom.International journal of molecular sciences · 2023Article
- Complete Plastid Genomes of Nine Species of Ranunculeae (Ranunculaceae) and Their Phylogenetic Inferences.Genes · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The chloroplast (plastid) arose via the endosymbiosis of a photosynthetic cyanobacterium by a nonphotosynthetic eukaryotic cell ∼1.5 billion years ago. Although the plastid underwent rapid evolution by genome reduction, its rate of molecular evolution is low and its genome organization is highly conserved. Here, we investigate the factors that have constrained the rate of molecular evolution of protein-coding genes in the plastid genome. Through phylogenomic analysis of 773 angiosperm plastid genomes, we show that there is substantial variation in the rate of molecular evolution between genes. We demonstrate that the distance of a plastid gene from the likely origin of replication influences the rate at which it has evolved, consistent with time and distance-dependent nucleotide mutation gradients. In addition, we show that the amino acid composition of a gene product constraints its substitution tolerance, limiting its mutation landscape and its corresponding rate of molecular evolution. Finally, we demonstrate that the mRNA abundance of a gene is a key factor in determining its rate of molecular evolution, suggesting an interaction between transcription and DNA repair in the plastid. Collectively, we show that the location, the composition, and the expression of a plastid gene can account for >50% of the variation in its rate of molecular evolution. Thus, these three factors have exerted a substantial limitation on the capacity for adaptive evolution in plastid-encoded genes and ultimately constrained the evolvability of the chloroplast.
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