ArticleGenome biology and evolution2015
Exploring the limits for reduction of plastid genomes: a case study of the mycoheterotrophic orchids Epipogium aphyllum and Epipogium roseum.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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78 citing papers in PubMed, 146 citations in OpenAlex.
- Phylogenomics Clarifies Plastome Reduction and Phylogenetic Relationships in Monotropoideae.Ecology and evolution · 2026Article
- Orchid genome evolution and trait innovation.Journal of integrative plant biology · 2026Review
- Comparative plastome analyses reveal life-form-associated selection signatures in Orchidaceae.BMC plant biology · 2026Article
- Mitogenome characterization and organellar genome evolution in achlorophyllous orchid Chamaegastrodia shikokiana Makino & F.Maek. (Orchidaceae).BMC plant biology · 2026Article
- Mycoheterotrophy and plastid genome evolution in the early-diverging epidendroid orchid tribe Nervilieae: independent transitions inAoB PLANTS · 2026Article
- Selective regime shifts and intracellular gene transfer in the organellar genomes of the mycoheterotrophic orchidFrontiers in plant science · 2026Article
- Plastome and transcriptome analysis reveals a degenerated photosynthesis-related pathway in the mycoheterotrophic vanilloid orchid Cyrtosia lindleyana.BMC plant biology · 2025Article
- The evolution of the plastid genomes in the holoparasitic Balanophoraceae.Proceedings. Biological sciences · 2025Article
- Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia.Annals of botany · 2024Article
- Pan-Chloroplast Genomes Reveal the Accession-Specific Marker forInternational journal of molecular sciences · 2024Article
- Analysis of Codon Usage Bias in the Plastid Genome ofCurrent issues in molecular biology · 2024Article
- Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation ofInternational journal of molecular sciences · 2024Article
- Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again.Genome biology and evolution · 2024Review
- Organelle Genomes ofInternational journal of molecular sciences · 2024Article
- Evolution ofFrontiers in plant science · 2024Article
- Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genusFrontiers in plant science · 2024Article
- Phylogenetic position and plastid genome structure ofFrontiers in plant science · 2024Article
- Characterization ofInternational journal of molecular sciences · 2023Article
- Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes.BMC genomics · 2023Article
- Characteristics and Comparative Analysis of Seven Complete Plastomes ofInternational journal of molecular sciences · 2023Article
18 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The question on the patterns and limits of reduction of plastid genomes in nonphotosynthetic plants and the reasons of their conservation is one of the intriguing topics in plant genome evolution. Here, we report sequencing and analysis of plastid genome in nonphotosynthetic orchids Epipogium aphyllum and Epipogium roseum, which, with sizes of 31 and 19 kbp, respectively, represent the smallest plastid genomes characterized by now. Besides drastic reduction, which is expected, we found several unusual features of these "minimal" plastomes: Multiple rearrangements, highly biased nucleotide composition, and unprecedentedly high substitution rate. Only 27 and 29 genes remained intact in the plastomes of E. aphyllum and E. roseum-those encoding ribosomal components, transfer RNAs, and three additional housekeeping genes (infA, clpP, and accD). We found no signs of relaxed selection acting on these genes. We hypothesize that the main reason for retention of plastid genomes in Epipogium is the necessity to translate messenger RNAs (mRNAs) of accD and/or clpP proteins which are essential for cell metabolism. However, these genes are absent in plastomes of several plant species; their absence is compensated by the presence of a functional copy arisen by gene transfer from plastid to the nuclear genome. This suggests that there is no single set of plastid-encoded essential genes, but rather different sets for different species and that the retention of a gene in the plastome depends on the interaction between the nucleus and plastids.
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