ArticlePloS one2015
Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
88 citing papers in PubMed, 156 citations in OpenAlex.
- Orchid genome evolution and trait innovation.Journal of integrative plant biology · 2026Review
- Comparative plastome analysis of the Vandenboschia radicans complex in Korea: insights into its evolutionary history.BMC plant biology · 2026Article
- Comparative plastome analyses reveal life-form-associated selection signatures in Orchidaceae.BMC plant biology · 2026Article
- Complete Chloroplast Genome of theEcology and evolution · 2026Article
- Repeated loss of plastid NDH during evolution of land plants.Annals of botany · 2026Review
- Comprehensive species sampling reveals pervasive pseudogenization and recurrent complete loss of plastid ndh genes in the genus Cymbidium (Orchidaceae).BMC plant biology · 2025Article
- Plastid phylogenomics of the parietal clade of Malpighiales: ancestral genome synteny and congruent signal across exons, introns and spacers in support of Salicaceae relationships.Annals of botany · 2025Article
- Comparative Chloroplast Genomics of Ten Collabieae Species Including Three Novel Genomes.Genes · 2025Article
- Comparative analysis of 18 chloroplast genomes reveals genomic diversity and evolutionary dynamics in subtribe Malaxidinae (Orchidaceae).BMC plant biology · 2025Article
- Comparative plastome evaluation, phylogenomic analysis, and DNA signatures of medicinally important malvaceous genera and their adulterants.Scientific reports · 2025Article
- Plastome and transcriptome analysis reveals a degenerated photosynthesis-related pathway in the mycoheterotrophic vanilloid orchid Cyrtosia lindleyana.BMC plant biology · 2025Article
- The complete chloroplast genomes of four Aspidopterys species and a comparison with other Malpighiaceae species.Scientific reports · 2025Article
- Orchid phylogenetics and evolution: history, current status and prospects.Annals of botany · 2025Review
- Rapid loss of plastidFrontiers in plant science · 2025Article
- Comparative chloroplast genomics of Caryophyllaceae species: insights into sequence variations and phylogenetic evolution.BMC plant biology · 2024Article
- Plastome Evolution and Comparative Analyses of a Recently Radiated GenusInternational journal of molecular sciences · 2024Article
- Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats.International journal of molecular sciences · 2024Article
- Article
- Article
- High-throughput sequencing yields the complete plastid genome of the endemic speciesMitochondrial DNA. Part B, Resources · 2024Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.