ArticlePloS one2020
Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae).
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Neotropical palms: from their conservation to economic potential.Frontiers in plant science · 2024Pooled it
- Mitogenome characterization and organellar genome evolution in achlorophyllous orchid Chamaegastrodia shikokiana Makino & F.Maek. (Orchidaceae).BMC plant biology · 2026Article
- Article
- Comprehensive characterization and phylogenetic analysis of the complete plastomes of two ant-orchids, Caularthron bicornutum and Myrmecophila thomsoniana.BMC plant biology · 2024Article
- Article
- Comparative Phylogenomic Study of Malaxidinae (Orchidaceae) Sheds Light on Plastome Evolution and Gene Divergence.International journal of molecular sciences · 2024Article
- Whole chloroplast genome sequence and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2024Article
- Kazakhstan tulips: comparative analysis of complete chloroplast genomes of four local and endangered species of the genusFrontiers in plant science · 2024Article
- Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes.BMC genomics · 2023Article
- Comparative Phylogenetic Analysis forInternational journal of molecular sciences · 2023Article
- Complete Chloroplast Genomes and Comparative Analyses of ThreeInternational journal of molecular sciences · 2023Article
- Phylogeny ofPlant diversity · 2023Article
- Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2023Article
- Phylogeny ofFrontiers in plant science · 2023Article
- Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology.Scientific reports · 2022Article
- The specific DNA barcodes based on chloroplast genes for species identification ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Orchid Phylotranscriptomics: The Prospects of Repurposing Multi-Tissue Transcriptomes for Phylogenetic Analysis and Beyond.Frontiers in plant science · 2022Article
- Molecular Phylogeny and Historical Biogeography ofFrontiers in plant science · 2022Article
- A Comprehensive Study of the GenusGenes · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. Three of them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.
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.