ArticlePeerJ2015
Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae).
Article in PeerJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 54 citations in OpenAlex.
- Genome architecture modulates 35S and 5S rDNA homogenization in Asteraceae.The Plant journal : for cell and molecular biology · 2026Article
- Intragenomic and Interspecific Polymorphism of 35S rDNA Internal Transcribed Spacer 1 (ITS1) inInternational journal of molecular sciences · 2026Article
- Nuclear Ribosomal ITS1-5.8S rDNA-ITS2 Region as a Phylogenetic Marker forInternational journal of molecular sciences · 2026Article
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?Heredity · 2023Review
- Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips.Archives of microbiology · 2022Review
- Strategies for molecular authentication of herbal products: from experimental design to data analysis.Chinese medicine · 2022Review
- Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences.BMC plant biology · 2021Article
- New data onInternational journal for parasitology. Parasites and wildlife · 2021Article
- Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros.Scientific reports · 2021Article
- Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain EndemicFrontiers in plant science · 2021Article
- Power and Weakness of Repetition - Evaluating the Phylogenetic Signal From Repeatomes in the FamilyFrontiers in plant science · 2021Article
- Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China.BMC plant biology · 2020Article
- Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms.Annals of botany · 2019Article
- Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom.Frontiers in microbiology · 2019Article
- Article
- Article
- Chloroplast Genome Evolution in Actinidiaceae: clpP Loss, Heterogenous Divergence and Phylogenomic Practice.PloS one · 2016Article
- Article
- Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species.Scientific reports · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual's consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the "noncoding" ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming).
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.