ArticleBMC evolutionary biology2013
Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations.
Article in BMC evolutionary biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed, 42 citations in OpenAlex.
- Article
- A customised target capture sequencing tool for molecular identification of Aloe vera and relatives.Scientific reports · 2021Article
- The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genusPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Telling plant species apart with DNA: from barcodes to genomes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species.Ecology and evolution · 2016Article
- DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market.Plant biotechnology journal · 2016Review
- Article
- Genomic repeat abundances contain phylogenetic signal.Systematic biology · 2015Article
- DNA barcodes successfully identified Macaronesian Lotus (Leguminosae) species within early diverged lineages of Cape Verde and mainland Africa.AoB PLANTS · 2014Article
- The explosive radiation of Cheirolophus (Asteraceae, Cardueae) in Macaronesia.BMC evolutionary biology · 2014Article
- The coding region of the UFGT gene is a source of diagnostic SNP markers that allow single-locus DNA genotyping for the assessment of cultivar identity and ancestry in grapevine (Vitis vinifera L.).BMC research notes · 2013Article
- Molecular phylogenetics of New Caledonian Diospyros (Ebenaceae) using plastid and nuclear markers.Molecular phylogenetics and evolution · 2013Article
- Primers for low-copy nuclear genes in the Hawaiian endemic Clermontia (Campanulaceae) and cross-amplification in Lobelioideae.Applications in plant sciences · 2013Article
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 at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA barcoding of land plants has relied traditionally on a small number of markers from the plastid genome. In contrast, low-copy nuclear genes have received little attention as DNA barcodes because of the absence of universal primers for PCR amplification.
resultsFrom pooled-species 454 transcriptome data we identified two variable intron-less nuclear loci for each of two species-rich genera of the Hawaiian flora: Clermontia (Campanulaceae) and Cyrtandra (Gesneriaceae) and compared their utility as DNA barcodes with that of plastid genes. We found that nuclear genes showed an overall greater variability, but also displayed a high level of heterozygosity, intraspecific variation, and retention of ancient alleles. Thus, nuclear genes displayed fewer species-diagnostic haplotypes compared to plastid genes and no interspecies gaps.
conclusionsThe apparently greater coalescence times of nuclear genes are likely to limit their utility as barcodes, as only a small proportion of their alleles were fixed and unique to individual species. In both groups, species-diagnostic markers from either genome were scarce on the youngest island; a minimum age of ca. two million years may be needed for a species flock to be barcoded. For young plant groups, nuclear genes may not be a superior alternative to slowly evolving plastid genes.
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.