Group‐specific polymerase chain reaction for DNA‐based analysis of species diversity and identity in dietary samples

@article{Jarman2004GroupspecificPC,
  title={Group‐specific polymerase chain reaction for DNA‐based analysis of species diversity and identity in dietary samples},
  author={S. Jarman and B. Deagle and N. Gales},
  journal={Molecular Ecology},
  year={2004},
  volume={13}
}
Unique DNA sequences are present in all species and can be used as biomarkers for the detection of cells from that species. These DNA sequences can most easily be detected using the polymerase chain reaction (PCR), which allows very small quantities of target DNA sequence to be amplified even when the target is mixed with large amounts of nontarget DNA. PCR amplification of DNA markers that are present in a wide range of species has proven very useful for studies of species diversity in… Expand

Topics from this paper

Earthworm primers for DNA-based gut content analysis and their cross-reactivity in a multi-species system
TLDR
A new group-specific primer pair for earthworms designed from cytochrome oxidase c subunit 1 (COI) sequences of 11 earthworm species found in Central Europe that can be used to detect consumption of earthworms by invertebrate predators is reported on. Expand
Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs
TLDR
A simple, robust and cheap method that is easily adaptable to many situations where a rare DNA template is to be PCR amplified in the presence of a higher concentration template with identical PCR primer binding sites is presented. Expand
Improving PCR detection of prey in molecular diet studies: importance of group‐specific primer set selection and extraction protocol performances
TLDR
The results clearly indicate that the A260/A280 absorbance ratio, which varies between extraction protocols, is positively correlated to the number of PCR amplifications of each prey taxon. Expand
New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach
TLDR
This work demonstrated that this new method for species identification using universal primers that amplify a very short but informative DNA fragment can be applied for diet analyses of a wide range of phytophagous species at large scales and is efficient for mammals, birds, insects and molluscs. Expand
A PCR‐based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces
TLDR
The DNA barcoding approach to diet analysis is extended to allow the inclusion of a wide taxonomic range of potential prey items and its potential generalization to other freshwater organisms may open new perspectives in food web ecology. Expand
A single mini-barcode test to screen for Australian mammalian predators from environmental samples
TLDR
The approach provides a cost-effective, time-efficient, and non-invasive tool that enables identification of all 8 medium-large mammal predators in Australia, including native and introduced species, using a single test. Expand
Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system
TLDR
This work investigates the occurrence of nuclear pseudogenes in fecal samples taken from bottlenose dolphins that were assayed for prey DNA with a universal primer technique and finds pseudogene in 13 of 15 samples and 1–5 pseudogene haplotypes per sample representing 5–100% of all amplicons produced. Expand
Group-Specific Multiplex PCR Detection Systems for the Identification of Flying Insect Prey
TLDR
The PCR assays presented here allow targeting prey at higher taxonomic levels such as family or order and therefore improve the ability to assess (trophic) interactions with flying insects in terrestrial and aquatic habitats. Expand
Molecular identification methods of fish species: reassessment and possible applications
  • F. Teletchea
  • Biology
  • Reviews in Fish Biology and Fisheries
  • 2009
TLDR
The tremendous advances in molecular biology in the past 10 years has rendered possible the study of DNA from virtually any substrates, offering new perspectives for the development of various applications, which will likely continue to increase in the future. Expand
Investigation on Natural Diets of Larval Marine Animals Using Peptide Nucleic Acid-Directed Polymerase Chain Reaction Clamping
The stomach contents of the larvae of marine animals are usually very small in quantity and amorphous, especially in invertebrates, making morphological methods of identification very difficult.Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 49 REFERENCES
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.
TLDR
Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. Expand
Novel universal primers establish identity of an enormous number of animal species for forensic application
TLDR
The primers described in this study universally amplify a specific segment of mitochondrial cytochrome b sequence from a sample of unknown origin and delineate its identity to the level of family, genus and species. Expand
Group‐specific polymerase chain reaction amplification of SSU rRNA‐encoding gene fragments from 12 microbial taxa
Starting from an alignment of all known representatives in GenBank, we designed group specific primers targeting SSU rRNA-encoding sequences of 12 microbial taxa known to contain insect pathogens andExpand
Group-Specific PCR Primers to Amplify 24S a-Subunit rRNA Genes from Kinetoplastida (Protozoa) Used in Denaturing Gradient Gel Electrophoresis
TLDR
The PCR-DGGE procedure developed in this study has been shown to be useful for distinguishing between different kinetoplastid species and may be a useful tool for evaluating the genetic diversity of this group in environmental samples, e.g., as a result of perturbation. Expand
Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.
  • T. Kocher, W. Thomas, +4 authors A. Wilson
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1989
TLDR
The polymerase chain reaction is used to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates, and the unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research. Expand
Rapid Identification of Adult and Naupliar Stages of Copepods Using DNA Hybridization Methodology
TLDR
A novel method of linking the probes to the plate with poly-T tail ensured the probes were positioned above the plate surface and available for hybridization; this significantly increased the sensitivity of the assay. Expand
Can multiple‐copy sequences of prey DNA be detected amongst the gut contents of invertebrate predators?
TLDR
Having demonstrated that shorter, multiple‐copy sequences survive digestion for a considerable period in the gut of a predator, the opportunity exists to develop new detection systems for studying predation in the field. Expand
PCR‐based gut content analysis of insect predators: using ribosomal ITS‐1 fragments from prey to estimate predation frequency
TLDR
A significant negative effect of time since feeding is found on the number of bands that could be detected in the guts of larvae and adult males and females of the generalist predator Coleomegilla maculata De Geer. Expand
PCR as a diagnostic and quantitative technique in veterinary parasitology.
TLDR
Specific attention is given to advances provided by multiplex PCR, fluorescence-based "real-time" PCR, and the utilization of PCR as a quantitative technique in the application of PCR methodology to parasite detection and differentiation and the diagnosis of disease. Expand
Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants.
TLDR
It was shown that the combination of molecular and statistical methods can be very useful to differentiate microbial communities. Expand
...
1
2
3
4
5
...