ArticleNucleic acids research2010
Identification of species by multiplex analysis of variable-length sequences.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Animal Species and Identity Testing: Developments, Challenges, and Applications to Non-Human Forensics.Genes · 2025Review
- Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism.Life (Basel, Switzerland) · 2024Article
- Simple and field-adapted species identification of biological specimens combining multiplex multienzyme isothermal rapid amplification, lateral flow dipsticks, and universal primers for initial rapid screening without standard PCR laboratory.International journal of legal medicine · 2024Article
- Application of a Multiplex PCR Assay for Molecular Identification of Pathogenic and Non-Pathogenic Leptospires based on lipL32 andArchives of Razi Institute · 2023Article
- Airway microecology in rifampicin-resistant and rifampicin-sensitive pulmonary tuberculosis patients.BMC microbiology · 2022Article
- Insertion-and-Deletion Mutations between the Genomes of SARS-CoV, SARS-CoV-2, and Bat Coronavirus RaTG13.Microbiology spectrum · 2022Article
- Molecular detection and genetic characterization of Coxiella-like endosymbionts in dogs and ticks infesting dogs in Northeast India.Experimental & applied acarology · 2022Article
- Molecular Detection and Phylogenetic Analysis ofArchives of Razi Institute · 2022Article
- Metagenomics analysis of the fecal microbiota in Ring-necked pheasants (Saudi journal of biological sciences · 2022Article
- Molecular Sexing and Species Detection of Antlered European Hunting Game for Forensic Purposes.Animals : an open access journal from MDPI · 2022Article
- An inter-laboratory study of DNA-based identity, parentage and species testing in animal forensic genetics.Forensic sciences research · 2022Article
- Development and validation of simultaneous identification of 26 mammalian and poultry species by a multiplex assay.International journal of legal medicine · 2022Article
- DNA Accounting: Tallying Genomes to Detect Adulterated Saffron.Foods (Basel, Switzerland) · 2021Article
- Current issues for mammalian species identification in forensic science: a review.International journal of legal medicine · 2021Review
- SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae:International journal of molecular sciences · 2020Article
- Diversity and Bioactive Potential of Actinobacteria Isolated from a Coastal Marine Sediment in Northern Portugal.Microorganisms · 2020Article
- Review
- Rapid Nanopore Assay for Carbapenem-ResistantFrontiers in microbiology · 2019Article
- Metagenomic of clinically diseased and healthy broiler affected with respiratory disease complex.Data in brief · 2018Article
- A TaqMan real-time PCR method based on alternative oxidase genes for detection of plant species in animal feed samples.PloS one · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups. We also demonstrate that the identification of prokaryotic and viral species with numeric profiles of fragment lengths is generally straightforward. A computational platform is presented to facilitate the planning of projects and includes a large data set with nearly 1800 numeric profiles for species in all domains of life (1556 for eukaryotes, 105 for prokaryotes and 130 for viruses). Finally, a SPInDel profiling kit for discrimination of 10 mammalian species was successfully validated on highly processed food products with species mixtures and proved to be easily adaptable to multiple screening procedures routinely used in molecular biology laboratories. These results suggest that SPInDel is a reliable and cost-effective method for broad-spectrum species identification that is appropriate for use in suboptimal samples and is amenable to different high-throughput genotyping platforms without the need for DNA sequencing.
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Registered trials
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