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Identification of species by multiplex analysis of variable-length sequences

Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A - Nucleic Acids Res. (2010)

Bottom Line: The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups.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.

Affiliation: Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal. fpereira@ipatimup.pt

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.

Discrimination of eutherian species using standard SPInDel profiles. (a) MDS plot obtained from the matrix of pairwise distances measured by the number of different loci between profiles. Species were labeled according to their taxonomic category. (b) UPGMA polar tree representing the phylogenetic relationship among the most represented eutherian groups. The input matrix and UPGMA tree were generated by the SPInDel workbench.
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Figure 4: Discrimination of eutherian species using standard SPInDel profiles. (a) MDS plot obtained from the matrix of pairwise distances measured by the number of different loci between profiles. Species were labeled according to their taxonomic category. (b) UPGMA polar tree representing the phylogenetic relationship among the most represented eutherian groups. The input matrix and UPGMA tree were generated by the SPInDel workbench.

Mentions: We tested the discriminatory efficiency of the SPInDel approach on the eutherian data set by PCA, considering profiles as variables. A multidimensional scaling (MDS) analysis was also performed with the R package ‘MASS’ (45), using the dissimilarity matrix obtained from the number of differences between profiles generated on the SPInDel workbench (Figure 4a and Supplementary Figure S7). The same matrix was used to construct a UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree (Figure 4b). An in-house developed algorithm was used to cluster profiles based on a dissimilarity matrix obtained from the number of differences between the profiles from different species. The output was exported in the Newick format from the SPInDel workbench and edited in the FigTree v1.3.1 software (http://tree.bio.ed.ac.uk/).Figure 4.

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Identification of species by multiplex analysis of variable-length sequences

Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A - Nucleic Acids Res. (2010)

Discrimination of eutherian species using standard SPInDel profiles. (a) MDS plot obtained from the matrix of pairwise distances measured by the number of different loci between profiles. Species were labeled according to their taxonomic category. (b) UPGMA polar tree representing the phylogenetic relationship among the most represented eutherian groups. The input matrix and UPGMA tree were generated by the SPInDel workbench.
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Figure 4: Discrimination of eutherian species using standard SPInDel profiles. (a) MDS plot obtained from the matrix of pairwise distances measured by the number of different loci between profiles. Species were labeled according to their taxonomic category. (b) UPGMA polar tree representing the phylogenetic relationship among the most represented eutherian groups. The input matrix and UPGMA tree were generated by the SPInDel workbench.
Mentions: We tested the discriminatory efficiency of the SPInDel approach on the eutherian data set by PCA, considering profiles as variables. A multidimensional scaling (MDS) analysis was also performed with the R package ‘MASS’ (45), using the dissimilarity matrix obtained from the number of differences between profiles generated on the SPInDel workbench (Figure 4a and Supplementary Figure S7). The same matrix was used to construct a UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree (Figure 4b). An in-house developed algorithm was used to cluster profiles based on a dissimilarity matrix obtained from the number of differences between the profiles from different species. The output was exported in the Newick format from the SPInDel workbench and edited in the FigTree v1.3.1 software (http://tree.bio.ed.ac.uk/).Figure 4.

Bottom Line: The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups.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.

Affiliation: Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal. fpereira@ipatimup.pt

ABSTRACT

Background: 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.

View Similar Images In: Results  - Collection
View Article: Pubmed Central -  PubMed
Show All Figures - Show MeSH
getmorefigures.php?pmc=3001097&rFormat=json&query=null&req=5