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Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda).

Ferri E, Barbuto M, Bain O, Galimberti A, Uni S, Guerrero R, Ferté H, Bandi C, Martin C, Casiraghi M - Front. Zool. (2009)

Bottom Line: Both alignment algorithm, gaps treatment, and the criteria used to define the threshold value were found to affect the performance of DNA barcoding with 12S rDNA marker.The results clearly show where DNA-based and morphological identifications are consistent, and where they are not.We propose DNA barcoding as a reliable, consistent, and democratic tool for species discrimination in routine identification of parasitic nematodes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Biotecnologie e Bioscienze, ZooPlantLab, Università degli Studi di Milano Bicocca, P,zza della Scienza 2, 20126 Milano, Italy. maurizio.casiraghi@unimib.it.

ABSTRACT

Background: We compared here the suitability and efficacy of traditional morphological approach and DNA barcoding to distinguish filarioid nematodes species (Nematoda, Spirurida). A reliable and rapid taxonomic identification of these parasites is the basis for a correct diagnosis of important and widespread parasitic diseases. The performance of DNA barcoding with different parameters was compared measuring the strength of correlation between morphological and molecular identification approaches. Molecular distance estimation was performed with two different mitochondrial markers (coxI and 12S rDNA) and different combinations of data handling were compared in order to provide a stronger tool for easy identification of filarioid worms.

Results: DNA barcoding and morphology based identification of filarioid nematodes revealed high coherence. Despite both coxI and 12S rDNA allow to reach high-quality performances, only coxI revealed to be manageable. Both alignment algorithm, gaps treatment, and the criteria used to define the threshold value were found to affect the performance of DNA barcoding with 12S rDNA marker. Using coxI and a defined level of nucleotide divergence to delimit species boundaries, DNA barcoding can also be used to infer potential new species.

Conclusion: An integrated approach allows to reach a higher discrimination power. The results clearly show where DNA-based and morphological identifications are consistent, and where they are not. The coherence between DNA-based and morphological identification for almost all the species examined in our work is very strong. We propose DNA barcoding as a reliable, consistent, and democratic tool for species discrimination in routine identification of parasitic nematodes.

No MeSH data available.


Related in: MedlinePlus

K2P distance graph of coxI filarioid nematodes. Frequency distribution of intraspecific and interspecific genetic divergences in morphologically identified filarioid nematodes. Graph shows 877 intraspecific and 21775 interspecific comparisons across 46 filarioid species. Distances were generated after alignment with MUSCLE, and calculated with MEGA (pairwise deletion), using Kimura's two parameter substitution model.
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Figure 2: K2P distance graph of coxI filarioid nematodes. Frequency distribution of intraspecific and interspecific genetic divergences in morphologically identified filarioid nematodes. Graph shows 877 intraspecific and 21775 interspecific comparisons across 46 filarioid species. Distances were generated after alignment with MUSCLE, and calculated with MEGA (pairwise deletion), using Kimura's two parameter substitution model.

Mentions: The minimum cumulative error is 0.62% (see Figure 1) at a threshold level of 4.8% (OT). ST (10 times intraspecific mean divergence) assumes the value of 5.0% and generates the same cumulative error (0.62%). As shown in K2P distance graph (Figure 2), using OT or ST, no overlap of intraspecific and interspecific nucleotide divergence occurs at distance values greater than threshold values (hence no false positive occur, type I errors). In contrast, as stated before, at distance values lower than OT or ST, a degree of overlap is observable (false negatives, type II errors). This percentage of false negatives (that represents the overall amount of cumulative error) are generated by two couples of congeneric species: 1) O. volvulus and O. ochengi (mean interspecific distance is 1.9%); 2) C. bulboidea and C. longa (mean interspecific distance is 0.2%). If O. volvulus and C. bulboidea are discarded from dataset, no overlap between intraspecific and interspecific distributions are observable, and the OT allows to reach 0% of cumulative error. In summary, identification based on molecular divergence threshold for coxI is coherent with morphological approach for 44 species out of 46.


Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda).

Ferri E, Barbuto M, Bain O, Galimberti A, Uni S, Guerrero R, Ferté H, Bandi C, Martin C, Casiraghi M - Front. Zool. (2009)

K2P distance graph of coxI filarioid nematodes. Frequency distribution of intraspecific and interspecific genetic divergences in morphologically identified filarioid nematodes. Graph shows 877 intraspecific and 21775 interspecific comparisons across 46 filarioid species. Distances were generated after alignment with MUSCLE, and calculated with MEGA (pairwise deletion), using Kimura's two parameter substitution model.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2657783&req=5

Figure 2: K2P distance graph of coxI filarioid nematodes. Frequency distribution of intraspecific and interspecific genetic divergences in morphologically identified filarioid nematodes. Graph shows 877 intraspecific and 21775 interspecific comparisons across 46 filarioid species. Distances were generated after alignment with MUSCLE, and calculated with MEGA (pairwise deletion), using Kimura's two parameter substitution model.
Mentions: The minimum cumulative error is 0.62% (see Figure 1) at a threshold level of 4.8% (OT). ST (10 times intraspecific mean divergence) assumes the value of 5.0% and generates the same cumulative error (0.62%). As shown in K2P distance graph (Figure 2), using OT or ST, no overlap of intraspecific and interspecific nucleotide divergence occurs at distance values greater than threshold values (hence no false positive occur, type I errors). In contrast, as stated before, at distance values lower than OT or ST, a degree of overlap is observable (false negatives, type II errors). This percentage of false negatives (that represents the overall amount of cumulative error) are generated by two couples of congeneric species: 1) O. volvulus and O. ochengi (mean interspecific distance is 1.9%); 2) C. bulboidea and C. longa (mean interspecific distance is 0.2%). If O. volvulus and C. bulboidea are discarded from dataset, no overlap between intraspecific and interspecific distributions are observable, and the OT allows to reach 0% of cumulative error. In summary, identification based on molecular divergence threshold for coxI is coherent with morphological approach for 44 species out of 46.

Bottom Line: Both alignment algorithm, gaps treatment, and the criteria used to define the threshold value were found to affect the performance of DNA barcoding with 12S rDNA marker.The results clearly show where DNA-based and morphological identifications are consistent, and where they are not.We propose DNA barcoding as a reliable, consistent, and democratic tool for species discrimination in routine identification of parasitic nematodes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Biotecnologie e Bioscienze, ZooPlantLab, Università degli Studi di Milano Bicocca, P,zza della Scienza 2, 20126 Milano, Italy. maurizio.casiraghi@unimib.it.

ABSTRACT

Background: We compared here the suitability and efficacy of traditional morphological approach and DNA barcoding to distinguish filarioid nematodes species (Nematoda, Spirurida). A reliable and rapid taxonomic identification of these parasites is the basis for a correct diagnosis of important and widespread parasitic diseases. The performance of DNA barcoding with different parameters was compared measuring the strength of correlation between morphological and molecular identification approaches. Molecular distance estimation was performed with two different mitochondrial markers (coxI and 12S rDNA) and different combinations of data handling were compared in order to provide a stronger tool for easy identification of filarioid worms.

Results: DNA barcoding and morphology based identification of filarioid nematodes revealed high coherence. Despite both coxI and 12S rDNA allow to reach high-quality performances, only coxI revealed to be manageable. Both alignment algorithm, gaps treatment, and the criteria used to define the threshold value were found to affect the performance of DNA barcoding with 12S rDNA marker. Using coxI and a defined level of nucleotide divergence to delimit species boundaries, DNA barcoding can also be used to infer potential new species.

Conclusion: An integrated approach allows to reach a higher discrimination power. The results clearly show where DNA-based and morphological identifications are consistent, and where they are not. The coherence between DNA-based and morphological identification for almost all the species examined in our work is very strong. We propose DNA barcoding as a reliable, consistent, and democratic tool for species discrimination in routine identification of parasitic nematodes.

No MeSH data available.


Related in: MedlinePlus