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Maurizio Casiraghi - One of the best experts on this subject based on the ideXlab platform.

  • DNA Barcoding: theoretical aspects and practical applications
    2020
    Co-Authors: Maurizio Casiraghi, Andrea Galimberti, Massimo Labra, Emanuele Ferri, Fabrizio De Mattia
    Abstract:

    DNA Barcoding is a molecular-based identification system, recently introduced in the scientific community. The method is not completely new to science, but the real innovation is not in the discrimination system itself: DNA Barcoding can be considered as the core of an integrated taxonomic system, where bioinformatics plays a key role. Time is now ripe for a real collaboration of all the different forces working in taxonomy, towards a “next generation systematics”. Index Terms — DNA Barcoding, DNA taxonomy, molecular identification, species identification. —————————— u ——————————

  • DNA Barcoding in mammals: what's new and where next?
    Hystrix-italian Journal of Mammalogy, 2015
    Co-Authors: Andrea Galimberti, Anna Sandionigi, Antonia Bruno, Adriana Bellati, Maurizio Casiraghi
    Abstract:

    DNA Barcoding is a universal molecular identification system of living beings for which efficacy and universality have been largely demonstrated in the last decade in many contexts. It is common to link DNA Barcoding to phylogenetic reconstruction, and there is indeed an overlap, but identification and phylogenetic positioning/classification are two different processes. In mammals, a better phylogenetic reconstruction, able to dig in fine details the relationships among biological entities, is really welcomed, but do we need DNA Barcoding too? In our opinion, the answer is positive, but not only for the identification power, nor for the supposed ability of DNA Barcoding to discover new species. We do need DNA Barcoding because it is a modern tool, able to create an integrated system, in which it is possible to link the many aspects of the biology of living beings starting from their identification. With 7000 species estimated and a growing interest in knowledge, exploitation and conservation, mammals are one of the best animal groups to achieve this goal. We organised our review to show how an integrative approach to taxonomy, leaded by DNA Barcoding, can be effective in the twenty-first century identification and/or description of species. Download the complete issue.

  • DNA Barcoding as a new tool for food traceability
    Food Research International, 2013
    Co-Authors: Andrea Galimberti, Fabrizio De Mattia, Alessia Losa, Ilaria Bruni, Silvia Federici, Maurizio Casiraghi, Stefano Martellos, Massimo Labra
    Abstract:

    Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA Barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA Barcoding in food traceability, and to delineate some best practices in the application of DNA Barcoding throughout the industrial pipeline. The use of DNA Barcoding for food safety and in the identification of commercial fraud is also discussed. © 2012 Elsevier Ltd.

  • DNA Barcoding as a new tool for food traceability
    Food Research International, 2013
    Co-Authors: Andrea Galimberti, Fabrizio De Mattia, Alessia Losa, Ilaria Bruni, Silvia Federici, Maurizio Casiraghi, Stefano Martellos, Massimo Labra
    Abstract:

    Abstract Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA Barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA Barcoding in food traceability, and to delineate some best practices in the application of DNA Barcoding throughout the industrial pipeline. The use of DNA Barcoding for food safety and in the identification of commercial fraud is also discussed.

  • Identification of poisonous plants by DNA Barcoding approach
    International Journal of Legal Medicine, 2010
    Co-Authors: Ilaria Bruni, Fabrizio De Mattia, Andrea Galimberti, Maurizio Casiraghi, Gabriele Galasso, Enrico Banfi, Massimo Labra
    Abstract:

    The plant exposures are one of the most frequent poisonings reported to poison control centres. The diagnosis of intoxicated patients is usually based on the morphological analysis of ingested plant portions; this procedure requires experience in systematic botany, because the plant identification is based on few evident traits. The objective of this research is to test DNA Barcoding approach as a new universal tool to identify toxic plants univocally and rapidly. Five DNA barcode regions were evaluated: three cpDNA sequences (trnH-psbA, rpoB and matK) and two nuclear regions (At103 and sqd1). The performance of these markers was evaluated in three plant groups: (1) a large collection of angiosperms containing different toxic substances, (2) congeneric species showing different degrees of toxicity and (3) congeneric edible and poisonous plants. Based on assessments of PCR, sequence quality and resolution power in species discrimination, we recommend the combination of plastidial and nuclear markers to identify toxic plants. Concerning plastidial markers, matK and trnH-psbA showed consistent genetic variability. However, in agreement with CBOL Plant Working Group, we selected matK as the best marker, because trnH-psbA showed some problems in sequences sizes and alignments. As a final and relevant observation, we also propose the combination of matK with a nuclear marker such as At103 to distinguish toxic hybrids form parental species. In conclusion, our data support the claim that DNA Barcoding is a powerful tool for poisonous plant identifications.

Andrea Galimberti - One of the best experts on this subject based on the ideXlab platform.

  • DNA Barcoding: theoretical aspects and practical applications
    2020
    Co-Authors: Maurizio Casiraghi, Andrea Galimberti, Massimo Labra, Emanuele Ferri, Fabrizio De Mattia
    Abstract:

    DNA Barcoding is a molecular-based identification system, recently introduced in the scientific community. The method is not completely new to science, but the real innovation is not in the discrimination system itself: DNA Barcoding can be considered as the core of an integrated taxonomic system, where bioinformatics plays a key role. Time is now ripe for a real collaboration of all the different forces working in taxonomy, towards a “next generation systematics”. Index Terms — DNA Barcoding, DNA taxonomy, molecular identification, species identification. —————————— u ——————————

  • DNA Barcoding in mammals: what's new and where next?
    Hystrix-italian Journal of Mammalogy, 2015
    Co-Authors: Andrea Galimberti, Anna Sandionigi, Antonia Bruno, Adriana Bellati, Maurizio Casiraghi
    Abstract:

    DNA Barcoding is a universal molecular identification system of living beings for which efficacy and universality have been largely demonstrated in the last decade in many contexts. It is common to link DNA Barcoding to phylogenetic reconstruction, and there is indeed an overlap, but identification and phylogenetic positioning/classification are two different processes. In mammals, a better phylogenetic reconstruction, able to dig in fine details the relationships among biological entities, is really welcomed, but do we need DNA Barcoding too? In our opinion, the answer is positive, but not only for the identification power, nor for the supposed ability of DNA Barcoding to discover new species. We do need DNA Barcoding because it is a modern tool, able to create an integrated system, in which it is possible to link the many aspects of the biology of living beings starting from their identification. With 7000 species estimated and a growing interest in knowledge, exploitation and conservation, mammals are one of the best animal groups to achieve this goal. We organised our review to show how an integrative approach to taxonomy, leaded by DNA Barcoding, can be effective in the twenty-first century identification and/or description of species. Download the complete issue.

  • DNA Barcoding as a new tool for food traceability
    Food Research International, 2013
    Co-Authors: Andrea Galimberti, Fabrizio De Mattia, Alessia Losa, Ilaria Bruni, Silvia Federici, Maurizio Casiraghi, Stefano Martellos, Massimo Labra
    Abstract:

    Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA Barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA Barcoding in food traceability, and to delineate some best practices in the application of DNA Barcoding throughout the industrial pipeline. The use of DNA Barcoding for food safety and in the identification of commercial fraud is also discussed. © 2012 Elsevier Ltd.

  • DNA Barcoding as a new tool for food traceability
    Food Research International, 2013
    Co-Authors: Andrea Galimberti, Fabrizio De Mattia, Alessia Losa, Ilaria Bruni, Silvia Federici, Maurizio Casiraghi, Stefano Martellos, Massimo Labra
    Abstract:

    Abstract Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA Barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA Barcoding in food traceability, and to delineate some best practices in the application of DNA Barcoding throughout the industrial pipeline. The use of DNA Barcoding for food safety and in the identification of commercial fraud is also discussed.

  • Identification of poisonous plants by DNA Barcoding approach
    International Journal of Legal Medicine, 2010
    Co-Authors: Ilaria Bruni, Fabrizio De Mattia, Andrea Galimberti, Maurizio Casiraghi, Gabriele Galasso, Enrico Banfi, Massimo Labra
    Abstract:

    The plant exposures are one of the most frequent poisonings reported to poison control centres. The diagnosis of intoxicated patients is usually based on the morphological analysis of ingested plant portions; this procedure requires experience in systematic botany, because the plant identification is based on few evident traits. The objective of this research is to test DNA Barcoding approach as a new universal tool to identify toxic plants univocally and rapidly. Five DNA barcode regions were evaluated: three cpDNA sequences (trnH-psbA, rpoB and matK) and two nuclear regions (At103 and sqd1). The performance of these markers was evaluated in three plant groups: (1) a large collection of angiosperms containing different toxic substances, (2) congeneric species showing different degrees of toxicity and (3) congeneric edible and poisonous plants. Based on assessments of PCR, sequence quality and resolution power in species discrimination, we recommend the combination of plastidial and nuclear markers to identify toxic plants. Concerning plastidial markers, matK and trnH-psbA showed consistent genetic variability. However, in agreement with CBOL Plant Working Group, we selected matK as the best marker, because trnH-psbA showed some problems in sequences sizes and alignments. As a final and relevant observation, we also propose the combination of matK with a nuclear marker such as At103 to distinguish toxic hybrids form parental species. In conclusion, our data support the claim that DNA Barcoding is a powerful tool for poisonous plant identifications.

Chenhong Li - One of the best experts on this subject based on the ideXlab platform.

  • multilocus DNA Barcoding species identification with multilocus data
    Scientific Reports, 2017
    Co-Authors: Jiamei Jiang, Shuli Song, Luke Tornabene, Ryan Chabarria, Gavin J P Naylor, Chenhong Li
    Abstract:

    Species identification using DNA sequences, known as DNA Barcoding has been widely used in many applied fields. Current Barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of Barcoding method does not always work when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus Barcoding framework that is based on gene capture and “next-generation” sequencing. We selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA Barcoding. We applied our method on two exemplar datasets each containing a pair of sister fish species: Siniperca chuatsi vs. Sini. kneri and Sicydium altum vs. Sicy. adelum, where the COI Barcoding approach failed. Both of our empirical and simulated results demonstrated that under limited gene flow and enough separation time, we could correctly identify species using multilocus Barcoding method. We anticipate that, as the cost of DNA sequencing continues to fall that our multilocus Barcoding approach will eclipse existing single-locus DNA Barcoding methods as a means to better understand the diversity of the living world.

  • multilocus DNA Barcoding species identification with multilocus data
    bioRxiv, 2017
    Co-Authors: Jiamei Jiang, Shuli Song, Luke Tornabene, Ryan Chabarria, Gavin J P Naylor, Chenhong Li
    Abstract:

    Species identification using DNA sequences, known as DNA Barcoding has been widely used in many applied fields. Current Barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of Barcoding is not always effective when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus Barcoding framework that is based on gene capture and "next-generation" sequencing and provide both empirical and simulation tests of its efficacy. We examine genetic distinctness in two pairs of fishes that are sister-species: Siniperca chuatsi vs. S. kneri and Sicydium altum vs. S. adelum, where the COI Barcoding approach failed species identification in both cases. Results revealed that distinctness between S. chuatsi and S. kneri increased as more independent loci were added. By contrast S. altum and S. adelum could not be distinguished even with all loci. Analyses of population structure and gene flow suggested that the two species of Siniperca diverged from each other a long time ago but have unidirectional gene flow, whereas the two species of Sicydium are not separated from each other and have high bidirectional gene flow. Simulations demonstrate that under limited gene flow ( 100000 generation), we can correctly identify species using more than 90 loci. Finally, we selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA Barcoding.

Massimo Labra - One of the best experts on this subject based on the ideXlab platform.

  • DNA Barcoding: theoretical aspects and practical applications
    2020
    Co-Authors: Maurizio Casiraghi, Andrea Galimberti, Massimo Labra, Emanuele Ferri, Fabrizio De Mattia
    Abstract:

    DNA Barcoding is a molecular-based identification system, recently introduced in the scientific community. The method is not completely new to science, but the real innovation is not in the discrimination system itself: DNA Barcoding can be considered as the core of an integrated taxonomic system, where bioinformatics plays a key role. Time is now ripe for a real collaboration of all the different forces working in taxonomy, towards a “next generation systematics”. Index Terms — DNA Barcoding, DNA taxonomy, molecular identification, species identification. —————————— u ——————————

  • DNA Barcoding as a new tool for food traceability
    Food Research International, 2013
    Co-Authors: Andrea Galimberti, Fabrizio De Mattia, Alessia Losa, Ilaria Bruni, Silvia Federici, Maurizio Casiraghi, Stefano Martellos, Massimo Labra
    Abstract:

    Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA Barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA Barcoding in food traceability, and to delineate some best practices in the application of DNA Barcoding throughout the industrial pipeline. The use of DNA Barcoding for food safety and in the identification of commercial fraud is also discussed. © 2012 Elsevier Ltd.

  • DNA Barcoding as a new tool for food traceability
    Food Research International, 2013
    Co-Authors: Andrea Galimberti, Fabrizio De Mattia, Alessia Losa, Ilaria Bruni, Silvia Federici, Maurizio Casiraghi, Stefano Martellos, Massimo Labra
    Abstract:

    Abstract Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA Barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA Barcoding in food traceability, and to delineate some best practices in the application of DNA Barcoding throughout the industrial pipeline. The use of DNA Barcoding for food safety and in the identification of commercial fraud is also discussed.

  • Identification of poisonous plants by DNA Barcoding approach
    International Journal of Legal Medicine, 2010
    Co-Authors: Ilaria Bruni, Fabrizio De Mattia, Andrea Galimberti, Maurizio Casiraghi, Gabriele Galasso, Enrico Banfi, Massimo Labra
    Abstract:

    The plant exposures are one of the most frequent poisonings reported to poison control centres. The diagnosis of intoxicated patients is usually based on the morphological analysis of ingested plant portions; this procedure requires experience in systematic botany, because the plant identification is based on few evident traits. The objective of this research is to test DNA Barcoding approach as a new universal tool to identify toxic plants univocally and rapidly. Five DNA barcode regions were evaluated: three cpDNA sequences (trnH-psbA, rpoB and matK) and two nuclear regions (At103 and sqd1). The performance of these markers was evaluated in three plant groups: (1) a large collection of angiosperms containing different toxic substances, (2) congeneric species showing different degrees of toxicity and (3) congeneric edible and poisonous plants. Based on assessments of PCR, sequence quality and resolution power in species discrimination, we recommend the combination of plastidial and nuclear markers to identify toxic plants. Concerning plastidial markers, matK and trnH-psbA showed consistent genetic variability. However, in agreement with CBOL Plant Working Group, we selected matK as the best marker, because trnH-psbA showed some problems in sequences sizes and alignments. As a final and relevant observation, we also propose the combination of matK with a nuclear marker such as At103 to distinguish toxic hybrids form parental species. In conclusion, our data support the claim that DNA Barcoding is a powerful tool for poisonous plant identifications.

Emanuele Ferri - One of the best experts on this subject based on the ideXlab platform.

  • DNA Barcoding: theoretical aspects and practical applications
    2020
    Co-Authors: Maurizio Casiraghi, Andrea Galimberti, Massimo Labra, Emanuele Ferri, Fabrizio De Mattia
    Abstract:

    DNA Barcoding is a molecular-based identification system, recently introduced in the scientific community. The method is not completely new to science, but the real innovation is not in the discrimination system itself: DNA Barcoding can be considered as the core of an integrated taxonomic system, where bioinformatics plays a key role. Time is now ripe for a real collaboration of all the different forces working in taxonomy, towards a “next generation systematics”. Index Terms — DNA Barcoding, DNA taxonomy, molecular identification, species identification. —————————— u ——————————

  • Integrated taxonomy: traditional approach and DNA Barcoding for the identification of filarioid worms and related parasites (Nematoda)
    Frontiers in Zoology, 2009
    Co-Authors: Emanuele Ferri, Andrea Galimberti, Michela Barbuto, Odile Bain, Ricardo Guerrero, Hubert Ferté, Claudio Bandi, Coralie Martin, Maurizio Casiraghi
    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.

  • integrated taxonomy traditional approach and DNA Barcoding for the identification of filarioid worms and related parasites nematoda
    Frontiers in Zoology, 2009
    Co-Authors: Emanuele Ferri, Andrea Galimberti, Michela Barbuto, Odile Bain, Ricardo Guerrero, Hubert Ferté, Claudio Bandi, Coralie Martin, Maurizio Casiraghi
    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.