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1.
PLoS One ; 15(8): e0237507, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32813726

RESUMO

DNA barcoding can identify biological species and provides an important tool in diverse applications, such as conserving species and identifying pathogens, among many others. If combined with statistical tests, DNA barcoding can focus taxonomic scrutiny onto anomalous species identifications based on morphological features. Accordingly, we put nonparametric tests into a taxonomic context to answer questions about our sequence dataset of the formal fungal barcode, the nuclear ribosomal internal transcribed spacer (ITS). For example, does DNA barcoding concur with annotated species identifications significantly better if expert taxonomists produced the annotations? Does species assignment improve significantly if sequences are restricted to lengths greater than 500 bp? Both questions require a figure of merit to measure of the accuracy of species identification, typically provided by the probability of correct identification (PCI). Many articles on DNA barcoding use variants of PCI to measure the accuracy of species identification, but do not provide the variants with names, and the absence of explicit names hinders the recognition that the different variants are not comparable from study to study. We provide four variant PCIs with a name and show that for fixed data they follow systematic inequalities. Despite custom, therefore, their comparison is at a minimum problematic. Some popular PCI variants are particularly vulnerable to errors in species annotation, insensitive to improvements in a barcoding pipeline, and unable to predict identification accuracy as a database grows, making them unsuitable for many purposes. Generally, the Fractional PCI has the best properties as a figure of merit for species identification. The fungal genus Ramaria provides unusual taxonomic difficulties. As a case study, it shows that a good taxonomic background can be combined with the pertinent summary statistics of molecular results to improve the identification of doubtful samples, linking both disciplines synergistically.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA Fúngico/análise , DNA Espaçador Ribossômico/análise , Fungos/classificação , Fungos/genética , Análise de Sequência de DNA/métodos , Teorema de Bayes , Modelos Estatísticos , Filogenia , Especificidade da Espécie
2.
PLoS One ; 15(8): e0231683, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32764752

RESUMO

Aquatic macroinvertebrates play a crucial role in freshwater ecosystems, but their diversity remains poorly known, particularly in the tropics. This "taxonomic void" limits our understanding of biodiversity patterns and processes in freshwater ecosystems, and the scale at which they operate. We used DNA barcoding to estimate lineage diversity (and the diversity of unique haplotypes) in 224 specimens of freshwater macroinvertebrates at a small spatial scale within the Panama Canal Watershed (PCW). In addition, we compiled available barcoding data to assess macroinvertebrate diversity at a broader spatial scale spanning the Isthmus of Panama. Consistently across two species delimitation algorithms (i.e., ABGD and GMYC), we found high lineage diversity within the PCW, with ~ 100-106 molecular operational taxonomic units (MOTUs) across 168 unique haplotypes. We also found a high lineage diversity along the Isthmus of Panama, but this diversity peaked within the PCW. However, our rarefaction/extrapolation approach showed that this diversity remains under-sampled. As expected, these results indicate that the diversity of Neotropical freshwater macroinvertebrates is higher than previously thought, with the possibility of high endemicity even at narrow spatial scales. Consistent with previous work on aquatic insects and other freshwater taxa in this region, geographic isolation is likely a main factor shaping these patterns of diversity. However, other factors such as habitat variability and perhaps local adaptation might be reshaping these patterns of diversity at a local scale. Although further research is needed to better understand the processes driving diversification in freshwater macroinvertebrates, we suggest that Neotropical streams hold a high proportion of hidden biodiversity. Understanding this diversity is crucial in the face of increasing human disturbance.


Assuntos
Biologia de Ecossistemas de Água Doce/métodos , Insetos/classificação , Invertebrados/genética , Animais , Biodiversidade , DNA/genética , Código de Barras de DNA Taxonômico/métodos , Ecossistema , Água Doce , Insetos/genética , Panamá , Zona do Canal do Panamá , Filogenia , Rios
3.
PLoS One ; 15(7): e0235682, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32645030

RESUMO

Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.


Assuntos
Chaperonina 60/genética , Código de Barras de DNA Taxonômico/métodos , Metagenômica/métodos , Microbiota/genética , Bactérias/genética , Feminino , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Vagina/microbiologia
4.
Proc Natl Acad Sci U S A ; 117(29): 17041-17048, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32632001

RESUMO

A central task in developmental biology is to learn the sequence of fate decisions that leads to each mature cell type in a tissue or organism. Recently, clonal labeling of cells using DNA barcodes has emerged as a powerful approach for identifying cells that share a common ancestry of fate decisions. Here we explore the idea that stochasticity of cell fate choice during tissue development could be harnessed to read out lineage relationships after a single step of clonal barcoding. By considering a generalized multitype branching process, we determine the conditions under which the final distribution of barcodes over observed cell types encodes their bona fide lineage relationships. We then propose a method for inferring the order of fate decisions. Our theory predicts a set of symmetries of barcode covariance that serves as a consistency check for the validity of the method. We show that broken symmetries may be used to detect multiple paths of differentiation to the same cell types. We provide computational tools for general use. When applied to barcoding data in hematopoiesis, these tools reconstruct the classical hematopoietic hierarchy and detect couplings between monocytes and dendritic cells and between erythrocytes and basophils that suggest multiple pathways of differentiation for these lineages.


Assuntos
Linhagem da Célula , Código de Barras de DNA Taxonômico/métodos , Animais , Linhagem da Célula/genética , Linhagem da Célula/fisiologia , Árvores de Decisões , Células Dendríticas/citologia , Eritrócitos/citologia , Hematopoese/genética , Hematopoese/fisiologia , Leucócitos/citologia , Modelos Biológicos , Biologia de Sistemas
5.
Science ; 368(6495): 1135-1140, 2020 06 05.
Artigo em Inglês | MEDLINE | ID: mdl-32499444

RESUMO

Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA Bacteriano/isolamento & purificação , DNA Fúngico/isolamento & purificação , Microbiologia Ambiental , Microbiota/genética , Esporos/genética , Sistemas CRISPR-Cas , DNA Bacteriano/genética , DNA Fúngico/genética , RNA Guia
6.
Bol. latinoam. Caribe plantas med. aromát ; 19(3): 300-313, mayo 2020. ilus, tab
Artigo em Inglês | LILACS | ID: biblio-1116300

RESUMO

Every 3 to 7 year angiosperms species of the flowering desert appear in the Atacama Region of Chile, as a result of the climatic phenomenon "El Niño". Our objective was to evaluate the universality of matK and rbcL barcode markers of these species, and validate their taxon through phylogenetic relationships. Argemone hunnemannii, Oenothera coquimbensis, Malesherbia humilis, Leucocoryne appendiculata, Loasa elongata, Nicotiana solanifolia, Stachys grandidentata, Aristolochia chilensis, Alstroemeria kingii and Adesmia eremophila, almost all classified as endemic to Chile, were collected in Pan de Azúcar and Llanos de Challe National Park (Atacama Region, Chile) at the end of October 2017. The phylogeny of these ten angiosperm species from the flowering desert was analyzed using rbcL and matK markers with the maximum likelihood and Bayesian inference methods. The results showed that 70% of the species can be distinguished with the matK or rbcL locus, however, 100% were distinguished using both loci. The phylogenetic results showed that the species formed clades with high reliability and high support with both the matK and rbcL genes, when comparing our results with sequences obtained from GenBank. The matK and rbcL genes are efficient markers for analyzing phylogenetic relationships and validating the taxonomy of flowering species.


Las especies de angiospermas del Desierto Florido de la Región de Atacama de Chile aparecen cada 3 a 7 años, influenciado por el fenómeno climático "El Niño". Nuestro objetivo fue evaluar la universalidad de los marcadores de código de barra matK y rbcL de estas especies, y validar su taxón por medio de relaciones filogenéticas. Las especies Argemone hunnemannii, Oenothera coquimbensis, Malesherbia humilis, Leucocoryne appendiculata, Loasa elongata, Nicotiana solanifolia, Stachys grandidentata, Aristolochia chilensis, Alstroemeria kingii y Adesmia eremophila son clasificadas la mayoría endémicas de Chile. Estas especies fueron colectadas en el Parque Nacional Pan de Azúcar y Llanos de Challe, Región de Atacama, Chile. La colecta se realizó a fines de octubre de 2017. Con los marcadores rbcL y matK se analizó la filogenia con los métodos máxima verosimilitud e inferencia bayesiana en diez especies de angiosperma del Desierto Florido. Los resultados mostraron que el 70% de las especies pueden ser distinguidas con un locus matK o rbcL, sin embargo, el 100% se distinguió usando ambos locus. Los resultados filogenéticos mostraron que las especies formaron clados con alta fiabilidad y alto soporte tanto con los genes matK y rbcL, al comparar con accesos de secuencias obtenidas de GenBank. Lo genes matK y rbcL son marcadores eficientes para analizar relaciones filogenéticas y validar el taxón de las especies de flor.


Assuntos
Filogenia , Plantas/genética , Deserto , Código de Barras de DNA Taxonômico/métodos , Ribulose-Bifosfato Carboxilase , Chile , Análise de Sequência de DNA
7.
PLoS One ; 15(5): e0233573, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32437469

RESUMO

The accuracy of the DNA barcoding tool depends on the existence of a comprehensive archived library of sequences reliably determined at species level by expert taxonomists. However, misidentifications are not infrequent, especially following large-scale DNA barcoding campaigns on diverse and taxonomically complex groups. In this study we used the species-rich flea beetle genus Longitarsus, that requires a high level of expertise for morphological species identification, as a case study to assess the accuracy of the DNA barcoding tool following several optimization procedures. We built a cox1 reference database of 1502 sequences representing 78 Longitarsus species, among which 117 sequences (32 species) were newly generated using a non-invasive DNA extraction method that allows keeping reference voucher specimens. Within this dataset we identified 69 taxonomic inconsistencies using barcoding gap analysis and tree topology methods. Threshold optimisation and a posteriori taxonomic revision based on newly generated reference sequences and metadata allowed resolving 44 sequences with ambiguous and incorrect identification and provided a significant improvement of the DNA barcoding accuracy and identification efficacy. Unresolved taxonomic uncertainties, due to overlapping intra- and inter-specific levels of divergences, mainly regards the Longitarsus pratensis species complex and polyphyletic groups L. melanocephalus, L. nigrofasciatus and L. erro. Such type of errors indicates either poorly established taxonomy or any biological processes that make mtDNA groups poorly predictive of species boundaries (e.g. recent speciation or interspecific hybridisation), thus providing directions for further integrative taxonomic and evolutionary studies. Overall, this study underlines the importance of reference vouchers and high-quality metadata associated to sequences in reference databases and corroborates, once again, the key role of taxonomists in any step of the DNA barcoding pipeline in order to generate and maintain a correct and functional reference library.


Assuntos
Besouros/genética , Código de Barras de DNA Taxonômico , Animais , Besouros/classificação , DNA/genética , DNA/isolamento & purificação , Código de Barras de DNA Taxonômico/métodos , Bases de Dados de Ácidos Nucleicos , Evolução Molecular
8.
PLoS One ; 15(5): e0233189, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32407365

RESUMO

A clear insight into the large-scale community structure of planktonic copepods is critical to understanding the mechanisms controlling diversity and biogeography of marine taxa in terms of their high abundance, ubiquity, and sensitivity to environmental changes. Here, we applied a 28S metabarcoding approach to large-scale communities of epipelagic and mesopelagic copepods at 70 stations across the Pacific Ocean and three stations in the Arctic Ocean. Major patterns of community structure and diversity, influenced by water mass structures, agreed with results from previous morphology-based studies. However, a large-scale metabarcoding approach could detect community changes even under stable environmental conditions, including changes in the north/south subtropical gyres and east/west areas within each subtropical gyre. There were strong effects of the epipelagic environment on mesopelagic communities, and community subdivisions were observed in the environmentally stable mesopelagic layer. In each sampling station, higher operational taxonomic unit (OTU) numbers and lower phylogenetic diversity were observed in the mesopelagic layer than in the epipelagic layer, indicating a recent rapid increase in species numbers in the mesopelagic layer. The phylogenetic analysis utilizing representative sequences of OTUs revealed trends of recent emergence of cold-water OTUs, which are mainly distributed at high latitudes with low water temperatures. Conversely, the high diversity of copepods at low latitudes was suggested to have been formed through long evolution under high water temperature conditions. The metabarcoding results suggest that evolutionary processes have strong impacts on current patterns of copepod diversity, and support the "out of the tropics" theory explaining latitudinal diversity gradients of copepods. Diversity patterns in both epipelagic and mesopelagic copepods was highly correlated to sea surface temperature; thus, predicted global warming may have a significant impact on copepod diversity in both layers.


Assuntos
Copépodes/genética , Código de Barras de DNA Taxonômico/métodos , Ecossistema , Animais , Sequência de Bases , Biodiversidade , Análise por Conglomerados , Modelos Lineares , Oceano Pacífico , Filogenia , Água do Mar , Temperatura
9.
J Food Sci ; 85(6): 1629-1634, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32468625

RESUMO

Tea, a popular aromatic infusion and food supplement, prepared from Camellia sinensis (L.) Kuntze leaves, is often subjected to adulteration with various undeclared inorganic and plant-derived materials. Cashew (Anacardium occidentale L.) nut husk is one of the most common plant tea adulterants. To date, there are limited DNA-based technologies for tea authentication and quantitative detection of adulterants. Herein, we used a universal plant DNA barcoding marker coupled with High Resolution Melting (Bar-HRM) analysis to authenticate tea products from cashew ground nut. Additionally, cashew-specific markers coupled with HRM technology were used to detect and quantify adulteration of tea with cashew DNA. This methodology can reliably detect admixtures as low as 1% v/v cashew in commercial tea products. Overall, our results demonstrate that the HRM technology is a strong molecular approach in tea authentication, capable of detecting very low adulterations in DNA admixtures. PRACTICAL APPLICATION: In this study, we established the use of high-resolution DNA-based technologies for the detection of cashew adulteration in tea, even in very low quantities. The technology could be applied to a greater range of plant-based tea adulterants. This work is expected to facilitate the traceability and authenticity of tea products and form the basis for the development of strategies against fraudulent practices.


Assuntos
Anacardium/genética , Camellia sinensis/genética , Contaminação de Alimentos/análise , Chá/química , Anacardium/química , Camellia sinensis/química , Código de Barras de DNA Taxonômico/métodos , DNA de Plantas/química , DNA de Plantas/genética , Contaminação de Alimentos/economia , Marcadores Genéticos , Chá/economia , Temperatura de Transição
10.
PLoS One ; 15(4): e0231717, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32298351

RESUMO

The fishes, which have currently named Aphanius Nardo, 1827 are the relict of the ancient ichthyofauna of the Tethys Sea. For a long time since 1827, the genus name has been subjected to revision by several researchers using mainly morphological features. Until recently, no comprehensive single- or multi-locus DNA barcoding study has been conducted on whole members of the family Aphaniidae. In the present study, by applying four conceptually different molecular species delimitation methods, including one distance-based method, one network-based and two topology-based methods, we examined a single-locus DNA barcode library (COI) diversity for the 268 sequences within the family Aphaniidae from the Old World (57 sequences are new in the present study and 211 sequences were retrieved from NCBI database). The molecular analyses revealed a clearer picture of intra-family relationships and allowed us to clarify the generic names, and also describe a new genus for the family Aphaniidae. Results supported distinction of three major clades related to three genera within this family: i) the first clade includes the A. mento group which are placed in a new genus, Paraphanius gen. nov., found in the Orontes (= Asi) and Tigris-Euphrates River drainage, the Levant in coastal waters and the Dead Sea basin, western Jordan, and in southern Turkey in the Mediterranean basins as well as in central Turkey. This clade positioned at the base of the phylogenetic tree, (ii) the second clade contains the A. dispar-like brackish water tooth-carps which are transferred to the genus Aphaniops Hoedeman, 1951 (type species, Lebias dispar), distributed in the coastal waters around the Red Sea and the Persian Gulf basins; and (iii) the third clade, the genus Aphanius Nardo, 1827 (type species Aphanius nanus = A. fasciatus) contains all the inland and inland-related tooth-carps, which are mainly distributed in the inland waters in Turkey and Iran and also in the inland-related drainages around the Mediterranean basin.


Assuntos
Ciprinodontiformes/classificação , Código de Barras de DNA Taxonômico/métodos , Complexo IV da Cadeia de Transporte de Elétrons/genética , Animais , Ciprinodontiformes/anatomia & histologia , Ciprinodontiformes/genética , História do Século XIX , História do Século XX , Oceano Índico , Irã (Geográfico) , Jordânia , Masculino , Filogenia , Turquia
11.
PLoS One ; 15(4): e0231436, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32298321

RESUMO

Molecular-based taxonomy, specifically DNA barcoding, has streamlined organism identification. For land plants, the recommended 2-locus barcode of rbcL and matK is not suitable for all groups, thus the second subunit of the nuclear internal transcribed spacer (ITS2) has received attention as a possible alternative. To date, evaluations of ITS2 have mostly been limited in scope to specific plant orders/families and single source material. Prior to using ITS2 to routinely characterize land plants present in environmental samples (i.e., DNA metabarcoding), a wet lab protocol optimized for bulk sample types is needed. To address this gap, in this study we determined the broad recoverability across land plants when using published ITS2 primer pairs, and subsequently optimized the PCR reaction constituents and cycling conditions for the best two performing primer pairs (ITS2F/ITSp4 and ITSp3/ITSu4). Using these conditions, both primer pairs were used to characterize land plants present in 17 diverse soils collected from across the US. The resulting PCR amplicons were prepared into libraries and pooled for sequencing on an Illumina® MiniSeq. Our existing bioinformatics workflow was used to process raw sequencing data and taxonomically assign unique ITS2 plant sequences by comparison to GenBank. Given strict quality criteria were imposed on sequences for inclusion in data analysis, only 43.6% and 7.5% of sequences from ITS2F/ITSp4 and ITSp3/ITSu4 respectively remained for taxonomic comparisons; ~7-11% of sequences originated from fungal co-amplification. The number of orders and families recovered did differ between primer pairs, with ITS2F/ITSp4 consistently outperforming ITSp3/ITSu4 by >15%. Primer pair bias was observed in the recovery of certain taxonomic groups; ITS2F/ITSp4 preferentially recovered flowering plants and grasses, whereas ITSp3/ITSu4 recovered more moss taxa. To maximize data recovery and reduce potential bias, we advocate that studies using ITS2 to characterize land plants from environmental samples such as soil use a multiple primer pair approach.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA Intergênico/genética , DNA de Plantas/genética , Metagenômica/métodos , Briófitas/classificação , Briófitas/genética , Código de Barras de DNA Taxonômico/normas , DNA Intergênico/química , DNA de Plantas/química , Gleiquênias/classificação , Gleiquênias/genética , Magnoliopsida/classificação , Magnoliopsida/genética , Metagenômica/normas , Reação em Cadeia da Polimerase/métodos , Reação em Cadeia da Polimerase/normas , Solo/química
12.
PLoS Biol ; 18(4): e3000667, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32298256

RESUMO

As biodiversity loss continues to accelerate, there is a critical need for education and biomonitoring across the globe. Portable technologies allow for in situ molecular biodiversity monitoring that has been historically out of reach for many researchers in habitat nations. In the realm of education, portable tools such as DNA sequencers facilitate in situ hands-on training in real-time sequencing and interpretation techniques. Here, we provide step-by-step protocols as a blueprint for a terrestrial conservation genetics field training program that uses low-cost, portable devices to conduct genomics-based training directly in biodiverse habitat countries.


Assuntos
Conservação dos Recursos Naturais/métodos , Genética/educação , Genética/instrumentação , Biodiversidade , Código de Barras de DNA Taxonômico/instrumentação , Código de Barras de DNA Taxonômico/métodos , Ecossistema , Feminino , Genética/organização & administração , Humanos , Masculino , Peru , Reação em Cadeia da Polimerase/instrumentação , Reação em Cadeia da Polimerase/métodos
13.
Proc Natl Acad Sci U S A ; 117(15): 8539-8545, 2020 04 14.
Artigo em Inglês | MEDLINE | ID: mdl-32217735

RESUMO

The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification and DNA metabarcoding. By using multispecies occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera and quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were nearly random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.


Assuntos
Biodiversidade , Código de Barras de DNA Taxonômico/métodos , DNA/análise , Ecossistema , Monitoramento Ambiental/métodos , Invertebrados/fisiologia , Áreas Alagadas , Animais , Meio Selvagem
14.
Nat Protoc ; 15(4): 1436-1458, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32132718

RESUMO

Embedded viral barcoding in combination with high-throughput sequencing is a powerful technology with which to track single-cell clones. It can provide clonal-level insights into cellular proliferation, development, differentiation, migration, and treatment efficacy. Here, we present a detailed protocol for a viral barcoding procedure that includes the creation of barcode libraries, the viral delivery of barcodes, the recovery of barcodes, and the computational analysis of barcode sequencing data. The entire procedure can be completed within a few weeks. This barcoding method requires cells to be susceptible to viral transduction. It provides high sensitivity and throughput, and enables precise quantification of cellular progeny. It is cost efficient and does not require any advanced skills. It can also be easily adapted to many types of applications, including both in vitro and in vivo experiments.


Assuntos
Rastreamento de Células/métodos , Células Clonais/citologia , Código de Barras de DNA Taxonômico/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Animais , Proliferação de Células/genética , DNA/genética , Vetores Genéticos/genética , Células HEK293 , Humanos , Lentivirus/genética , Camundongos
15.
Food Chem ; 318: 126501, 2020 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-32131042

RESUMO

Mold identification at the species level in environmental samples is a major challenge. Molecular techniques have been widely used for fungal classification, but as most primers are genus-specific, it is laborious to identify unknown samples. In this study, a PCR-based method for the identification of mold at the species level was developed. Therefore, common sequencing primers and combinations of them, targeting specific DNA regions, were tested. Here we present a combination of eight primer pairs to identify mold within a single PCR run. The approach correctly identified mold of unknown species from samples taken at a local bakery, including Penicillium chrysogenum, Penicillium citrinum, Cladosporium sphaerospermum, Paecilomyces formosus, Rhizopus oryzae and Aspergillus niger. Results obtained from the PCR method were successfully validated by chromatographic mycotoxin and microscopy analysis. Findings highlight DNA barcoding as an appropriate tool for mold identification; however, its efficacy is essentially dependent on DNA quality and primer selection.


Assuntos
Código de Barras de DNA Taxonômico/métodos , Fungos/isolamento & purificação , Reação em Cadeia da Polimerase/métodos , Pão/microbiologia , DNA Fúngico/genética , Contaminação de Alimentos/análise , Manipulação de Alimentos , Fungos/genética , Fungos/metabolismo , Micotoxinas/metabolismo
16.
PLoS One ; 15(3): e0229512, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32163430

RESUMO

Seafood mislabeling occurs in a wide range of seafood products worldwide, resulting in public distrust, economic fraud, and health risks for consumers. We quantified the extent of shrimp mislabeling in coastal and inland North Carolina. We used standard DNA barcoding procedures to determine the species identity of 106 shrimp sold as "local" by 60 vendors across North Carolina. Thirty-four percent of the purchased shrimp was mislabeled, and surprisingly the percentage did not differ significantly between coastal and inland counties. One third of product incorrectly marketed as "local" was in fact whiteleg shrimp: an imported and globally farmed species native to the eastern Pacific, not found in North Carolina waters. In addition to the negative ecosystem consequences of shrimp farming (e.g., the loss of mangrove forests and the coastal buffering they provide), North Carolina fishers-as with local fishers elsewhere-are negatively impacted when vendors label farmed, frozen, and imported shrimp as local, fresh, and wild-caught.


Assuntos
Aquicultura/ética , Aquicultura/métodos , Penaeidae/genética , Animais , Conservação dos Recursos Naturais/métodos , Código de Barras de DNA Taxonômico/métodos , Ecossistema , North Carolina , Penaeidae/classificação , Alimentos Marinhos/análise , Alimentos Marinhos/economia , Frutos do Mar/análise , Frutos do Mar/classificação
17.
PLoS One ; 15(3): e0229390, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32142513

RESUMO

Habitat degradation and summer droughts severely restrict feeding options for the endangered southern hairy-nosed wombat (SHNW; Lasiorhinus latifrons). We reconstructed SHNW summer diets by DNA metabarcoding from feces. We initially validated rbcL and ndhJ diet reconstructions using autopsied and captive animals. Subsequent diet reconstructions of wild wombats broadly reflected vegetative ground cover, implying local rather than long-range foraging. Diets were all dominated by alien invasives. Chemical analysis of alien food revealed Carrichtera annua contains high levels of glucosinolates. Clinical examination (7 animals) and autopsy (12 animals) revealed that the most degraded site also contained most individuals showing signs of glucosinolate poisoning. We infer that dietary poisoning through the ingestion of alien invasives may have contributed to the recent population crashes in the region. In floristically diverse sites, individuals appear to be able to manage glucosinolate intake by avoidance or episodic feeding but this strategy is less tractable in the most degraded sites. We conclude that recovery of the most affected populations may require effective Carrichtera management and interim supplementary feeding. More generally, we argue that protection against population decline by poisoning in territorial herbivores requires knowledge of their diet and of those food plants containing toxic principles.


Assuntos
Código de Barras de DNA Taxonômico/métodos , Dieta/efeitos adversos , Marsupiais/fisiologia , Plantas Tóxicas/genética , Plantas Tóxicas/toxicidade , Estações do Ano , Animais , Ecossistema , Fezes/química , Comportamento Alimentar , Marsupiais/genética
18.
PLoS One ; 15(3): e0229353, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32163447

RESUMO

In the last few years, DNA barcoding became an established method for species identification in biodiversity inventories and monitoring studies. Such studies depend on the access to a comprehensive reference data base, covering all relevant taxa. Here we present a comprehensive DNA barcode inventory of all amphibian and reptile species native to Austria, except for the putatively extinct Vipera ursinii rakosiensis and Lissotriton helveticus, which has been only recently reported for the very western edge of Austria. A total of 194 DNA barcodes were generated in the framework of the Austrian Barcode of Life (ABOL) initiative. Species identification via DNA barcodes was successful for most species, except for the hybridogenetic species complex of water frogs (Pelophylax spp.) and the crested newts (Triturus spp.), in areas of sympatry. However, DNA barcoding also proved powerful in detecting deep conspecific lineages, e.g. within Natrix natrix or the wall lizard (Podarcis muralis), resulting in more than one Barcode Index Number (BIN) per species. Moreover, DNA barcodes revealed the presence of Natrix helvetica, which has been elevated to species level only recently, and genetic signatures of the Italian water frog Pelophylax bergeri in Western Austria for the first time. Comparison to previously published DNA barcoding data of European amphibians and reptiles corroborated the results of the Austrian data but also revealed certain peculiarities, underlining the particular strengths and in the case of the genus Pelophylax also the limitations of DNA barcoding. Consequently, DNA barcoding is not only powerful for species identification of all life stages of most Austrian amphibian and reptile species, but also for the detection of new species, the monitoring of gene flow or the presence of alien populations and/or species. Thus, DNA barcoding and the data generated in this study may serve both scientific and national or even transnational conservation purposes.


Assuntos
Anfíbios/genética , Biodiversidade , Código de Barras de DNA Taxonômico/métodos , DNA/genética , Biblioteca Gênica , Répteis/genética , Animais , Áustria , DNA/isolamento & purificação , Filogenia , Padrões de Referência , Especificidade da Espécie
19.
Bull Entomol Res ; 110(4): 521-534, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32037992

RESUMO

Pear psyllids (Hemiptera: Psylloidea: Psyllidae: Cacopsylla spp.) belong to the most serious pests of pear (Pyrus spp.). They damage pear trees by excessive removal of phloem sap, by soiling the fruits with honeydew which, in turn, provides a substrate for sooty mould, and by transmission of Candidatus Phytoplasma spp., the causal agents of the pear decline disease. The morphological similarity, the presence of seasonal dimorphism that affects adult colour, size and wing morphology and uncritical use of species names, led to much confusion in the taxonomy of pear psyllids. As a result, pear psyllids have been frequently misidentified. Many of the entries attributed to Cacopsylla pyricola and other species in the GenBank are misidentifications which led to additional, unnecessary confusion. Here we analysed DNA barcodes of 11 pear psyllid species from eastern Asia, Europe and Iran using four mitochondrial gene fragments (COI 658 bp, COI 403 bp, COI-tRNAleu-COII 580 bp and 16S rDNA 452 bp). The efficiency of identification was notably high and considerable barcoding gaps were observed in all markers. Our results confirm the synonymies of the seasonal forms of Cacopsylla jukyungi ( = C. cinereosignata, winter form) and C. maculatili ( = C. qiuzili, summer form) previously suggested based on morphology. Some previous misidentifications (C. chinensis from China, Japan and Korea = misidentification of C. jukyungi; C. pyricola and C. pyrisuga from East Asia = misidentification of C. jukyungi and C. burckhardti, respectively; C. pyricola from Iran = misidentification of C. bidens, C. pyri and Cacopsylla sp.) are also corrected. There is no evidence for the presence of European pear psyllid species in East Asia.


Assuntos
Hemípteros/química , Hemípteros/genética , Animais , Código de Barras de DNA Taxonômico/métodos , Genes de Insetos , Genes Mitocondriais , Especificidade da Espécie
20.
BMC Genomics ; 21(1): 184, 2020 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-32106809

RESUMO

A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the identification of a range of fungal species in the vast majority of samples. In the HumanMycobiomeScan pipeline, sequence reads are mapped against a reference database containing fungal genome sequences only. We argue that using reference databases comprised of a single taxonomic group leads to an unacceptably high number of false-positives due to: (i) mapping to conserved genetic regions in reference genomes, and (ii) sequence contamination in the assembled reference genomes. To demonstrate this, we replaced the HumanMycobiomeScan's fungal reference database with one containing genome sequences of amphibians and reptiles and re-analysed their case study. The classification pipeline recovered all species present in the reference database, revealing turtles (Geoemydidae), bull frogs (Pyxicephalidae) and snakes (Colubridae) as the most abundant herpetological taxa in the human gut. We also re-analysed their case study using a kingdom-agnostic pipeline. This revealed that while the gut of hunter-gatherers and Western subjects may be colonized by a range of microbial eukaryotes, only three fungal families were retrieved. These results highlight the pitfalls of using taxon-specific reference databases for metagenome classification, even when they are comprised of curated whole genome data. We propose that databases containing all domains of life provide the most suitable option for metagenomic species profiling, especially when targeting microbial eukaryotes.


Assuntos
Biologia Computacional/métodos , Código de Barras de DNA Taxonômico/métodos , Fezes/microbiologia , Metagenômica/métodos , Anfíbios/classificação , Anfíbios/genética , Animais , Bactérias/classificação , Bactérias/genética , Curadoria de Dados , Dieta , Fezes/química , Fungos/classificação , Fungos/genética , Humanos , Itália , Répteis/classificação , Répteis/genética , Tanzânia
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