A universal DNA barcode for the Tree of Life DOI Creative Commons
Bruno A. S. de Medeiros, Liming Cai, Peter J. Flynn

и другие.

Опубликована: Янв. 18, 2024

Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods do not reflect genomic complexity, may lack sufficient variation, rely on limited loci that are universal across the Tree of Life. Here, we develop a novel method uses exceptionally low-coverage genome skim data to create “varKode”, two-dimensional image representing landscape species. Using these varKodes, then train neural networks for precise taxonomic identification. Applying an expertly annotated dataset including hundreds newly sequenced samples from plant clade Malpighiales, demonstrate >91% precision when identifying species or genera. Remarkably, high accuracy remains despite minimal amounts lead failure applying alternative methods. We further illustrate broad utility varKodes several focal clades eukaryotes prokaryotes. As final test, classify entire NCBI eukaryote sequence-read archive identify its 861 constituent families with >95% utilizing less than 10 Mbp per sample. Enhanced computational efficiency scalability, inputs robust degraded DNA, modularity development make varKoding ideal approach science.

Язык: Английский

Multiple tests on saffron find new adulterant materials and reveal that Ist grade saffron is rare in the market DOI

V. C. Khilare,

Anita Tiknaik, B. Aditya Prakash

и другие.

Food Chemistry, Год журнала: 2018, Номер 272, С. 635 - 642

Опубликована: Авг. 22, 2018

Язык: Английский

Процитировано

49
Authentication of berries and berry‐based food products DOI Creative Commons
Heikki M. Salo, Nga Nguyen, Emmi Alakärppä

и другие.

Comprehensive Reviews in Food Science and Food Safety, Год журнала: 2021, Номер 20(5), С. 5197 - 5225

Опубликована: Авг. 1, 2021

Abstract Berries represent one of the most important and high‐valued group modern‐day health‐beneficial “superfoods” whose dietary consumption has been recognized to be beneficial for human health a long time. In addition being delicious, berries are rich in nutrients, vitamins, several bioactive compounds, including carotenoids, flavonoids, phenolic acids, hydrolysable tannins. However, due their high value, berry‐based products often subject fraudulent adulteration, commonly economical gain, but also unintentionally misidentification species. Deliberate adulteration comprises substitution high‐value with lower value counterparts mislabeling product contents. As is deceptive toward customers presents risk public health, food authentication through different methods applied as countermeasure. Although many have developed terms fast, sensitive, reliable, low‐cost analysis myriad species, application on still limited. The present review provides an overview development analytical chemistry methods, such isotope ratio analysis, liquid gas chromatography, spectroscopy, well DNA‐based electronic sensors, products. We provide earlier use recent advances these discuss drawbacks related application.

Язык: Английский

Процитировано

41
DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates DOI Creative Commons
Rahul Jamdade, Kareem A. Mosa, Ali El‐Keblawy

и другие.

Diversity, Год журнала: 2022, Номер 14(4), С. 262 - 262

Опубликована: Март 30, 2022

The need for herbal medicinal plants is steadily increasing. Hence, the accurate identification of plant material has become vital safe usage, avoiding adulteration, and trading. DNA barcoding shown to be a valuable molecular tool plants, ensuring safety efficacy materials therapeutic significance. Using morphological characters in genera with closely related species, species delimitation often difficult. Here, we evaluated capability nuclear barcode ITS2 plastid barcodes rbcL matK identify 20 medicinally important Caryophyllales. In our analysis, applied an integrative approach discrimination using pairwise distance-based unsupervised operational taxonomic unit “OTU picking” methods, viz., ABGD (Automated Barcode Gap Analysis) ASAP (Assemble Species by Automatic Partitioning). Along OTU picking Supervised Machine Learning methods (SML) were also implemented recognize divergent taxa. Our results indicated that was more successful distinguishing between examined implying it could used detect contamination adulteration these plants. Moreover, this study suggests combination than one method assist resolution morphologically similar or

Язык: Английский

Процитировано

24
Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships DOI Creative Commons

Chenqian Tang,

Xin Chen, Yunfei Deng

и другие.

BMC Plant Biology, Год журнала: 2022, Номер 22(1)

Опубликована: Окт. 22, 2022

Abstract Background Sorbus sensu stricto ( s.s. ) is a genus with important economical values because of its beautiful leaves, and flowers especially the colorful fruits. It belongs to tribe Maleae family Rosaceae, comprises about 90 species mainly distributed in China. There on-going dispute infrageneric classification delimitation as are morphologically similar. With aim shedding light on circumscription taxa within genus, phylogenetic analyses were performed using 29 chloroplast (cp) genomes (16 newly sequenced) representing two subgenera eight sections. Results The 16 cp sequenced range between 159,646 bp 160,178 length. All samples examined 22 re-annotated lato s.l. contain 113 unique genes 19 these duplicated inverted repeat (IR). Six hypervariable regions including trnR - atpA , petN psbM rpl32-trnL trnH psbA trnT trnL ndhC-trnV screened 44–53 SSRs 14–31 dispersed repeats identified potential molecular markers. Phylogenetic under ML/BI indicated that polyphyletic, but other five segregate genera, Aria Chamaemespilus Cormus Micromeles Torminalis monophyletic. Two major clades four sub-clades resolved full-support s.s . not consistent existing classification. subgenera, subg. Albocarmesinae supported monophyletic when S. tianschanica transferred from hupehensis var. paucijuga respectively. current at sectional level by analysis genome phylogeny. Conclusion Phylogenomic useful for inferring relationships Though structure highly conserved sequences used most promising molecule makers population genetics, studies.

Язык: Английский

Процитировано

24
A universal DNA barcode for the Tree of Life DOI Creative Commons
Bruno A. S. de Medeiros, Liming Cai, Peter J. Flynn

и другие.

Опубликована: Янв. 18, 2024

Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods do not reflect genomic complexity, may lack sufficient variation, rely on limited loci that are universal across the Tree of Life. Here, we develop a novel method uses exceptionally low-coverage genome skim data to create “varKode”, two-dimensional image representing landscape species. Using these varKodes, then train neural networks for precise taxonomic identification. Applying an expertly annotated dataset including hundreds newly sequenced samples from plant clade Malpighiales, demonstrate >91% precision when identifying species or genera. Remarkably, high accuracy remains despite minimal amounts lead failure applying alternative methods. We further illustrate broad utility varKodes several focal clades eukaryotes prokaryotes. As final test, classify entire NCBI eukaryote sequence-read archive identify its 861 constituent families with >95% utilizing less than 10 Mbp per sample. Enhanced computational efficiency scalability, inputs robust degraded DNA, modularity development make varKoding ideal approach science.

Язык: Английский

Процитировано

6