DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (, , , , , and ) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose and as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., , , , , , , and ). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.
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http://dx.doi.org/10.3389/fpls.2021.782663 | DOI Listing |
Biodivers Data J
January 2025
Dynafor, INRAE, INP, ENSAT, 31326, Castanet Tolosan, France Dynafor, INRAE, INP, ENSAT, 31326 Castanet Tolosan France.
Background: DNA barcoding and metabarcoding are now powerful tools for studying biodiversity and especially the accurate identification of large sample collections belonging to diverse taxonomic groups. Their success depends largely on the taxonomic resolution of the DNA sequences used as barcodes and on the reliability of the reference databases. For wild bees, the barcode sequences coverage is consistently growing in volume, but some incorrect species annotations need to be cared for.
View Article and Find Full Text PDFPlant Divers
November 2024
CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China.
Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next generation barcodes in plants. However, conserved DNA barcoding markers, including complete plastid genome and nuclear ribosomal DNA (nrDNA) sequences, are inadequate for accurate species identification. Skmer, a recently proposed approach that estimates genetic distances among species based on unassembled genome skims, has been proposed to effectively improve species discrimination rate.
View Article and Find Full Text PDFZhongguo Zhong Yao Za Zhi
December 2024
Experimental Research Center, China Academy of Chinese Medical Sciences Beijing 100700, China.
The chloroplast genome is an important tool for studying plant classification, evolution, and the heterologous production of secondary metabolites and protein drugs. With advancements in sequencing technology and reductions in sequencing costs, chloroplast genome data have rapidly accumulated. However, existing chloroplast genome databases suffer from issues such as incomplete data, inadequate management, and inconsistent, inaccurate information, posing significant challenges for the development and utilization of the chloroplast genome.
View Article and Find Full Text PDFBiodivers Data J
January 2025
Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, China Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University Baoding China.
Background: The genus Pocock, 1901 previously included 25 known species and one subspecies from Asia, 12 species and one subspecies were reported in China.
New Information: Five new species of Pocock, 1901 from southern China are described: (♂♀) from Hainan, (♂♀) from Chongqing, (♂♀) from Hunan, (♂) from Sichuan and (♂♀) from south part of Shaanxi. DNA barcodes of the new species described herein are provided.
Sci Rep
January 2025
National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry, State Institute of Pharmaceutical Industry, 201203, Shanghai, People's Republic of China.
In Traditional Chinese Medicine (TCM), the medicinal leech is vital for treatments to promote blood circulation and eliminate blood stasis. However, the prevalence of counterfeit leech products in the market undermines the quality and efficacy of these remedies. Traditional DNA barcoding techniques, such as the COI barcode, have been limited in their application due to amplification challenges.
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