DNA barcoding in herbal medicine:Retrospective and prospective / 药物分析学报

DNA barcoding has been widely used for herb identification in recent decades,enabling safety and innovation in the field of herbal medicine.In this article,we summarize recent progress in DNA bar-coding for herbal medicine to provide ideas for the further development and application of this tech-nology.Most importantly,the standard DNA barcode has been extended in two ways.First,while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples,super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic levels.Second,mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials.In addition,some mo-lecular techniques,such as high-throughput sequencing and isothermal amplification,are combined with DNA barcodes for species identification,which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding era.Furthermore,standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference se-quences for species identification,which increases the accuracy and credibility of species discrimination based on DNA barcodes.In summary,DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.

A novel biological sources consistency evaluation method reveals high level of biodiversity within wild natural medicine: A case study of Amynthas earthworms as "Guang Dilong"

For wild natural medicine, unanticipated biodiversity as species or varieties with similar morphological characteristics and sympatric distribution may co-exist in a single batch of medical materials, which affects the efficacy and safety of clinical medication. DNA barcoding as an effective species identification tool is limited by its low sample throughput nature. In this study, combining DNA mini-barcode, DNA metabarcoding and species delimitation method, a novel biological sources consistency evaluation strategy was proposed, and high level of interspecific and intraspecific variations were observed and validated among 5376 Amynthas samples from 19 sampling points regarded as "Guang Dilong" and 25 batches of proprietary Chinese medicines. Besides Amynthas aspergillum as the authentic source, 8 other Molecular Operational Taxonomic Units (MOTUs) were elucidated. Significantly, even the subgroups within A. aspergillum revealed here differ significantly on chemical compositions and biological activity. Fortunately, this biodiversity could be controlled when the collection was limited to designated areas, as proved by 2796 "decoction pieces" samples. This batch biological identification method should be introduced as a novel concept regarding natural medicine quality control, and to offer guidelines for in-situ conservation and breeding bases construction of wild natural medicine.

Identification of processed Chinese medicinal materials using DNA mini-barcoding / 中国天然药物

Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and identification of processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA mini-barcoding, based on the sequencing of a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In the present study, six DNA barcode loci including ITS2, psbA-trnH, rbcL, matK, trnL (UAA) intron and its P6 loop, were employed for the authentication of 45 processed samples belonging to 15 species. We evaluated the amplification efficiency of each locus. We also examined the identification accuracy of the potential mini-barcode locus, of trnL (UAA) intron P6 loop. Our results showed that the five primary barcode loci were successfully amplified in only 8.89%-20% of the processed samples, while the amplification rates of the trnL (UAA) intron P6 loop were higher, at 75.56% successful amplification. We compared the mini-barcode sequences with Genbank using the Blast program. The analysis showed that 45.23% samples could be identified to genus level, while only one sample could be identified to the species level. We conclude that trnL (UAA) p6 loop is a candidate mini-barcode that has shown its potential and may become a universal mini-barcode as complementary barcode for authenticity testing and will play an important role in medicinal materials control.

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

Accurate identification is essential for any study exploring biodiversity. Unfortunately, museum type specimens preserved for more than a hundred years are often not informative enough for precise identification of the species represented by the name-bearing type. The use of ancient DNA can help solve taxonomic problems when name-bearing types no longer have diagnostic morphological features that allow for an accurate identification of the species involved. That is the case for Deuterodon pedri, an endemic species from a small drainage in the rio Doce basin in Minas Gerais, Brazil, for which the type material is in poor condition. Specimens of D. pedri were collected in 1865 by the Thayer Expedition to Brazil and fixed in spirits, enabling them to yield viable DNA. As the morphology alone of the type material does not allow for an accurate identification, we used both morphological and ancient DNA (aDNA) methods to decisively establish the identity of D. pedri. This identification allowed us to recognize the species among recently collected specimens and then, based on them, redescribe the species. A genetype for the lectotype of D. pedri is presented.(AU)

Uma identificação acurada é fundamental para qualquer estudo que explora a biodiversidade. Infelizmente, espécimes de museu descritos há mais de cem anos, algumas vezes não são informativos o suficiente para uma identificação precisa da espécie representada pelo tipo. O uso de DNA antigo pode ajudar a resolver problemas taxonômicos, quando espécimes tipos não apresentam mais as características morfológicas diagnósticas que permitem a identificação precisa das espécies. Esse é o caso de Deuterodon pedri, uma espécie endêmica de uma pequena drenagem na bacia do rio Doce, em Minas Gerais, Brasil cujo material tipo encontra-se em condições precárias. Espécimes de D. pedri foram coletados em 1865 pela Expedição Thayer ao Brasil e fixados em “cachaça”, o que permite apresentar DNA viável. Como apenas o exame morfológico do material tipo não permitiria a identificação precisa, nós usamos ambos os dados de análises morfológicas e DNA antigo (aDNA) para estabelecer decisivamente a identidade de D. pedri. Esta identificação permitiu reconhecer a espécie entre exemplares coletados recentemente e, com base neles, redescrever a espécie. É apresentado um genetipo para o lectótipo de D. pedri.(AU)

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments / Historia, aplicaciones, aspectos metodológicos y perspectivas para el uso del ADN ambiental (ADNa) en ecosistemas marinos y de agua dulce

Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980’s and phytoplankton communities in the water column since the early-1990’s. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.

El material genético que liberan los organismos en los componentes no vivos del ecosistema (aire, suelo, agua y sedimentos) recibe el nombre de ADN ambiental (ADNa) (eDNA, por su nombre en inglés). Este ADN previamente definido como ADN particulado ha sido utilizado desde mediados de la década de los ochenta y principios de los noventas para describir la composición de las comunidades microbianas en sedimentos marinos y de comunidades microbianas y fitoplanctónicas en la columna de agua. Recientemente el ADNa es utilizado principalmente para la detección y monitoreo de especies invasoras y en peligro. No obstante, existen múltiples áreas en las que este método puede ser utilizado como por ejemplo en ciencias forenses, ecología de poblaciones y comunidades, y taxonomía. Esta revisión proporciona información sobre esta nueva herramienta molecular, sus actuales y futuras aplicaciones, historia, principales consideraciones metodológicas y áreas emergentes para su uso en ecología y conservación de ambientes marinos y de agua dulce.