Identification of Angelica acutiloba, A. sinensis, and other Chinese medicinal Apiaceae plants by DNA barcoding.

Crude drug Angelicae acutilobae radix is one of the most important crude drugs in Japanese traditional medicine and is used mainly for the treatment of gynecological disorders. In the listing in the Japanese Pharmacopoeia XVIII, Angelicae acutilobae radix is defined as the root of Angelica acutiloba (Apiaceae), which has long been produced on an industrial scale in Japan. With the aging of farmers and depopulation of production areas, the domestic supply has recently declined and the majority of the supply is now imported from China. Due to having only slightly different morphological and chemical characteristics for the Apiaceae roots used to produce dried roots for Chinese medicines, the plant species originating the crude drug Apiaceae roots may be incorrectly identified. In particular, Angelicae sinensis radix, which is widely used in China, and Angelicae acutilobae radix are difficult to accurately identify by morphology and chemical profiles. Thus, in order to differentiate among Angelicae acutilobae radix and other radixes originated from Chinese medicinal Apiaceae plants, we established DNA markers. Using DNA sequences for the chloroplast psbA-trnH intergenic spacer and nuclear internal transcribed spacer regions, Angelicae acutilobae radix and other Chinese Apiaceae roots, including Angelicae sinensis radix, can be definitively identified.

Population genetic structure of wild Angelica acutiloba, A. acutiloba var. iwatensis, and their hybrids by atpF-atpA intergenic spacer in chloroplast DNA and genome-wide SNP analysis using MIG-seq.

Sampling surveys of Angelica acutiloba and A. acutiloba var. iwatensis, which are medicinal plants endemic to Japan, were conducted in the Chubu region in the central area of the main island of Japan. A. acutiloba grows in riverbeds in mountainous areas, while A. acutiloba. var. iwatensis grows on slopes near mountain ridges at 1000 m above sea level or on constantly collapsing rocky slopes and bare fields on developed land along asphalt roads in valleys of mountainous areas. Specimens of two wild Angelica species collected in this region were examined for maternal lineage by DNA polymorphism analysis of the atpF-atpA region for chloroplast DNA using direct sequencing and genomic component analysis by genome-wide SNP using MIG-seq. In this study area, while all A. acutiloba populations were monophyletic in both maternal and ancestral lineages, A. acutiloba var. iwatensis were genetically heterogeneous due to being composed of three maternal and three ancestral lineages to various degrees. In addition, a natural hybrid population with maternal lineage presumed to be A. acutiloba and paternal lineage A. acutiloba var. iwatensis was also found. In the present study, we report that the combined method of atpF-atpA and MIG-seq analyses is a useful tool for determining the population genetic structure of two wild Angelica species and for identifying hybrids.

Genetic and Chemical Diversity of Commercial Japanese Valerian.

In order to investigate the relationship between the chemical composition of essential oils and haplotypes of the psbA-trnH intergenic spacer region of chloroplast DNA (psbA-trnH) in Valerianae Fauriei Radix (Japanese Valerian; JV), we analyzed the DNA sequence and GC-MS metabolome of JV from Japanese markets and of herbal specimens from related species. DNA analysis revealed that JV products from Japan consisted of three haplotypes, namely AH-1, -2 and -5 reported in our previous study. The GC-MS metabolome revealed five chemotypes (J1, J2, C, K and O), of which J1, J2 and C were detected in the JV products from Japan. Chemotypes J1 and J2, with kessyl glycol diacetate (KGD) as the main volatile component, were found in the products of Japanese origin whereas chemotype C, with 1-O-acetyl-2,10-bisaboladiene-1,6-diol (ABD), was found in the products of Chinese and Korean origin. The haplotypes were correlated with the chemotypes: haplotype AH-1 for chemotype J1, AH-2 for chemotype J2 and AH-5 for chemotype C, suggesting that the chemical diversity of JV is not attributed to the environmental factors rather to the genetic factors. Since KGD and ABD were reported to have sedative effects and nerve growth factor (NGF)-potentiating effects, respectively, understanding the chemotypes and selecting an appropriate one would be important for the application of JV. The psbA-trnH haplotypes could be useful DNA markers for the quality control and standardization of JV.

Characterization of inter-annual changes in soil microbial flora of Panax ginseng cultivation fields in Shimane Prefecture of Western Japan by DNA metabarcoding using next-generation sequencing.

Panax ginseng C.A.Mey. (Araliaceae) cultivation suffers from the inability to cultivate the same fields continuously for long durations due to replant failure. The main cause of replant failure is considered to be the annual change in the soil microbial flora, especially the invasion and settlement of pathogenic microorganisms of soil-borne diseases. We analyzed the soil bacterial and fungal flora and inter-annual changes in their composition over 5 years in ginseng cultivation fields on Daikonshima Island, Shimane Prefecture of Western Japan by DNA metabarcoding using next-generation sequencing. Bacteria such as Sphingomonas sp., Bacillus sp., and Betaproteobacteria and the fungus Mortierella sp. were consistently detected throughout the cultivation period. The inter-annual compositional changes of the bacterial flora, especially two members of the family Burkholderiaceae, one member of the phylum Actinobacteria, one member of the genus Candidatus Koribacter, and one member of the genus Sphingomonas, corresponded to the cultivation period, whereas those of the fungal flora showed random changes, suggesting that the growth of ginseng may be greatly affected by changes in the bacterial flora. Therefore, a greater understanding of the bacterial flora could provide valuable information for the cultivation of ginseng. The absence of pathogenic microorganisms associated with soil-borne diseases, which have been reported as causative agents of the main diseases of ginseng, in all soil sampling sites throughout the entire cultivation period in this study proves, for the first time, that traditional cultivation management employing empirical methods and chemical control is an effective approach to control these pathogens. Therefore, the DNA metabarcoding of the bacterial flora could provide valuable information for cultivation management, specifically in detecting and controlling soil-borne pathogens responsible for ongoing cultivation damage in long-term cultivation of medicinal plants.

Identification of Valeriana fauriei and other Eurasian medicinal valerian by DNA polymorphisms in psbA-trnH intergenic spacer sequences in chloroplast DNA.

In order to differentiate among Valeriana fauriei Briq. and other Eurasian medicinal valerian (V. dioica L., V. hardwickii Wall., V. jatamansi Jones, and V. officinalis L.), we attempted to establish DNA markers. DNA sequences for the psbA-trnH intergenic spacer region of chloroplast DNA (psbA-trnH) and 18S ribosomal RNA, internal transcribed spacer 1 (ITS1), 5.8S ribosomal RNA, internal transcribed spacer 2 (ITS2), and 28S ribosomal RNA of nuclear DNA in V. fauriei and other Eurasian medicinal valerian were compared. Using partial sequences of psbA-trnH (nucleotide positions 1-75 from the 5' end of the intergenic spacer region), V. fauriei and other Eurasian medicinal valerian could be correctly identified to the species level. In addition, the partial sequences of psbA-trnH in V. fauriei contained five different haplotypes, and it was possible to distinguish the origins of valerian from Japan and Eurasia (China and Korea). On the other hand, individuals had heterogeneous sequences of ITS1 and ITS2, making it impossible to use direct sequencing and DNA markers of ITS1 and ITS2 to distinguish species and origins of V. fauriei and other Eurasian medicinal valerian.

Ecological, phylogenetical, and pharmacognostical characteristics of Aconitum kiyomiense endemic to Hida highlands, Takayama city, Gifu Prefecture, Japan.

Aconitum kiyomiense Kadota (Ranunculaceae) is endemic to Takayama city, Gifu Prefecture, central Japan. We collected specimens from marshes and flood plains at altitudes ranging from 852 to 1085 m and from a new habitat consisting of a mesic meadow in the subalpine belt (1681 m). Glabrous pedicels and flowering sequence of inflorescence were used for identification, but intra-species variations in the pilus of pedicels (glabrous, pilose, and chimeric types) were observed. Although the flowering sequence has been reported as both indeterminate and determinate, all specimens in the present study were determinate. No intra-species variation was detected via partial nuclear internal transcribed space, and sequences did not match another 17 East Eurasian continent subgenus Aconitum species. The chloroplast trnL-trnF intergenic spacer region (trnL-trnF) showed three different haplotypes. The trnL-trnF dominant haplotype sequence was identical to that of A. kusnezoffii growing on the Eurasian continent, suggesting that A. kiyomiense is more primitive than other Japanese aconitum and a relic species of the Eurasian continent. We report the first detection of aconitine alkaloids in the tuberous roots, which exhibited aconitine alkaloid contents varying from 0.32 to 4.05 mg/g dry weight (mg/g) for aconitine, 0.02 to 4.12 mg/g for hypaconitine, undetectable to 0.05 mg/g for jesaconitine, and 0.42 to 3.76 mg/g for mesaconitine. The variation of aconitine alkaloid components and contents appeared to be random and did not vary with inflorescence phenotype, trnL-trnF haplotype, environmental habitat conditions, or the geographic region of the collection sites. Since most populations showed no genetic intra-variation, it will be necessary to maintain the continuity of habitats and designate areas for conservation of genetic diversity at the population level.