Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers

Deep Learning Network of Amomum villosum Quality Classification and Origin Identification Based on X-ray Technology

A machine vision system based on a convolutional neural network (CNN) was proposed to sort Amomum villosum using X-ray non-destructive testing technology in this study. The Amomum villosum fruit network (AFNet) algorithm was developed to identify the internal structure for quality classification and origin identification in this manuscript. This network model is composed of experimental features of Amomum villosum. In this study, we adopted a binary classification method twice consecutive to identify the origin and quality of Amomum villosum. The results show that the accuracy, precision, and specificity of the AFNet for quality classification were 96.33%, 96.27%, and 100.0%, respectively, achieving higher accuracy than traditional CNN under the condition of faster operation speed. In addition, the model can also achieve an accuracy of 90.60% for the identification of places of origin. The accuracy of multi-category classification performed later with the consistent network structure is lower than that of the cascaded CNNs solution. With this intelligent feature recognition model, the internal structure information of Amomum villosum can be determined based on X-ray technology. Its application will play a positive role to improve industrial production efficiency.

Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification

BACKGROUND

Species in genus Amomum always have important medicinal and economic values. Classification of Amomum using morphological characters has long been a challenge because they exhibit high similarity. The main goals of this study were to mine genetic markers from cp genomes for Amomum species identification and discover their evolutionary history through comparative analysis.

RESULTS

Three species Amomum villosum, Amomum maximum and Amomum longipetiolatum were sequenced and annotated for the complete chloroplast (cp) genomes, and the cp genomes of A. longipetiolatum and A. maximum were the first reported. Three cp genomes exhibited typical quadripartite structures with 163,269-163,591 bp in length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs and 3 rRNAs genes. 113-152 SSRs and 99 long repeats were identified in the three cp genomes. By designing specific primers, we amplified the highly variable loci and the mined genetic marker ccsA exhibited a relatively high species identification resolution in Amomum. The nonsynonymous and synonymous substitution ratios (Ka/Ks) in Amomum and Alpinia showed that most genes were subjected to a purifying selection. Phylogenetic analysis revealed the evolutionary relationships of Amomum and Alpinia species and proved that Amomum is paraphyletic. In addition, the sequenced sample of A. villosum was found to be a hybrid, becoming the first report of natural hybridization of this genus. Meanwhile, the high-throughput sequencing-based ITS2 analysis was proved to be an efficient tool for interspecific hybrid identification and with the help of the chloroplast genome, the hybrid parents can be also be determined.

CONCLUSION

The comparative analysis and mined genetic markers of cp genomes were conducive to species identification and evolutionary relationships of Amomum.

DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances

Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.

Essential oil components in the seed masses of Amomum xanthioides and its related species from Southeast Asia and China

Previously, to develop an objective identification method for Amomi Semen (AS), the nucleotide sequences of nrDNA ITS region and two cpDNA regions of nine Amomum taxa specimens from Southeast Asia and China were determined, and the generated phylogenetic tree showed six taxa specimens were divided into four groups. In this study, 51 crude drug samples of AS in Japanese markets were classified into four groups or species based on their ITS sequences. Approximately 67% of samples were derived from A. villosum var. xanthioides or A. xanthioides, A. villosum var. villosum and A. longiligulare prescribed in Japanese Pharmacopoeia, and the rest were mixed with A. uliginosum and A. microcarpum. Subsequently, the essential oil compositions of Amomum taxa specimens and AS samples were determined by GC-MS to characterize each group or species. Group 1(A. xanthioides) samples were characterized by containing higher amount of camphor(6) than bornyl acetate(9), and a specific germacrene D-4-ol; group 2(Chinese A. villosum var. villosum and var. xanthioides) by containing higher amount of 9 than 6, a specific isobornyl acetate; group 3(Laotian A. villosum var. villosum and A. longiligulare) by containing higher amount of 6 than 9, and a characteristic neointermedeol, except for A. longiligulare specimen from Hainan, China; group 4(A. uliginosum) by containing equivalent amount of 6 and 9, and the specific (E,E)-farnesyl acetate and (E,E)-farnesol. A. microcarpum samples were discriminated from the above groups by absence of 6 and 9, and with higher amount of (E)-nerolidol. There was a good correlation between genetic classification and chemical discrimination.

Genetic diversity of Amomum xanthioides and its related species from Southeast Asia and China

Amomum Semen, the seed mass of Amomum xanthioides, has been imported from Southeast Asia and China and used for the treatment of gastric and intestinal disorders. A. xanthioides has been treated as a synonym of A. villosum var. xanthioides. Furthermore, A. villosum var. villosum, A. villosum var. xanthioides, or A. longiligulare have been described as the botanical origin of Amomi Fructus, which is a similar crude drug in Chinese Pharmacopoeia. Under these circumstances, the botanical origin of Amomum Semen was changed to A. villosum var. xanthioides, A. villosum var. villosum, or A. longiligulare in Supplement II to the 17th edition of the Japanese Pharmacopoeia. To develop an objective identification method for Amomum Semen and to confirm the phylogenetic relationship among Amomum taxa, the nucleotide sequences of the nuclear ribosomal DNA internal transcribed spacer region and chloroplast DNA partial matK-trnK and trnH-psbA intergenic spacer regions were determined in specimens collected from Southeast Asia and China, including those from the type localities of each taxon. Six taxa were divided into four groups. A. xanthioides from Myanmar belonging to group 1 was discriminated from A. villosum var. xanthioides from China of group 2. A. villosum and its varieties were divided into two groups: group 2 included those from China, and group 3 consisted of A. villosum from Laos. A. longiligulare from China and Laos and A. uliginosum from Laos belonged to group 3 and group 4, respectively. These findings illustrate the phylogenetic basis for the need for taxonomical reorganization among the Amomum species.

A Comparison of Two Monoterpenoid Synthases Reveals Molecular Mechanisms Associated With the Difference of Bioactive Monoterpenoids Between Amomum villosum and Amomum longiligulare

The fruits of Amomum villosum and Amomum longiligulare are both used medicinally as Fructus Amomi the famous traditional Chinese medicine, however, the medicinal quality of A. villosum is better than that of A. longiligulare. Volatile terpenoids in the seeds, especially bornyl acetate and borneol, are the medicinal components of Fructus Amomi. The volatile terpenoids and transcriptome of developing seeds of A. villosum and A. longiligulare were compared in this study. The result revealed that the bornyl acetate and borneol contents were higher in A. villosum than in A. longiligulare. Additionally, six terpenoid synthase genes (AlTPS1-AlTPS6) were screened from the transcriptome of A. longiligulare, and AlTPS2 and AlTPS3 were found to share 98 and 83% identity with AvTPS2 and AvBPPS (bornyl diphosphate synthase) from A. villosum, respectively. BPPS is the key enzyme for the biosynthesis of borneol and bornyl acetate. Biochemical assays improved that AlTPS2 had an identical function to AvTPS2 as linalool synthase; however, AlTPS3 produced camphene as the major product and bornyl diphosphate (BPP) as the secondary product, whereas AvBPPS produced BPP as its major product. There was only one different amino acid between AlTPS3 (A496) and AvBPPS (G495) in their conserved motifs, and the site-directed mutation of A496G in DTE motif of AlTPS3 changed the major product from camphene to BPP. Molecular docking suggests that A496G mutation narrows the camphene-binding pocket and decreases the BPP-binding energy, thus increases the product BPP selectivity of enzyme. In addition, the expression level of AvBPPS was significantly higher than that of AlTPS3 in seeds, which was consistent with the related-metabolites contents. This study provides insight into the TPS-related molecular bases for the biosynthesis and accumulation differences of the bioactive terpenoids between A. villosum and A. longiligulare. BPPS, the key gene involved in the biosynthesis of the active compound, was identified as a target gene that could be applied for the quality-related identification and breeding of Fructus Amomi.

Chemotaxonomic Monitoring of Genetically Authenticated Amomi Fructus Using High-Performance Liquid Chromatography-Diode Array Detector with Chemometric Analysis

Amomi Fructus is widely used to treat digestive disorders, and Amomum villosum, A. villosum var. xanthioides, and A. longiligulare are permitted medicinally in national pharmacopeias. However, there are a variety of adulterants present in herbal markets owing to their morphological similarities to the genuine Amomum species. Forty-two Amomi Fructus samples from various origins were identified using internal transcribed spacer and chloroplast barcoding analyses, and then their chromatographic profiles were compared using chemometric analysis for chemotaxonomic monitoring. Among the Amomi Fructus samples, A. villosum, A. longiligulare, A. ghaticum, and A. microcarpum were confirmed as single Amomum species, whereas a mixture of either these Amomum species or with another Amomum species was observed in 15 samples. Chemotaxonomic monitoring results demonstrated that two medicinal Amomum samples, A. villosum and A. longiligulare, were not clearly distinguished from each other, but were apparently separated from other non-medicinal Amomum adulterants. A. ghaticum and A. microcarpum samples were also chemically different from other samples and formed their own species groups. Amomum species mixtures showed diverse variations of chemical correlations according to constituent Amomum species. Genetic authentication-based chemotaxonomic monitoring methods are helpful in classifying Amomi Fructus samples by their original species and to distinguish genuine Amomum species from the adulterants.

The complete chloroplast genome sequence of Amomum villosum Lour

Amomum villosum Lour. (Zingiberaceae) is an important edible and medicinal crop. The complete chloroplast (cp) genome of A. villosum was determined using Illumina sequencing platform. The size of whole cp genome was 164,069 bp, containing a small single copy (SSC) region of 15,353 bp and a large single copy (LSC) region of 88,798 bp, which were separated by a pair of inverted repeat (IRs) regions (29,959 bp). The A. villosum cp genome contained 133 genes, including eight ribosomal RNA genes (4 rRNA species), 38 transfer RNA genes (30 tRNA species) and 87 protein-coding genes (79 PCG species). The overall GC content of A. villosum cp genome is 36.05%. To investigate the evolution status of A. villosum, as well as Zingiberales, a phylogenetic tree with A. villosum and other 21 species was constructed based on their complete chloroplast genomes. Phylogenetic analysis revealed that A. villosum was closely related to Amomum krervanh.