Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria

Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma comosa and C. latifolia

Members of the Curcuma genus, a crop in the Zingiberaceae, are widely utilized rhizomatous herbs globally. There are two distinct species, C. comosa Roxb. and C. latifolia Roscoe, referred to the same vernacular name "Wan Chak Motluk" in Thai. C. comosa holds economic importance and is extensively used as a Thai traditional medicine due to its phytoestrogenic properties. However, its morphology closely resembles that of C. latifolia, which contains zederone, a compound known for its hepatotoxic effects. They are often confused, which may affect the quality, efficacy and safety of the derived herbal materials. Thus, DNA markers were developed for discriminating C. comosa from C. latifolia. This study focused on analyzing core DNA barcode regions, including rbcL, matK, psbA-trnH spacer and ITS2, of the authentic C. comosa and C. latifolia species. As a result, no variable nucleotides in core DNA barcode regions were observed. The complete chloroplast (cp) genome was introduced to differentiate between the two species. The comparison revealed that the cp genomes of C. comosa and C. latifolia were 162,272 and 162,289 bp, respectively, with a total of 133 identified genes. The phylogenetic analysis revealed that C. comosa and C. latifolia exhibited a very close relationship with other Curcuma species. The cp genome of C. comosa and C. latifolia were identified for the first time, providing valuable insights for species identification and evolutionary research within the Zingiberaceae family.

Characterization of the complete chloroplast genome of Helicteres hirsuta Lour. 1790 (Helicteriodeae: Malvaceae)

Helicteres hirsuta Lour. 1790 is a precious medicinal plant species, especially for treating chronic liver diseases. Genomic data on H. hirsuta are limited. Therefore, this current study aimed to characterize the chloroplast genome of H. hirsuta and reconstruct the phylogenetic relationship among Helicteroideae taxa. Consequently, the complete chloroplast genome of H. hirsuta was 163,404 bp in length and contained 113 unique genes (79 protein-coding genes, 30 tRNA genes, and four rRNA genes). Notably, two introns of clpP gene of H. hirsuta were lost in comparison to that of other Helicteroideae species. The phylogenetic tree based on chloroplast genomes of eleven Helicteroideae species revealed that H. hirsuta was closely related to Reevesia species. In conclusion, our study described the first complete chloroplast genome of H. hirsuta, which is essential for tracing evolutionary history in the Helicteroideae subfamily.

Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications

The genus Argentina Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within Argentina owing to limited sampling of Argentina taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on Argentina from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of Argentina. The Argentina cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 Argentina cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in Argentina were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions (trnH-GUG-psbA, trnG-GCC-trnfM-CAU, trnD-GUC-trnY-GUA, rpl32-trnL-UAG, atpH-atpI, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, ndhF-rpl32, trnR-UCU-atpA, and accD-psaI) were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of Argentina. Our results indicated that Argentina is monophyletic. In the current sampling, the A. smithiana - A. anserina clade was sister to the remainder of Argentina. Our results corroborated the previous taxonomic treatments to transfer A. phanerophlebia and A. micropetala from the genus Sibbaldia L. to Argentina. Our results showed close relationships among A. stenophylla, A. microphylla, A. taliensis, and A. tatsienluensis, congruent with previous studies based on the morphology of these species. Twenty-six genes (rps3, rps15, rps16, rps19, rpl16, rpl20, rpl22, rpoA, rpoB, rpoC1, rpoC2, atpA, atpF, psbB, psbF, ndhA, ndhB, ndhC, ndhD, ndhF, rbcL, accD, ccsA, matK, ycf1, ycf2) were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in Argentina species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of Argentina.

Comparative analysis of medicinal plants Scutellaria baicalensis and common adulterants based on chloroplast genome sequencing

BACKGROUND

Scutellaria baicalensis Georgi has been extensively used as a medicinal herb in China for over 2000 years. They may be intentionally or inadvertently substituted or blended with comparable species in the local market, threatening clinical medication safety. Molecular markers are effective tools to prevent misidentification and eliminate doping and falsification among Scutellaria plants. This study screened four highly variable regions to identify Scutellaria and its adulterants. In addition, a phylogenetic analysis was performed using the complete cp genome combined with published Scutellaria species samples. Moreover, a comparative analysis of the cp genomes was conducted to investigate the cp genome evolution of S. baicalensis.

RESULTS

The complete cp genome of five species of Scutellaria was sequenced for the first time, and four previously published Scutellaria species were re-sequenced. They all exhibited a conserved quadripartite structure in their cp genomes, including two distinct regions, namely a small and large single copy region, respectively, and two inverted repeats encompassing the majority of ribosomal RNA genes. Furthermore, the nine species exhibited high conservation from aspects of the genome structure, codon usage, repeat sequences, and gene content. Four highly variable regions (matK-rps16, ndhC-trnV-UAC, psbE-petL, and rps16-trnQ-UUG) may function as potential molecular markers for differentiating S. baicalensis from its adulterants. Additionally, the monophyly of Scutellaria was ascertained and could be reclassified into two subgenera, subgenus Anaspis and subgenus Scutellaria, as evidenced by the phylogenetic analyses on sequences of cp genome and shared protein-coding sequences. According to the molecular clock analysis, it has been inferred that the divergence of Scutellaria occurred at approximately 4.0 Mya during the Pliocene Epoch.

CONCLUSION

Our study provides an invaluable theoretical basis for further Scutellaria species identification, phylogenetics, and evolution analysis.

The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification

Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.

Research on image recognition of three Fritillaria cirrhosa species based on deep learning

Based on the deep learning method, a network model that can quickly and accurately identify the species of Fritillaria cirrhosa species was constructed. The learning method based on deep residual convolutional neural network was used to input the unprocessed original image directly as input, and the features of the image were extracted through convolution and pooling operations. On this basis, the ResNet34 model was improved, and the additional fully connected layer was added in front of the Softmax classifier to improve the learning ability of the network model. Total of 3915 images of three kinds of Fritillaria cirrhosa were used as data sources for the experiments, among which 160 images of each type were randomly selected to form the validation set. The final training set recognition accuracy rate was 95.8%, the validation set accuracy rate reached 92.3%, and the test set accuracy rate was 88.7%. The image recognition method of Fritillaria cirrhosa based on deep learning proposed in this paper is effective and feasible, which can quickly and accurately identify the species of Fritillaria cirrhosa species, and provides a new idea for the intelligent recognition of Chinese medicinal materials.

DNA barcoding in herbal medicine: Retrospective and prospective

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 barcoding for herbal medicine to provide ideas for the further development and application of this technology. 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 molecular 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 sequences 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.

Complete Chloroplast Genome of Four Thai Native Dioscorea Species: Structural, Comparative and Phylogenetic Analyses

The chloroplast genomes of Dioscorea brevipetiolata, D. depauperata, D. glabra, and D. pyrifolia are 153,370–153,503 bp in size. A total of 113 genes were predicted, including 79 protein-coding sequences (CDS), 30 tRNA, and four rRNA genes. The overall GC content for all four species was 37%. Only mono-, di-, and trinucleotides were present in the genome. Genes adjacent to the junction borders were similar in all species analyzed. Eight distinct indel variations were detected in the chloroplast genome alignment of 24 Dioscorea species. At a cut-off point of Pi = 0.03, a sliding window analysis based on 25 chloroplast genome sequences of Dioscorea species revealed three highly variable regions, which included three CDS (trnC, ycf1, and rpl32), as well as an intergenic spacer region, ndhF-rpl32. A phylogenetic tree based on the complete chloroplast genome sequence displayed an almost fully resolved relationship in Dioscorea. However, D. brevipetiolata, D. depauperata, and D. glabra were clustered together with D. alata, while D. pyrifolia was closely related to D. aspersa. As Dioscorea is a diverse genus, genome data generated in this study may contribute to a better understanding of the genetic identity of these species, which would be useful for future taxonomic work of Dioscorea.

Complete chloroplast genomes of 11 Sabia samples: Genomic features, comparative analysis, and phylogenetic relationship

The genus Sabia is a woody climber belonging to the family Sabiaceae, order Proteales. Several species of this genus have been utilized as medicines for treating diseases, such as rheumatic arthritis, traumatism, hepatitis, etc. However, the lack of molecular data has prevented the accurate identification and refinement of taxonomic relationships in this genus. In this study, chloroplast genomes of 11 samples of the genus Sabia were assembled and analyzed. These chloroplast genomes showed a typical quadripartite structure and ranged in length from 160,956 to 162,209 bp. The structure of the genomes was found to be relatively conserved, with 130 genes annotated, including 85 coding genes, 37 tRNA genes, and eight rRNA genes. A total of 78-98 simple sequence repeats and 52-61 interspersed repeats were detected. Sequence alignment revealed 11 highly variable loci in chloroplast genomes. Among these loci, ndhF-ndhD achieved a remarkably higher resolution than the other regions. In addition, phylogenetic analysis indicated that Sect. Pachydiscus and Sect. Sabia of Sabia did not form two separate monophyletic groups. The divergence time calculated based on the Reltime method indicated that the evolutionary branches of Sabia and Meliosma started to form approximately 85.95 million years ago (Mya), and the species within Sabia began to diverge approximately 7.65 Mya. In conclusion, our study provides a basis for comprehensively exploring the phylogenetic relationships of Sabia. It also provides a methodological basis and data support for establishing a standardized and scientific identification system for this genus.

Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species

Artemisia Linn. is a large genus within the family Asteraceae that includes several important medicinal plants. Because of their similar morphology and chemical composition, traditional identification methods often fail to distinguish them. Therefore, developing an effective identification method for Artemisia species is an urgent requirement. In this study, we analyzed 15 chloroplast (cp) genomes, including 12 newly sequenced genomes, from 5 Artemisia species. The cp genomes from the five Artemisia species had a typical quadripartite structure and were highly conserved across species. They had varying lengths of 151,132-151,178 bp, and their gene content and codon preferences were similar. Mutation hotspot analysis identified four highly variable regions, which can potentially be used as molecular markers to identify Artemisia species. Phylogenetic analysis showed that the five Artemisia species investigated in this study were sister branches to each other, and individuals of each species formed a monophyletic clade. This study shows that the cp genome can provide distinguishing features to help identify closely related Artemisia species and has the potential to serve as a universal super barcode for plant identification.

Application of Analytical Technologies in the Discrimination and Authentication of Herbs from Fritillaria: A Review

Medicinal plants of Fritillaria are widely distributed in numerous countries around the world and possess excellent antitussive and expectorant effects. In particular, Fritillariae Bulbus (FB) as a precious traditional medicine has thousands of years of medical history in China. Herbs of Fritillaria have a high market value and demand while limited by harsh growing circumstances and scarce wild resources. As a consequence, fraudulent behaviors are regularly engaged by the unscrupulous merchants in an attempt to reap greater profits. It is of an urgent need to evaluate the quality of Fritillaria herbs and their products using various analytical instruments and techniques. This review has scrutinized approximately 160 articles from 1995 to 2022 published on the investigation of Fritillaria herbs and related herbal products. The botanical classification of genus Fritillaria, types of counterfeits, technologies applied for differentiating Fritillaria species were comprehensively summarized and discussed in the current review. Molecular and chromatographic identification were the dominant technologies in the authentication of Fritillaria herbs. Additionally, we brought some potential and promising technologies and analytical strategies into attention, which are worthy attempting in the future researches. This review could conduce to excellent reference value for further investigations of the authenticity assessment of Fritillaria species.

Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis

Corydalis is one of the few lineages that have been reported to have extensive large-scale chloroplast genome (cp-genome) rearrangements. In this study, novel cp-genome rearrangements of Corydalis pinnata, C. mucronate, and C. sheareri are described. C. pinnata is a narrow endemic species only distributed at Qingcheng Mountain in southwest China. Two independent relocations of the same four genes (trnM-CAU-rbcL) were found relocated from the typically posterior part of the large single-copy region to the front of it. A uniform inversion of an 11-14-kb segment (ndhB-trnR-ACG) was found in the inverted repeat region; and extensive losses of accD, clpP, and trnV-UAC genes were detected in all cp-genomes of all three species of Corydalis. In addition, a phylogenetic tree was reconstructed based on 31 single-copy orthologous proteins in 27 cp-genomes. This study provides insights into the evolution of cp-genomes throughout the genus Corydalis and also provides a reference for further studies on the taxonomy, identification, phylogeny, and genetic transformation of other lineages with extensive rearrangements in cp-genomes.

Comparative chloroplast genomes and phylogenetic analyses of Pinellia

Background

Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.

Methods and results

We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.

Conclusions

The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.

Supplementary Information

The online version of this article (10.1007/s11033-022-07617-5) contains supplementary material, which is available to authorized users.

Comparative Analysis of Chloroplast Genomes of Dalbergia Species for Identification and Phylogenetic Analysis

Dalbergia L.f. is a pantropical genus consisting of 269 species of trees, shrubs, and woody lianas. This genus is listed in CITES Appendices because of illegal logging and trafficking driven by the high economic value of its heartwood. Some species are also used medicinally. Species identification of Dalbergia timber and herbs is challenging but essential for CITES implementation. Molecular methods had been developed for some timber species, mostly from Madagascar and Southeast Asia, but medicinal species in south China were usually not included in those studies. Here, we sequenced and assembled the chloroplast genomes of five Dalbergia species native to Hong Kong, four of which are medicinal plants. Our aim is to find potential genetic markers for the identification of medicinal Dalbergia species based on divergence hotspots detected in chloroplast genomes after comparative and phylogenetic analysis. Dalbergia chloroplast genomes displayed the typical quadripartite structure, with the 50 kb inversion found in most Papilionoideae lineages. Their sizes and gene content are well conserved. Phylogenetic tree of Dalbergia chloroplast genomes showed an overall topology similar to that of ITS sequences. Four divergence hotspots (trnL(UAA)-trnT(UGU), ndhG-ndhI, ycf1a and ycf1b) were identified and candidate markers for identification of several Dalbergia species were suggested.

DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates

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

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

Background

Viola philippica Cav. is the only original plant for Violae Herba, as described in the Chinese Pharmacopoeia. The quality of this crude drug is affected by several adulterants from congeneric Viola species, and the authentic plant origin of Violae Herba is still controversial. Genome-based identification offers abundant genetic information and potential molecular markers that can be used for the authentication of closely related species. This study aims to investigate the certified origin of Violae Herba and to develop more effective markers for these easily confused species at the genetic level.

Methods

We compared the morphology and chemical composition of 18 batches of commercial samples and six widespread medicinal Viola plants used as Violae Herba or its substitutes by TLC and HPLC-Triple-TOF–MS/MS analyses. The complete chloroplast genomes of these species were sequenced and analyzed, including the general features, repeat sequences, mutational hotspots and phylogeny. The complete chloroplast genomes used as superbarcodes and some specific barcodes screened from mutational hotspots were tested for their ability to distinguish Viola species.

Results

A comparative study showed that Violae Herba is a multi-origin traditional Chinese medicine. Commercial decoction pieces and the standard reference drug were mainly derived from V. prionantha, clashing with the record in the Chinese Pharmacopoeia. Chloroplast genome analyses of V. philippica and five adulterants indicated that sequence divergence was relatively low within Viola species. By tree-based approaches, the complete chloroplast genomes showed a better discrimination ability and phylogenetic resolution for each Viola species. These results indicate that the whole chloroplast genomes can be used as superbarcodes to differentiate Viola medicinal plants. More specific DNA barcodes could be further developed from the Viola chloroplast genomes for more efficient and rapid identification of commercial Violae Herba and its adulterants.

Conclusions

This study has implications for chloroplast genome-based phylogenetic analysis and the authentication of multiple Viola species used as Violae Herba. The legal origin recorded in the Chinese Pharmacopoeia should be further revised to V. prionantha, in line with the commercial Violae Herba in the TCM markets.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13020-022-00585-9.

Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae)

The genus Styrax L. consists of approximately 130 species distributed in the Americas, eastern Asia, and the Mediterranean region. The phylogeny and evolutionary history of this genus are not clear. Knowledge of the phylogenetic relationships and the method for species identification will be critical for the evolution of this genus. In this study, we sequenced the chloroplast genome of 17 Styrax samples and added 17 additional chloroplast genome sequences from GenBank. The data were used to investigate chloroplast genome evolution, infer phylogenetic relationships, and access the species identification rate within Styrax. The Styrax chloroplast genome contains typical quadripartite structures, ranging from 157,641 bp to 159,333 bp. The chloroplast genome contains 114 unique genes. The P distance among the Styrax species ranged from 0.0003 to 0.00611. Seventeen small inversions and SSR sites were discovered in the Styrax chloroplast genome. By comparing with the chloroplast genome sequences, six mutation hotspots were identified, and the markers ycf1b and trnT-trnL were identified as the best Styrax-specific DNA barcodes. The specific barcodes and superbarcode exhibited higher discriminatory power than universal barcodes. Chloroplast phylogenomic results improved the resolution of the phylogenetic relationships of Styrax compared to previous analyses.

DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes

The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.