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Yuan B, He G, Dong W. The first complete mitochondrial genome of the genus Laelaps with novel gene arrangement reveals extensive rearrangement and phylogenetics in the superfamily Dermanyssoidea. EXPERIMENTAL & APPLIED ACAROLOGY 2024:10.1007/s10493-024-00943-2. [PMID: 39017744 DOI: 10.1007/s10493-024-00943-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/26/2024] [Indexed: 07/18/2024]
Abstract
We collected 56 specimens of Laelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507 bp in size and contains 37 genes and a control region of 2380 bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2 bp and 16 spacer regions ranging from 1 to 48 bp. We analyzed 13 protein-coding genes of L. chini mitogenome and found that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species of gamasid mites in the superfamily Dermanyssoidea from Genbank and the L. chini mitochondrial genome to analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species of gamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea.
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Affiliation(s)
- Bili Yuan
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Gangxian He
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Wenge Dong
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China.
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Karbarz M, Szlachcikowska D, Zapał A, Leśko A. Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach. Genes (Basel) 2024; 15:689. [PMID: 38927625 PMCID: PMC11202981 DOI: 10.3390/genes15060689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.
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Affiliation(s)
| | - Dominika Szlachcikowska
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, 35-225 Rzeszów, Poland
| | - Angelika Zapał
- Institute of Biology, University of Rzeszow, 35-959 Rzeszów, Poland
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Lonare N, Patil G, Waghmare S, Bhor R, Hardikar H, Tembe S. DNA Barcoding of Invasive Terrestrial Plant Species in India. Mol Biotechnol 2024:10.1007/s12033-024-01102-z. [PMID: 38430432 DOI: 10.1007/s12033-024-01102-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
Invasive plants are known to cause biodiversity loss and pose a major risk to human health and environment. Identification of invasive plants and distinguishing them from native species has been relied on morphological examination. Stringent requirement of floral characters and decreasing number of expert taxonomists are making conventional morphology-based identification system tedious and resource-intensive. DNA barcoding may help in quick identification of invasive species if distinct sequence divergence pattern at various taxonomic levels is observed. The present work evaluates the utility of four molecular markers; rbcL, matK, their combination (rbcL + matK), and psbA-trnH for identification of 37 invasive plant species from India and also in distinguishing them from 97 native species. A psbA-trnH locus was found to be of restricted utility in this work as it was represented by the members of a single family. A hierarchical increase in K2P mean divergence across different taxonomic levels was found to be the maximum for matK alone followed by rbcL + matK and rbcL alone, respectively. NJ clustering analysis, however, confirmed the suitability of combined locus (rbcL + matK) over individual rbcL and matK as the DNA barcode. RbcL showed the lowest resolution power among the three markers studied. MatK exhibited much better performance compared to rbcL alone in identifying most of the species accurately although it failed to show monophyly of genus Dinebra. Two families; Asteraceae and Poaceae, remained polyphyletic in the trees constructed by all three markers. Combined locus (rbcL + matK) was found to be the most suitable marker as it raised the resolution power of both the markers and could identify more than 90% of genera correctly. Phylogenetic tree constructed by Maximum-Parsimony method using combined locus as a molecular marker exhibited the best resolution, thus, supporting the significance of two-locus combination of rbcL + matK for barcoding invasive plant species from India. Present study contributes to the global barcode data of invasive plant species by adding fifty-one new sequences to it. Effective barcoding of additional number of native as well as invasive plant species from India is possible using this dual locus if it is combined with one or more new molecular plastid markers. Expansion of barcode database with a focus on barcode performance optimisation to improve discrimination ability at species level can be undertaken in future.
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Affiliation(s)
- Nayan Lonare
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Gayatri Patil
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Suprriya Waghmare
- IMT Technologies Pvt. Ltd, Kondhwa Khurd, Pune, Maharashtra, 411048, India
| | - Reshma Bhor
- IMT Technologies Pvt. Ltd, Kondhwa Khurd, Pune, Maharashtra, 411048, India
| | - Hrishikesh Hardikar
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Sanket Tembe
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India.
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Choudhary A, Shekhawat D, Pathania J, Sita K, Sharma S, Chawla A, Jaiswal V. Exploring DNA barcode for accurate identification of threatened Aconitum L. species from Western Himalaya. Mol Biol Rep 2024; 51:75. [PMID: 38175298 DOI: 10.1007/s11033-023-08927-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Aconitum species, belonging to Ranunculaceae, have high medicinal importance but due to their overexploitation come under IUCN (International Union for Conservation of Nature) red list. The precise identification of the Aconitum species is equally important because they are used in herbal formulations. The present study aimed to develop an efficient DNA barcode system for the authentic identification of Aconitum species. METHODS AND RESULTS A set of 92 barcode gene sequences (including 12 developed during the present study and 80 retrieved from NCBI) of 5 Aconitum species (A. heterophyllum, A. vialoceum, A. japonicum, A. napellus, and A. stapfianum) were analyzed using three methods (tree-based, distance-based, and similarity-based) for species discrimination. The PWG-distance method was found most effective for species discrimination. The discrimination rate of PWG- distance ranged from 33.3% (rbcL + trnH-psbA) to 100% (ITS, rbcL + ITS, ITS + trnH-psbA and rbcL + ITS + trnH-psbA). Among DNA barcodes and their combinations, the ITS marker had the highest degree of species discrimination (NJ-40%, PWG-100% and BLAST-40%), followed by trnH-psbA (NJ-20%, PWG-60% and BLAST-20%). ITS also had higher barcoding gap as compared to other individual barcodes and their combinations. Further, we also analyzed six Aconitum species (A. balfourii, A. ferox, A. heterophyllum, A. rotundifolium, A. soongaricum and A. violaceum) existing in Western Himalaya. These species were distinguished clearly through tree-based method using the ITS barcode gene with 100% species resolution. CONCLUSION ITS showed the best species discrimination power and was used to develop species-specific barcodes for Aconitum species. DNA barcodes developed during the present study can be used to identify Aconitum species.
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Affiliation(s)
- Anita Choudhary
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Deepika Shekhawat
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Jyotsna Pathania
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Kumari Sita
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shailika Sharma
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Amit Chawla
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Vandana Jaiswal
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Fu QL, Mo ZQ, Xiang XG, Milne RI, Jacquemyn H, Burgess KS, Sun YN, Yan H, Qiu L, Yang BY, Tan SL. Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae). BMC PLANT BIOLOGY 2023; 23:645. [PMID: 38097946 PMCID: PMC10722739 DOI: 10.1186/s12870-023-04663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND The genus Triplostegia contains two recognized species, T. glandulifera and T. grandiflora, but its phylogenetic position and species delimitation remain controversial. In this study, we assembled plastid genomes and nuclear ribosomal DNA (nrDNA) cistrons sampled from 22 wild Triplostegia individuals, each from a separate population, and examined these with 11 recently published Triplostegia plastomes. Morphological traits were measured from herbarium specimens and wild material, and ecological niche models were constructed. RESULTS Triplostegia is a monophyletic genus within the subfamily Dipsacoideae comprising three monophyletic species, T. glandulifera, T. grandiflora, and an unrecognized species Triplostegia sp. A, which occupies much higher altitude than the other two. The new species had previously been misidentified as T. glandulifera, but differs in taproot, leaf, and other characters. Triplotegia is an old genus, with stem age 39.96 Ma, and within it T. glandulifera diverged 7.94 Ma. Triplostegia grandiflora and sp. A diverged 1.05 Ma, perhaps in response to Quaternary climate fluctuations. Niche overlap between Triplostegia species was positively correlated with their phylogenetic relatedness. CONCLUSIONS Our results provide new insights into the species delimitation of Triplostegia, and indicate that a taxonomic revision of Triplostegia is needed. We also identified that either rpoB-trnC or ycf1 could serve as a DNA barcode for Triplostegia.
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Affiliation(s)
- Qing-Li Fu
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Hans Jacquemyn
- KU Leuven, Department of Biology, Plant Conservation and Population Biology, B-3001, Leuven, Belgium
| | - Kevin S Burgess
- College of Letters and Sciences, Columbus State University, University System of Georgia, Columbus, GA, 31907-5645, USA
| | - Ya-Nan Sun
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Hua Yan
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Li Qiu
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Bo-Yun Yang
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Shao-Lin Tan
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China.
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Wang C, Tang Y, Li Y, Hu C, Li J, Lyu A. Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii. BMC Genomics 2023; 24:488. [PMID: 37633914 PMCID: PMC10463391 DOI: 10.1186/s12864-023-09604-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023] Open
Abstract
WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species.
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Affiliation(s)
- Cheng Wang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yafang Tang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai, 264200, China
| | - Chao Hu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Jingyi Li
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Ang Lyu
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Science, Wuhan, 430064, China.
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Chang Y, Zhang R, Ma Y, Sun W. A haplotype-resolved genome assembly of Rhododendron vialii based on PacBio HiFi reads and Hi-C data. Sci Data 2023; 10:451. [PMID: 37438373 DOI: 10.1038/s41597-023-02362-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
Rhododendron vialii (subgen. Azaleastrum) is an evergreen shrub with high ornamental value. This species has been listed as a plant species with extremely small populations (PSESP) for urgent protection by China's Yunnan provincial government in 2021, due to anthropogenic habitat fragmentation. However, limited genomic resources hinder scientifically understanding of genetic threats that the species is currently facing. In this study, we assembled a high-quality haplotype-resolved genome of R. vialii based on PacBio HiFi long reads and Hi-C reads. The assembly contains two haploid genomes with sizes 532.73 Mb and 521.98 Mb, with contig N50 length of 35.67 Mb and 34.70 Mb, respectively. About 99.92% of the assembled sequences could be anchored to 26 pseudochromosomes, and 14 gapless assembled chromosomes were included in this assembly. Additionally, 60,926 protein-coding genes were identified, of which 93.82% were functionally annotated. This is the first reported genome of R. vialii, and hopefully it will lay the foundations for further research into the conservation genomics and horticultural domestication of this ornamentally important species.
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Affiliation(s)
- Yuhang Chang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, 650201, China.
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, 650201, China.
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Hu L, Tate JA, Gardiner SE, MacKay M. Ploidy variation in Rhododendron subsection Maddenia and its implications for conservation. AOB PLANTS 2023; 15:plad016. [PMID: 37197711 PMCID: PMC10184449 DOI: 10.1093/aobpla/plad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023]
Abstract
Polyploidy, which is common in plants, can confound taxon recognition and hence conservation assessments. In the taxonomically complex genus Rhododendron, 25 % of the over 1,300 taxa are considered under threat and 27 % Near Threatened or Data Deficient, with their taxonomy needing to be resolved urgently. Although ploidy levels of Rhododendron taxa range from diploid (2x) to dodecaploid (12x) according to previous reports, the extent of polyploidy across the genus has not been examined. We first summarized the taxonomic distribution of polyploids in the genus based on the literature. Then as a case study, we estimated ploidy levels of 47 taxa in subsection Maddenia (subgenus Rhododendron, section Rhododendron) using flow cytometry, together with verification of meiotic chromosome counts for representative taxa. The summary of reported ploidy in Rhododendron indicates that polyploidy is most common in subgenera Pentanthera and Rhododendron. In subsection Maddenia, all examined taxa are diploids except for the R. maddenii complex that shows a high ploidy variation (2-8x, 12x). We investigated ploidy level of 12 taxa in subsection Maddenia for the first time, and estimated genome sizes of two Rhododendron species. Knowledge of ploidy levels will inform phylogenetic analysis of unresolved species complexes. Overall, our study of subsection Maddenia provides a model for examining multiple issues including taxonomic complexity, ploidy variation and geographic distribution in relation to biodiversity conservation.
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Affiliation(s)
- Ling Hu
- Corresponding author’s e-mail address:
| | - Jennifer A Tate
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant and Food Research Limited, Fitzherbert Science Centre, Palmerston North 4472, New Zealand
| | - Marion MacKay
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
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Song F, Deng YF, Yan HF, Lin ZL, Delgado A, Trinidad H, Gonzales-Arce P, Riva S, Cano-Echevarría A, Ramos E, Aroni YP, Rivera S, Arakaki M, Ge XJ. Flora diversity survey and establishment of a plant DNA barcode database of Lomas ecosystems in Peru. Sci Data 2023; 10:294. [PMID: 37208352 DOI: 10.1038/s41597-023-02206-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
Lomas formations or "fog oases" are islands of vegetation in the desert belt of the west coast of South America, with a unique vegetation composition among the world's deserts. However, plant diversity and conservation studies have long been neglected, and there exists a severe gap in plant DNA sequence information. To address the lack of DNA information, we conducted field collections and laboratory DNA sequencing to establish a DNA barcode reference library of Lomas plants from Peru. This database provides 1,207 plant specimens and 3,129 DNA barcodes data corresponding with collections from 16 Lomas locations in Peru, during 2017 and 2018. This database will facilitate both rapid species identification and basic studies on plant diversity, thereby enhancing our understanding of Lomas flora's composition and temporal variation, and providing valuable resources for conserving plant diversity and maintaining the stability of the fragile Lomas ecosystems.
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Affiliation(s)
- Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yun-Fei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhe-Li Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Amalia Delgado
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Huber Trinidad
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Paúl Gonzales-Arce
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Sebastián Riva
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Asunción Cano-Echevarría
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Elmer Ramos
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Yaquelin Pamela Aroni
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Soledad Rivera
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Mónica Arakaki
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Chen S, Yin X, Han J, Sun W, Yao H, Song J, Li X. DNA barcoding in herbal medicine: Retrospective and prospective. J Pharm Anal 2023; 13:431-441. [PMID: 37305789 PMCID: PMC10257146 DOI: 10.1016/j.jpha.2023.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/07/2023] [Accepted: 03/25/2023] [Indexed: 06/13/2023] Open
Abstract
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.
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Affiliation(s)
- Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xianmei Yin
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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11
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Ye LJ, Möller M, Luo YH, Zou JY, Zheng W, Liu J, Li DZ, Gao LM. Variation in gene expression along an elevation gradient of Rhododendron sanguineum var. haemaleum assessed in a comparative transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1133065. [PMID: 37025136 PMCID: PMC10070981 DOI: 10.3389/fpls.2023.1133065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Selection along environmental gradients may play a vital role in driving adaptive evolution. Nevertheless, genomic variation and genetic adaptation along environmental clines remains largely unknown in plants in alpine ecosystems. To close this knowledge gap, we assayed transcriptomic profiles of late flower bud and early leaf bud of Rhododendron sanguineum var. haemaleum from four different elevational belts between 3,000 m and 3,800 m in the Gaoligong Mountains. By comparing differences in gene expression of these samples, a gene co-expression network (WGCNA) was constructed to identify candidate genes related to elevation. We found that the overall gene expression patterns are organ-specific for the flower and leaf. Differentially expressed unigenes were identified in these organs. In flowers, these were mainly related to terpenoid metabolism (RsHMGR, RsTPS), while in leaves mainly related to anthocyanin biosynthesis (RsCHS, RsF3'5'H). Terpenoids are the main components of flower scent (fragrance) likely attracting insects for pollination. In response to fewer pollinators at higher elevation zone, it seems relatively less scent is produced in flower organs to reduce energy consumption. Secondary metabolites in leaves such as anthocyanins determine the plants' alternative adaptive strategy to extreme environments, such as selective pressures of insect herbivory from environmental changes and substrate competition in biosynthesis pathways at high elevations. Our findings indicated that the gene expression profiles generated from flower and leaf organs showed parallel expression shifts but with different functionality, suggesting the existence of flexibility in response strategies of plants exposed to heterogeneous environments across elevational gradients. The genes identified here are likely to be involved in the adaptation of the plants to these varying mountainous environments. This study thus contributes to our understanding of the molecular mechanisms of adaptation in response to environmental change.
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Affiliation(s)
- Lin-Jiang Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory of Plant Resources and Biodiversity of Jiangxi Province, Jingdezhen University, Jingdezhen, Jiangxi, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
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12
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Jia YH, He F, Shen ZL, Xie XH, Lv SJ, Jiang BX, Yang GX, Yan YC, Wu ZH, Wu YY. Molecular characterization of a chalcone synthase gene RhCHS from Rhododendron × hybridum Hort. Gene X 2023; 857:147176. [PMID: 36627095 DOI: 10.1016/j.gene.2023.147176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/11/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Chalcone synthase (CHS) plays a vital role in anthocyanin biosynthesis pathway, which is associated with petal color of flower. To date, lots of CHS genes have been obtained from plants, while few were from Rhododendron genus. In this study we got a new CHS gene named RhCHS (MW358095) from Rhododendron × hybridum Hort. It had a 2040 bp coding region consisting of two exons and one intron. By using the deduced RhCHS protein as a query sequence, 15 CHS homologous family genes with sequence similarity from 60% to 98%, designated as RgCHS-D(x), were retrieved from the genome assembly of Rhododendron griersonianum (RGv1.1) by TBlastN. 12 CHS family genes were found locating in No.9 chromosome arranged in clusters, while only 3 of them exhibited in No.1, 2, and 8 chromosomes, respectively. The results revealed gene duplication of CHS in evolutionary process. Multiple alignment of the deduced amino acid sequence of RhCHS showed high similarity of the active site, the catalytic residue, and the signature motif, the conserved characteristics of which were also exhibited in the tertiary structure prediction of the RhCHS, as well as the phylogenetic tree, all these demonstrated the RhCHS belonging to the type III PKS superfamily. HPLC-MS/MS of flower petals detected the total concentration of CC, DC, and PelC. These anthocyanidins showed an overall increasing trend during the flowering period and reached the peak in the full-blooming stage, which was consistence with the changeable rule of RhCHS expression level. The promoter, which was 1507 bp exhibiting high β-glucuronidase (GUS) staining activity, was predicted containing many cis-acting elements, especially light and transcription factor such as bHLH, MYB, WRKY, Dof, and ERF. In short, this study may provide the help to Rhododendron × hybridum Hort. not only in the mechanism research of petals color exhibition, but also in molecular breeding of CHS practice value.
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Affiliation(s)
- Yong-Hong Jia
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Fan He
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Zi-Li Shen
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Xiao-Hong Xie
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Si-Jia Lv
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Bao-Xin Jiang
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Guo-Xia Yang
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Yi-Cheng Yan
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Ze-Hang Wu
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Yue-Yan Wu
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China.
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13
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Nie S, Zhao SW, Shi TL, Zhao W, Zhang RG, Tian XC, Guo JF, Yan XM, Bao YT, Li ZC, Kong L, Ma HY, Chen ZY, Liu H, El-Kassaby YA, Porth I, Yang FS, Mao JF. Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color. HORTICULTURE RESEARCH 2023; 10:uhac241. [PMID: 36643737 PMCID: PMC9832866 DOI: 10.1093/hr/uhac241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/17/2022] [Indexed: 05/09/2023]
Abstract
The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
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Affiliation(s)
- Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden
| | - Ren-Gang Zhang
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang 261322, China
| | - Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai-Yao Ma
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhao-Yang Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hui Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
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14
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Sang YL, Dai L, Wang P, Chen LJ, Jiao ML, Liu JY, Zhang NZ, Fan GW, Hao YJ, Wang XL. Investigation of insecticidal activity of two Rhododendron species on stored-product insects. JOURNAL OF PLANT DISEASES AND PROTECTION : SCIENTIFIC JOURNAL OF THE GERMAN PHYTOMEDICAL SOCIETY (DPG) 2023; 130:371-382. [PMID: 35965943 PMCID: PMC9361267 DOI: 10.1007/s41348-022-00654-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 07/20/2022] [Indexed: 05/03/2023]
Abstract
This study was designed to investigate the insecticidal activity of the essential oils (EOs) and extracts from Rhododendron rufum and Rhododendron przewalskii. The EOs were extracted from the leaves of R. Rufum and R. przewalskii by hydro-distillation and their chemical components were analyzed by gas chromatography-mass spectrometry (GC-MS). The repellency, contact toxicity and antifeedant activity of the EOs and extracts were evaluated against Sitophilus oryzae and Tribolium castaneum along with those of their main components. A total of nine compounds were identified from the EO of R. Rufum, and the most abundant component was myristicin (79.72%). The EO of R. Rufum exhibited repellent activities at different levels and its main compound myristicin showed contact toxicity and repellent effects against S. oryzae and T. castaneum. Meanwhile, by bioassay-guided fractionation, four compounds with strong antifeedant activities against T. castaneum, 24-methylenecycloartanyl-2'E, 4'Z-tetradecadienoate (1), methyl thyrsiflorin B acetate (2), friedelin (3) and Excoecarin R1 methyl ester (4) were separated and identified from the ethanol extract of R. przewalskii for the first time. Considering the significant anti-insect activities, the EOs and extracts of R. Rufum and R. przewalskii might be used in integrated pest strategies, establishing a good perspective for the comprehensive use of natural plant resources of Rhododendron genus.
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Affiliation(s)
- Yu-Li Sang
- College of Pharmacy, Liaoning University, No.66 Middle Chongshan Road, Shenyang, 110036 Liaoning China
| | - Lu Dai
- College of Pharmacy, Liaoning University, No.66 Middle Chongshan Road, Shenyang, 110036 Liaoning China
| | - Pei Wang
- College of Pharmacy, Liaoning University, No.66 Middle Chongshan Road, Shenyang, 110036 Liaoning China
| | - Li-Jiang Chen
- College of Pharmacy, Liaoning University, No.66 Middle Chongshan Road, Shenyang, 110036 Liaoning China
| | - Mei-Ling Jiao
- College of Pharmacy, Liaoning University, No.66 Middle Chongshan Road, Shenyang, 110036 Liaoning China
| | - Jing-Yu Liu
- College of Pharmacy, Liaoning University, No.66 Middle Chongshan Road, Shenyang, 110036 Liaoning China
| | - Nai-Zhi Zhang
- College of Pharmacy, Liaoning University, No.66 Middle Chongshan Road, Shenyang, 110036 Liaoning China
| | - Guang-Wen Fan
- College of Pharmacy, Liaoning University, No.66 Middle Chongshan Road, Shenyang, 110036 Liaoning China
| | - Yan-Jun Hao
- Liaoning Academy of Traditional Chinese Medicine, Liaoning University of Traditional Chinese Medicine, No.79 East Chongshan Road, Shenyang, 110032 Liaoning China
| | - Xiu-Lan Wang
- Inner Mongolia Institute of Mongolian Medicine Engineering Technology, Inner Mongolia University for Nationalities, No.536 West Huolinhe Street, Tongliao, 028000 China
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15
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Ma W, Yu T, Wang W, Wang F, Ji H, Mu C. The complete chloroplast genome of Rhododendron calophytum Franch (Ericaceae). Mitochondrial DNA B Resour 2022. [DOI: 10.1080/23802359.2022.2106161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Wenbao Ma
- Ecological Restoration and Conservation of Forests and Wetlands Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu, China
| | - Tao Yu
- CECEP Eco-Product Development Research Center, Beijing, China
| | - Wanjiang Wang
- Ecological Restoration and Conservation of Forests and Wetlands Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu, China
| | - Fei Wang
- West China Subalpine Botanical Garden, Dujiangyan, China
| | - Huijuan Ji
- Ecological Restoration and Conservation of Forests and Wetlands Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu, China
| | - Changlong Mu
- Ecological Restoration and Conservation of Forests and Wetlands Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu, China
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16
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Lu G, Qiao J, Wang L, Liu H, Wu G, Zhu Y, Zhao Y, Xie G, Qin M. An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin. Chin Med 2022; 17:32. [PMID: 35241112 PMCID: PMC8892722 DOI: 10.1186/s13020-022-00585-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/11/2022] [Indexed: 11/14/2022] Open
Abstract
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.
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Affiliation(s)
- Gengyu Lu
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
| | - Juanjuan Qiao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
| | - Long Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 China
| | - Hui Liu
- Yangzhou Center for Food and Drug Control, Yangzhou, 225000 China
| | - Gang Wu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 China
| | - Yan Zhu
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
| | - Guoyong Xie
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
| | - Minjian Qin
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 China
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17
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Chen Q, Hu H, Zhang D. DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:764255. [PMID: 35283910 PMCID: PMC8914171 DOI: 10.3389/fpls.2022.764255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/21/2022] [Indexed: 05/10/2023]
Abstract
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.
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Affiliation(s)
- Qi Chen
- College of Pharmacy, Dali University, Dali, China
| | - Haisu Hu
- College of Pharmacy, Dali University, Dali, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, China
- Institute of Materia Medica, Dali University, Dali, China
- *Correspondence: Dequan Zhang,
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18
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Wang J, Fu CN, Mo ZQ, Möller M, Yang JB, Zhang ZR, Li DZ, Gao LM. Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in Cephalotaxus (Cephalotaxaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:768810. [PMID: 35599857 PMCID: PMC9116380 DOI: 10.3389/fpls.2022.768810] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/07/2022] [Indexed: 05/17/2023]
Abstract
Species of Cephalotaxus have great economic and ecological values. However, the taxonomy and interspecific phylogenetic relationships within the genus have been controversial and remained not fully resolved until now. To date, no study examined the efficiency of the complete plastome as super-barcode across Cephalotaxus species with multiple samples per taxon. In this study, we have evaluated the complete plastome in species discrimination and phylogenetic resolution in Cephalotaxus by including 32 individuals of all eight recognized species and five varieties following Farjon's classification (2010) with multiple samples per taxon. Our results indicated that not all species recognized in recent taxonomic revisions of Cephalotaxus could be distinguished and not all were monophyletic. Based on the plastome phylogeny, a new taxonomic classification for the genus comprising nine species and two varieties, including a cryptic species, was proposed. The phylogeny also resolved all interspecific relationships. Compared to the plastome based classification, standard DNA barcodes, alone or in combination, only recognized a maximum of seven out of the nine species. Moreover, two highly variable single loci, ycf1 and rps16, each alone achieved full species discrimination. With the moderate length of 1079 bp, rps16 is proposed as a specific barcode to discriminate Cephalotaxus species. The super-barcodes and specific barcode candidates will aid in the identification of endangered Cephalotaxus species, and to help focus conservation measures.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
- *Correspondence: Lian-Ming Gao,
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Abstract
Growing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2, matK, rbcL, trnH-psbA and their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matK exhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.
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20
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Zheng W, Yan LJ, Burgess KS, Luo YH, Zou JY, Qin HT, Wang JH, Gao LM. Natural hybridization among three Rhododendron species (Ericaceae) revealed by morphological and genomic evidence. BMC PLANT BIOLOGY 2021; 21:529. [PMID: 34763662 PMCID: PMC8582147 DOI: 10.1186/s12870-021-03312-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/02/2021] [Indexed: 06/08/2023]
Abstract
BACKGROUND Natural hybridization can influence the adaptive response to selection and accelerate species diversification. Understanding the composition and structure of hybrid zones may elucidate patterns of hybridization processes that are important to the formation and maintenance of species, especially for taxa that have experienced rapidly adaptive radiation. Here, we used morphological traits, ddRAD-seq and plastid DNA sequence data to investigate the structure of a Rhododendron hybrid zone and uncover the hybridization patterns among three sympatric and closely related species. RESULTS Our results show that the hybrid zone is complex, where bi-directional hybridization takes place among the three sympatric parental species: R. spinuliferum, R. scabrifolium, and R. spiciferum. Hybrids between R. spinuliferum and R. spiciferum (R. ×duclouxii) comprise multiple hybrid classes and a high proportion of F1 generation hybrids, while a novel hybrid taxon between R. spinuliferum and R. scabrifolium dominated the F2 generation, but no backcross individuals were detected. The hybrid zone showed basically coincident patterns of population structure between genomic and morphological data. CONCLUSIONS Natural hybridization exists among the three Rhododendron species in the hybrid zone, although patterns of hybrid formation vary between hybrid taxa, which may result in different evolutionary outcomes. This study represents a unique opportunity to dissect the ecological and evolutionary mechanisms associated with adaptive radiation of Rhododendron species in a biodiversity hotspot.
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Affiliation(s)
- Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Li-Jun Yan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
- College of Vocational and Technical Education, Yunnan Normal University, 650092, Kunming, Yunnan, China
| | - Kevin S Burgess
- Department of Biology, Columbus State University, University System of Georgia, 31907-5645, Columbus, GA, USA
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Ji-Hua Wang
- The Flower Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, 674100, Lijiang, Yunnan, China.
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21
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Xia XM, Yang MQ, Li CL, Huang SX, Jin WT, Shen TT, Wang F, Li XH, Yoichi W, Zhang LH, Zheng YR, Wang XQ. Spatiotemporal evolution of the global species diversity of Rhododendron. Mol Biol Evol 2021; 39:6413646. [PMID: 34718707 PMCID: PMC8760938 DOI: 10.1093/molbev/msab314] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here, we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3,437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multispecies subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southward from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, that is, elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.
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Affiliation(s)
- Xiao-Mei Xia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao-Qin Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cong-Li Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Xin Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ting-Ting Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fei Wang
- West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Sichuan 611834, China
| | - Xiao-Hua Li
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiangxi 332900, China
| | - Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, Chiba 271-8510, Japan
| | - Le-Hua Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiangxi 332900, China
| | - Yuan-Run Zheng
- West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Sichuan 611834, China.,State Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Liu Y, Zhang M, Chen X, Chen X, Hu Y, Gao J, Pan W, Xin Y, Wu J, Du Y, Zhang X. Developing an efficient DNA barcoding system to differentiate between Lilium species. BMC PLANT BIOLOGY 2021; 21:465. [PMID: 34645404 PMCID: PMC8513328 DOI: 10.1186/s12870-021-03229-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Lilium is an important ornamental bulb, possesses medicinal properties, and is also edible. Species within the Lilium genus share very similar morphology and macroscopic characteristics, thus they cannot be easily and clearly distinguished from one another. To date, no efficient species-specific markers have been developed for classifying wild lily species, which poses an issue with further characterizing its medicinal properties. RESULTS To develop a simple and reliable identification system for Lilium, 45 representative species from 6 sections were used to develop a DNA barcoding system, which was based on DNA sequence polymorphisms. In this study, we assessed five commonly used DNA barcode candidates (ITS, rbcL, ycf1b, matK and psbA-trnH) and five novel barcode candidates obtained from highly variable chloroplast genomic regions (trnL-trnF, trnS-trnG, trnF-ndhJ, trnP-psaJ-rpI33 and psbB-psbH). We showed that a set of three novel DNA barcodes (ITS + trnP-psaJ-rpI33 + psbB-psbH) could be efficiently used as a genetic marker to distinguish between lily species, as assessed by methods including DNAsp, BI and ML tree, and Pair Wise Group (PWG). CONCLUSIONS A rapid and reliable DNA barcoding method was developed for all 45 wild Lilium species by using ITS, trnP-psaJ-rpI33, and psbB-psbH as DNA barcoding markers. The method can be used in the classification of wild Lilium species, especially endangered species, and also provides an effective method for selective lily breeding.
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Affiliation(s)
- Yixin Liu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Mingfang Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xuqing Chen
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xi Chen
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yue Hu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Junlian Gao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wenqiang Pan
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China
| | - Yin Xin
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China
| | - Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China.
| | - Yunpeng Du
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Xiuhai Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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23
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Khan G, Nolzen J, Schepker H, Albach DC. Incongruent phylogenies and their implications for the study of diversification, taxonomy, and genome size evolution of Rhododendron. AMERICAN JOURNAL OF BOTANY 2021; 108:1957-1981. [PMID: 34668570 DOI: 10.1002/ajb2.1747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 05/20/2023]
Abstract
PREMISE Classification of taxa depends on the quality of inferred phylogenies. Rhododendron, a highly species-rich genus (>1156 species) of woody plants, has a highly debated infrageneric classification, due to its huge diversity, homoplasy in key characters, and incongruence among data sets. We provide a broad coverage of representative species to resolve Rhododendron infrageneric phylogeny and highlight the areas of incongruence. We further investigate the effect of polyploidy and genome size evolution on diversification of Rhododendron. METHODS We generated two plastid and two nuclear loci for 260 Rhododendron species. We analyzed the loci separately as well as concatenated, utilizing both likelihood and Bayesian methods. We tested incongruence both among the data sets and with previous studies. We estimated genome sizes for 125 species through flow cytometry. RESULTS Our results suggest stronger support for larger subgenera; however, the smaller subgenera pose several problems; for example, R. tomentosum (former genus Ledum) occupies incongruent positions based on different DNA regions. The main shift to higher diversification in the genus occurs in the Himalayan/Southeast Asian clade of R. subg. Hymenanthes. We found that polyploidy occurs in almost all subgenera but most frequently within R. subg. Rhododendron sections Rhododendron and Schistanthe. CONCLUSIONS We endorse the recognition of five major clades at the subgeneric level, but a number of species cannot be confidently assigned to these clades due to incongruency. With regard to genome size evolution, results support previous reports that genome sizes of tropical plants are lower than those of colder and temperate regions and that genome downsizing promotes diversification.
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Affiliation(s)
- Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Strasse 9-11, Oldenburg, 26111, Germany
| | - Jennifer Nolzen
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Strasse 9-11, Oldenburg, 26111, Germany
| | - Hartwig Schepker
- Stiftung Bremer Rhododendronpark, Deliusweg 40, Bremen, 28359, Germany
| | - Dirk C Albach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Strasse 9-11, Oldenburg, 26111, Germany
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24
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Bhatt P, Thaker V. A comparative study on 193 plastomes of Poaceae for validity and implications of individual barcode genes and concatenated protein coding sequences with selected plastomes of grasses from the desert of India. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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25
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Chang YH, Yao G, Neilsen J, Liu DT, Zhang L, Ma YP. Rhododendron kuomeianum (Ericaceae), a new species from northeastern Yunnan (China), based on morphological and genomic data. PLANT DIVERSITY 2021; 43:292-298. [PMID: 34485771 PMCID: PMC8390914 DOI: 10.1016/j.pld.2021.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 04/07/2021] [Accepted: 04/13/2021] [Indexed: 05/20/2023]
Abstract
Rhododendron kuomeianum Y.H. Chang, J. Nielsen & Y.P. Ma, a new species of Rhododendron (Ericaceae) within subsect. Maddenia in sect. Rhododendron from Yiliang County, NE Yunnan, China, is described and illustrated. The new species is similar to R. valentinianum, but it can be easily distinguished by its sparse scales on the abaxial surface of the leaf blade, fewer flowers per inflorescence and white corolla with pale red margins. There are also differences in the widths of calyx lobes, leaf blade shape and indumentum characteristics of the petiole between the new species and Rhododendron linearilobum. We confirmed that R. kuomeianum is a new species closely related to R. valentinianum and R. changii with phylogenomic studies of 10 species within this subsection based on restriction site-associated DNA sequencing (RAD-seq) data. These phylogenomic analyses also clarified additional taxonomic problems in this subsection previously raised by morphological analysis. Our findings make a strong case for using next-generation sequencing to explore phylogenetic relationships and identify new species, especially in plants groups with complicated taxonomic problems.
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Affiliation(s)
- Yu-Hang Chang
- Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gang Yao
- Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jens Neilsen
- Dobbies Garden Centre, UK-DD2 Perth, Scotland, UK
| | - De-Tuan Liu
- Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lu Zhang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650051, China
| | - Yong-Peng Ma
- Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Corresponding author. Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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26
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Fu CN, Mo ZQ, Yang JB, Cai J, Ye LJ, Zou JY, Qin HT, Zheng W, Hollingsworth PM, Li DZ, Gao LM. Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron. Mol Ecol Resour 2021; 22:404-414. [PMID: 34310851 DOI: 10.1111/1755-0998.13479] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/22/2021] [Accepted: 07/05/2021] [Indexed: 12/01/2022]
Abstract
Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3-4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.
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Affiliation(s)
- Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lin-Jiang Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | | | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
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27
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The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron. BMC Genomics 2021; 22:376. [PMID: 34022814 PMCID: PMC8141123 DOI: 10.1186/s12864-021-07704-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background The genus Rhododendron L. has been widely cultivated for hundreds of years around the world. Members of this genus are known for great ornamental and medicinal value. Owing to advances in sequencing technology, genomes and transcriptomes of members of the Rhododendron genus have been sequenced and published by various laboratories. With increasing amounts of omics data available, a centralized platform is necessary for effective storage, analysis, and integration of these large-scale datasets to ensure consistency, independence, and maintainability. Results Here, we report our development of the Rhododendron Plant Genome Database (RPGD; http://bioinfor.kib.ac.cn/RPGD/), which represents the first comprehensive database of Rhododendron genomics information. It includes large amounts of omics data, including genome sequence assemblies for R. delavayi, R. williamsianum, and R. simsii, gene expression profiles derived from public RNA-Seq data, functional annotations, gene families, transcription factor identification, gene homology, simple sequence repeats, and chloroplast genome. Additionally, many useful tools, including BLAST, JBrowse, Orthologous Groups, Genome Synteny Browser, Flanking Sequence Finder, Expression Heatmap, and Batch Download were integrated into the platform. Conclusions RPGD is designed to be a comprehensive and helpful platform for all Rhododendron researchers. Believe that RPGD will be an indispensable hub for Rhododendron studies.
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Ye LJ, Mӧller M, Luo YH, Zou JY, Zheng W, Wang YH, Liu J, Zhu AD, Hu JY, Li DZ, Gao LM. Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex. BMC PLANT BIOLOGY 2021; 21:204. [PMID: 33910529 PMCID: PMC8082929 DOI: 10.1186/s12870-021-02977-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/08/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND The Rhododendron sanguineum complex is endemic to alpine mountains of northwest Yunnan and southeast Tibet of China. Varieties in this complex exhibit distinct flower colors even at the bud stage. However, the underlying molecular regulations for the flower color variation have not been well characterized. Here, we investigated this via measuring flower reflectance profiles and comparative transcriptome analyses on three coexisting varieties of the R. sanguineum complex, with yellow flush pink, bright crimson, and deep blackish crimson flowers respectively. We compared the expression levels of differentially-expressed-genes (DEGs) of the anthocyanin / flavonoid biosynthesis pathway using RNA-seq and qRT-PCR data. We performed clustering analysis based on transcriptome-derived Single Nucleotide Polymorphisms (SNPs) data, and finally analyzed the promoter architecture of DEGs. RESULTS Reflectance spectra of the three color morphs varied distinctively in the range between 400 and 700 nm, with distinct differences in saturation, brightness, hue, and saturation/hue ratio, an indirect measurement of anthocyanin content. We identified 15,164 orthogroups that were shared among the three varieties. The SNP clustering analysis indicated that the varieties were not monophyletic. A total of 40 paralogous genes encoding 12 enzymes contributed to the flower color polymorphism. These anthocyanin biosynthesis-related genes were associated with synthesis, modification and transportation properties (RsCHS, RsCHI, RsF3H, RsF3'H, RsFLS, RsANS, RsAT, RsOMT, RsGST), as well as genes involved in catabolism and degradation (RsBGLU, RsPER, RsCAD). Variations in sequence and cis-acting elements of these genes might correlate with the anthocyanin accumulation, thus may contribute to the divergence of flower color in the R. sanguineum complex. CONCLUSIONS Our results suggested that the varieties are very closely related and flower color variations in the R. sanguineum complex correlate tightly with the differential expression levels of genes involved in the anabolic and catabolic synthesis network of anthocyanin. Our study provides a scenario involving intricate relationships between genetic mechanisms for floral coloration accompanied by gene flow among the varieties that may represent an early case of pollinator-mediated incipient sympatric speciation.
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Affiliation(s)
- Lin-Jiang Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | | | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Yue-Hua Wang
- School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - An-Dan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Yunnan Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China.
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Xu J, Luo H, Nie S, Zhang RG, Mao JF. The complete mitochondrial and plastid genomes of Rhododendron simsii, an important parent of widely cultivated azaleas. Mitochondrial DNA B Resour 2021; 6:1197-1199. [PMID: 33796782 PMCID: PMC7995824 DOI: 10.1080/23802359.2021.1903352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/08/2021] [Indexed: 12/03/2022] Open
Abstract
The genus Rhododendron of the heather family (Ericaceae) is well known and widely cultivated for their highly ornamental value. The most widely cultivated Rhododendron species is Rhododendron simsii (Indoor azalea). In this study, we assembled the complete linear mitochondrial genome (GenBank accession number MW030508) and quadripartite plastid genome (GenBank accession number MW030509). The mitochondrial genome is 802,707 bp in length with containing 53 unique genes (33 protein-coding, 17 tRNA, and 3 rRNA genes), while the 152,214 bp long plastid genome is smaller and containing 105 unique genes (4 rRNA, 26 tRNA, and 75 protein-coding genes). Phylogenetic analysis showed that the same species relationship with APG system as well as the low supports of branches which is the common characteristic of resolved Ericales phylogenetics.
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Affiliation(s)
- Jie Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hang Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ren-Gang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd., Beijing, China
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Lv YN, Yang CY, Shi LC, Zhang ZL, Xu AS, Zhang LX, Li XL, Li HT. Identification of medicinal plants within the Apocynaceae family using ITS2 and psbA-trnH barcodes. Chin J Nat Med 2021; 18:594-605. [PMID: 32768166 DOI: 10.1016/s1875-5364(20)30071-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Indexed: 02/02/2023]
Abstract
To ensure the safety of medications, it is vital to accurately authenticate species of the Apocynaceae family, which is rich in poisonous medicinal plants. We identified Apocynaceae species by using nuclear internal transcribed spacer 2 (ITS2) and psbA-trnH based on experimental data. The identification ability of ITS2 and psbA-trnH was assessed using specific genetic divergence, BLAST1, and neighbor-joining trees. For DNA barcoding, ITS2 and psbA-trnH regions of 122 plant samples of 31 species from 19 genera in the Apocynaceae family were amplified. The PCR amplification for ITS2 and psbA-trnH sequences was 100%. The sequencing success rates for ITS2 and psbA-trnH sequences were 81% and 61%, respectively. Additional data involved 53 sequences of the ITS2 region and 38 sequences of the psbA-trnH region were downloaded from GenBank. Moreover, the analysis showed that the inter-specific divergence of Apocynaceae species was greater than its intra-specific variations. The results indicated that, using the BLAST1 method, ITS2 showed a high identification efficiency of 97% and 100% of the samples at the species and genus levels, respectively, via BLAST1, and psbA-trnH successfully identified 95% and 100% of the samples at the species and genus levels, respectively. The barcode combination of ITS2/psbA-trnH successfully identified 98% and 100% of samples at the species and genus levels, respectively. Subsequently, the neighbor joining tree method also showed that barcode ITS2 and psbA-trnH could distinguish among the species within the Apocynaceae family. ITS2 is a core barcode and psbA-trnH is a supplementary barcode for identifying species in the Apocynaceae family. These results will help to improve DNA barcoding reference databases for herbal drugs and other herbal raw materials.
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Affiliation(s)
- Ya-Na Lv
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Chun-Yong Yang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Lin-Chun Shi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zhong-Lian Zhang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - An-Shun Xu
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Li-Xia Zhang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xue-Lan Li
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Hai-Tao Li
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Mao X, Wang J, Shrestha N, Ma Y, Liu J. Species Identification in the Rhododendron vernicosum- R. decorum Species Complex (Ericaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:608964. [PMID: 33584768 PMCID: PMC7876077 DOI: 10.3389/fpls.2021.608964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Delimitating species boundaries is the primary aim of biological classification and could be critical for evaluating the evolving process of species and conserving biodiversity. Rhododendron is an iconic group with an extraordinary diversity in southwest China. However, it remains unknown whether the recorded species therein comprise independently evolving lineages or artificially delimitated morphological entities. In this study, we carried out species delimitation of four Rhododendron species in the R. vernicosum-R. decorum species complex based on morphological analyses and population genetic data from nuclear simple sequence repeats (SSR) markers. We randomly selected a total of 105 specimens of different individuals identified as four species across their distributional ranges to examine the statistically distinct phenotypic clusters based on 19 morphological traits. Similarly, we genotyped 55 individuals of four species from 21 populations using 15 SSR markers. The morphological analyses sorted R. decorum and the other three species into two different phenotypic clusters. The genetic clusters were consistent with the morphological clusters. However, we also recovered the third genetic cluster, comprising six R. vernicosum populations and containing the admixed genetic compositions of the other two distinct genetic clusters. This hybrid group was morphologically similar to the typical R. vernicosum (including the samples from its type specimen locality and both R. verruciferum and R. gonggashanense) but with more genetic ancestry from R. decorum. Based on our findings, we identify two distinct species and one putative hybrid group due to introgression in the R. vernicosum-R. decorum species complex. We propose to merge R. verruciferum and R. gonggashanense into R. vernicosum based on genetic compositions and our morphological analyses. The hybrid group inferred from our findings, however, needs further investigations.
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Affiliation(s)
- Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ji Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Yazhen Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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32
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Zhao B, Xiong C, Wu L, Xiang L, Shi Y, Sun W, Chen S. DNA barcoding coupled with high resolution melting for rapid identification of Ardisia gigantifolia and its toxic adulterants. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1885993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Bo Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Chao Xiong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
- Department of Food and Drug Resources & Health Food Innovation, School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, Hubei, PR China
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
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33
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Zhao B, Xiong C, Li J, Zhang D, Shi Y, Sun W, Duan X. Species Quantification in Complex Herbal Formulas-Vector Control Quantitative Analysis as a New Method. Front Pharmacol 2020; 11:488193. [PMID: 33324200 PMCID: PMC7725679 DOI: 10.3389/fphar.2020.488193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/16/2020] [Indexed: 11/17/2022] Open
Abstract
Product mislabeling and/or species fraud in Traditional Chinese Medicine (TCM) not only decrease TCM quality, but also pose a potential health issue to the end user. Up to now, methods to control TCM quality have been developed to detect specific metabolites or identify the original species. However, species quantification in complex herbal formulas is rarely concerned. Here, we reported a simple Vector Control Quantitative Analysis (VCQA) method for flexible and accurate multiplex species quantification in traditional Chinese herbal formulas. We developed PCR-based strategy to quickly generate the integrated DNA fragments from multiple targeted species, which can be assembled into the quantitative vector in one round of cloning by Golden Gate ligation and Gateway recombination technique. With this method, we recruited the nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region for the quantification of Ligusticum sinense “Chuanxiong,” Angelica dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav., Notopterygium incisum K. C. Ting ex H. T. Chang, Asarum sieboldii Miq., Saposhnikovia divaricata (Turcz.) Schischk., Nepeta cataria L., Mentha canadensis L., and Glycyrrhiza uralensis Fisch. ex DC. in ChuanXiong ChaTiao Wan, a classic Chinese herbal formula with very long historical background. We found that, firstly, VCQA method could eliminate the factors affecting such as the variations in DNA extracts when in combination with the use of universal and species-specific primers. Secondly, this method detected the limit of quantification of A. sieboldii Miq. in formula products down to 1%. Thirdly, the stability of quality of ChuanXiong ChaTiao Wan formula varies significantly among different manufacturers. In conclusion, VCQA method has the potential power and can be used as an alternative method for species quantification of complex TCM formulas.
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Affiliation(s)
- Bo Zhao
- College of Pharmacy, Guilin Medical University, Guilin, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Xiong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jingjian Li
- College of Pharmacy, Guilin Medical University, Guilin, China
| | - Deng Zhang
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoqun Duan
- College of Pharmacy, Guilin Medical University, Guilin, China
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34
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Sijimol K, Dev SA, Sreekumar VB. DNA barcoding supports existence of morphospecies complex in endemic bamboo genus Ochlandra Thwaites of the Western Ghats, India. J Genet 2020. [DOI: 10.1007/s12041-020-01227-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhang X, Qin H, Xie W, Ma Y, Sun W. Comparative population genetic analyses suggest hybrid origin of R hododendron pubicostatum, an endangered plant species with extremely small populations endemic to Yunnan, China. PLANT DIVERSITY 2020; 42:312-318. [PMID: 33094202 PMCID: PMC7567756 DOI: 10.1016/j.pld.2020.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 05/08/2023]
Abstract
Gene flow between sympatric congeneric plants is thought to be very common and may pose serious threats to endangered species. In the present study, we evaluate the genetic diversity and divergence of three sympatric Rhododendron species in Jiaozi Mountain using newly developed microsatellites through the Illumina MiSeq sequencing approach. Genetic diversity of all three Rhododendron species studied was moderate in comparison to genetic parameters previously reported from species of this genus. Interestingly, genetic structure analysis of the three species identified a possible hybrid origin of the threatened Rh. pubicostatum. This sympatry should be considered a unimodal hybrid zone, since R h. pubicostatum is predominant here. Unimodal hybrid zones are uncommon in Rhododendron, despite the fact that hybridization frequently occurs in the genus. Issues pertaining to the conservation of R h. pubicostatum resulting from admixture of genetic material from its parental species are discussed.
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Affiliation(s)
- Xuemei Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hantao Qin
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Weijia Xie
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, 650201, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, China
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Le DT, Zhang YQ, Xu Y, Guo LX, Ruan ZP, Burgess KS, Ge XJ. The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens. PLoS One 2020; 15:e0235569. [PMID: 32735584 PMCID: PMC7394517 DOI: 10.1371/journal.pone.0235569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/17/2020] [Indexed: 12/29/2022] Open
Abstract
The palm family (Arecaceae) is of high ecological and economic value, yet identification in the family remains a challenge for both taxonomists and horticulturalists. The family consists of approximately 2600 species across 181 genera and DNA barcoding may be a useful tool for species identification within the group. However, there have been few systematic evaluations of DNA barcodes for the palm family. In the present study, five DNA barcodes (rbcL, matK, trnH-psbA, ITS, ITS2) were evaluated for species identification ability across 669 samples representing 314 species and 100 genera in the Arecaceae, employing four analytical methods. The ITS gene region was found to not be a suitable barcode for the palm family, due in part, to low recovery rates and paralogous gene copies. Among the four analyses used, species resolution for ITS2 was much higher than that achieved with the plastid barcodes alone (rbcL, matK, trnH-psbA), and the barcode combination ITS2 + matK + rbcL gave the highest resolution among all single barcodes and their combinations, followed by ITS2 + matK. Among 669 palm samples analyzed, 110 samples (16.3%) were found to be misidentified. The 2992 DNA barcode sequences generated in this study greatly enriches the existing identification toolbox available to plant taxonomists that are interested in researching genetic relationships among palm taxa as well as for horticulturalists that need to confirm palm collections for botanical garden curation and horticultural applications. Our results indicate that the use of the ITS2 DNA barcode gene region provides a useful and cost-effective tool to confirm the identity of taxa in the Palm family.
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Affiliation(s)
- Duc-Thanh Le
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Li-Xiu Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Kevin S. Burgess
- Department of Biology, Columbus State University, University System of Georgia, Columbus, Georgia, United States of America
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Oyebanji OO, Chukwuma EC, Bolarinwa KA, Adejobi OI, Adeyemi SB, Ayoola AO. Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers. J Biosci 2020. [DOI: 10.1007/s12038-020-00061-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Yu H, Miao S, Xie G, Guo X, Chen Z, Favre A. Contrasting Floristic Diversity of the Hengduan Mountains, the Himalayas and the Qinghai-Tibet Plateau Sensu Stricto in China. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Whitehurst LE, Cunard CE, Reed JN, Worthy SJ, Marsico TD, Lucardi RD, Burgess KS. Preliminary application of DNA barcoding toward the detection of viable plant propagules at an initial, international point-of-entry in Georgia, USA. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02204-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Zhang D, Jiang B. Species identification in complex groups of medicinal plants based on DNA barcoding: a case study on Astragalus spp. (Fabaceae) from southwest China. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01119-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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He T, Jiao L, Wiedenhoeft AC, Yin Y. Machine learning approaches outperform distance- and tree-based methods for DNA barcoding of Pterocarpus wood. PLANTA 2019; 249:1617-1625. [PMID: 30825008 DOI: 10.1007/s00425-019-03116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/20/2019] [Indexed: 05/10/2023]
Abstract
Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal logging and associated trade, and the development of reliable and efficient analytical methods is essential for its extensive application in the trade of wood and in the forensics of natural materials more broadly. In this study, 120 DNA sequences of four barcodes (ITS2, matK, ndhF-rpl32, and rbcL) generated in our previous study and 85 downloaded from National Center for Biotechnology Information (NCBI) were collected to establish a reference data set for six commercial Pterocarpus woods. MLAs (BLOG, BP-neural network, SMO and J48) were compared with distance- (TaxonDNA) and tree-based (NJ tree) methods based on identification accuracy and cost-effectiveness across these six species, and also were applied to discriminate the CITES-listed species Pterocarpus santalinus from its anatomically similar species P. tinctorius for forensic identification. MLAs provided higher identification accuracy (30.8-100%) than distance- (15.1-97.4%) and tree-based methods (11.1-87.5%), with SMO performing the best among the machine learning classifiers. The two-locus combination ITS2 + matK when using SMO classifier exhibited the highest resolution (100%) with the fewest barcodes for discriminating the six Pterocarpus species. The CITES-listed species P. santalinus was discriminated successfully from P. tinctorius using MLAs with a single barcode, ndhF-rpl32. This study shows that MLAs provided higher identification accuracy and cost-effectiveness for forensic application over other analytical methods in DNA barcoding of Pterocarpus wood.
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Affiliation(s)
- Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and National Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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Fu CN, Wu CS, Ye LJ, Mo ZQ, Liu J, Chang YW, Li DZ, Chaw SM, Gao LM. Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide. Sci Rep 2019; 9:2773. [PMID: 30808961 PMCID: PMC6391452 DOI: 10.1038/s41598-019-39161-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/02/2018] [Indexed: 01/17/2023] Open
Abstract
Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In Pseudotaxus and Taxus, we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by "trnQ-IRs". These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in Taxus. Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all Taxus species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that accD and rrn16-rrn23 are promising special barcodes to discriminate yew species. Our newly developed Taxus plastomic sequences provide a resource for super-barcodes and conservation genetics of several endangered yews and serve as comprehensive data to improve models of plastome complexity in Taxaceae as a whole and authenticate Taxus species.
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Affiliation(s)
- Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Lin-Jiang Ye
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Yu-Wen Chang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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Ren F, Wang Y, Xu Z, Li Y, Xin T, Zhou J, Qi Y, Wei X, Yao H, Song J. DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae. Ecol Evol 2019; 9:1934-1945. [PMID: 30847083 PMCID: PMC6392370 DOI: 10.1002/ece3.4886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/02/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya-Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA-trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P-distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia-recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well-supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.
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Affiliation(s)
- Feng‐Ming Ren
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Chongqing Institute of Medicinal Plant Cultivation, Research and Utilization on Characteristic Biological Resources of Sichuan and Chongqing Co‐construction LabChinese Medicine Breeding and Evaluation Engineering Technology Research Center of ChongqingChongqingChina
| | - Ying‐Wei Wang
- Beijing Botanical Garden, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Zhi‐Chao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Tian‐Yi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jian‐Guo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yao‐Dong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Xue‐Ping Wei
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jing‐Yuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
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Yang J, Feng L, Yue M, He YL, Zhao GF, Li ZH. Species delimitation and interspecific relationships of the endangered herb genus Notopterygium inferred from multilocus variations. Mol Phylogenet Evol 2019; 133:142-151. [PMID: 30639766 DOI: 10.1016/j.ympev.2019.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 01/29/2023]
Abstract
Species identification and discrimination is the basis of biodiversity research. In general, it is considered that numerous nucleotide variations (e.g., whole chloroplast genomes) can identify species with higher resolution than a few loci, e.g., partial chloroplast or nuclear gene fragments. In this study, we tested this hypothesis by sampling population genetics samples of the endangered herb genus Notopterygium. We sequenced the complete plastomes, five nuclear gene regions, three chloroplast DNA fragments, and a nuclear internal transcribed spacer (nrITS) region for 18 populations sampled throughout most of the geographic ranges of all six Notopterygium species. Species identification analysis showed that four DNA barcodes (matK, rbcL, trnS-trnG, and nrITS) and/or combinations of these markers achieved Notopterygium species discrimination at higher resolution than the general plastomes and nuclear gene sequences. In particular, nrITS had the highest discriminatory power among all of the individual markers. Molecular data sets and morphological evidence indicated that all six Notopterygium species could be reclassified unambiguously to four putative species clades. N. oviforme and N. franchetii had the closest relationship. Molecular dating showed that the origin and divergence of Notopterygium species was significantly associated with geological and climatic fluctuations during the middle of the Pliocene. In conclusion, our results suggest that a few nucleotide variations can achieve species discrimination with higher resolution than numerous plastomes and general nuclear gene fragments when discerning related Notopterygium species.
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Affiliation(s)
- Jiao Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan-Ling He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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Li QJ, Wang X, Wang JR, Su N, Zhang L, Ma YP, Chang ZY, Zhao L, Potter D. Efficient Identification of Pulsatilla (Ranunculaceae) Using DNA Barcodes and Micro-Morphological Characters. FRONTIERS IN PLANT SCIENCE 2019; 10:1196. [PMID: 31649688 PMCID: PMC6794950 DOI: 10.3389/fpls.2019.01196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/30/2019] [Indexed: 05/04/2023]
Abstract
Pulsatilla (Ranunculaceae) comprises about 40 species, many of which have horticultural and/or medicinal importance. However, the recognition and identification of wild Pulsatilla species is difficult due to the presence of complex morphological characters. DNA barcoding is a powerful molecular tool capable of rapidly and accurately distinguishing between species. Here, we assessed the effectiveness of four commonly used DNA barcoding loci-rbcL (R), trnH-psbA ( T ), matK (M), and ITS (I)-to identify species of Pulsatilla from a comprehensive sampling group. Among the four barcoding single loci, the nuclear ITS marker showed the highest interspecific distances and the highest rate of correct identification. Among the eleven combinations, the chloroplast multi-locus R+T and R+M+T combinations were found to have the best species discrimination rate, followed by R+M. Overall, we propose that the R+M+T combination and the ITS marker on its own are, respectively, the best multi- and single-locus barcodes for discriminating among species of Pulsatilla. The phylogenetic analysis was able to distinguish species of Pulsatilla to the subgenus level, but the analysis also showed relatively low species resolution. This may be caused by incomplete lineage sorting and/or hybridization events in the evolutionary history of the genus, or by the resolution limit of the candidate barcodes. We also investigated the leaf epidermis of eight representative species using scanning electronic microscopy. The resulting micro-morphological characters were valuable for identification of related species. Using additional genome fragments, or even whole chloroplast genomes combined with micro-morphological data may permit even higher resolution of species in Pulsatilla.
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Affiliation(s)
- Qiu-jie Li
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Xi Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Jun-ru Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Na Su
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Ling Zhang
- College of Life Sciences, Tarim University, Alaer, China
| | - Yue-ping Ma
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Zhao-yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
- *Correspondence: Liang Zhao,
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, Davis, CA, United States
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Wang S, Leus L, Van Labeke MC, Van Huylenbroeck J. Prediction of Lime Tolerance in Rhododendron Based on Herbarium Specimen and Geochemical Data. FRONTIERS IN PLANT SCIENCE 2018; 9:1538. [PMID: 30405673 PMCID: PMC6206291 DOI: 10.3389/fpls.2018.01538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
Rhododendrons are typically known to be calcifuges that cannot grow well in lime soils. Data on lime tolerance of different taxa in Rhododendron are scarce. Habitats of naturally distributed specimens of genus Rhododendron were compiled as Chinese text-based locations from the Chinese Virtual Herbarium. The locations were then geocoded into latitude/longitude pairs and subsequently connected to soil characteristics including pH and CaCO3 from the Harmonized World Soil Database (HWSD). Using the upper quartile values of pH > 7.2 and CaCO3 > 2% weight in topsoil as threshold, we predicted the lime tolerant taxa. A dataset of 31,146 Rhododendron specimens including the information on taxonomy, GPS locations and soil parameters for both top- and subsoil was built. The majority of the specimens were distributed in soils with moderately acidic pH and without presence of CaCO3. 76 taxa with potential lime tolerance were predicted out of 525 taxa. The large scale data analysis based on combined data of geocoded herbarium specimens and HWSD allows identification of valuable Rhododendron species, subspecies or botanical varieties with potential tolerance to lime soils with higher pH. The predicted tolerant taxa are valuable resources for an in-depth evaluation of lime tolerance or for further use in horticulture and breeding.
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Affiliation(s)
- Shusheng Wang
- Plant Sciences Unit, Applied Genetics and Breeding, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, China
| | - Leen Leus
- Plant Sciences Unit, Applied Genetics and Breeding, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Johan Van Huylenbroeck
- Plant Sciences Unit, Applied Genetics and Breeding, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
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Tan S, Luo Y, Hollingsworth PM, Burgess KS, Xu K, Li D, Gao L. DNA barcoding herbaceous and woody plant species at a subalpine forest dynamics plot in Southwest China. Ecol Evol 2018; 8:7195-7205. [PMID: 30073078 PMCID: PMC6065341 DOI: 10.1002/ece3.4254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/05/2018] [Accepted: 05/14/2018] [Indexed: 01/13/2023] Open
Abstract
Although DNA barcoding has been widely used to identify plant species composition in temperate and tropical ecosystems, relatively few studies have used DNA barcodes to document both herbaceous and woody components of forest plot. A total of 201 species (72 woody species and 129 herbaceous species) representing 135 genera distributed across 64 families of seed plants were collected in a 25 ha CForBio subalpine forest dynamics plot. In total, 491 specimens were screened for three DNA regions of the chloroplast genome (rbcL, matK, and trnH-psbA) as well as the internal transcribed spacers (ITS) of nuclear ribosomal DNA. We quantified species resolution for each barcode separately or in combination using a ML tree-based method. Amplification and sequencing success were highest for rbcL, followed by trnH-psbA, which performed better than ITS and matK. The rbcL + ITS barcode had slightly higher species resolution rates (88.60%) compared with rbcL + matK (86.60%) and rbcL + trnH-psbA (86.01%). The addition of trnH-psbA or ITS to the rbcL + matK barcode only marginally increased species resolution rates, although in combination the four barcodes had the highest discriminatory power (90.21%). The situations where DNA barcodes did not discriminate among species were typically associated with higher numbers of co-occurring con-generic species. In addition, herbaceous species were much better resolved than woody species. Our study represents one of the first applications of DNA barcodes in a subalpine forest dynamics plot and contributes to our understanding of patterns of genetic divergence among woody and herbaceous plant species.
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Affiliation(s)
- Shao‐Lin Tan
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesKunming, YunnanChina
| | - Ya‐Huang Luo
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
| | | | - Kevin S. Burgess
- Department of BiologyCollege of Letters and SciencesColumbus State UniversityUniversity System of GeorgiaColumbusGeorgia
| | - Kun Xu
- Lijiang Forest Ecosystem Research StationKunming Institute of BotanyChinese Academy of SciencesLijiangChina
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesKunming, YunnanChina
| | - Lian‐Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- Lijiang Forest Ecosystem Research StationKunming Institute of BotanyChinese Academy of SciencesLijiangChina
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Wang X, Gussarova G, Ruhsam M, de Vere N, Metherell C, Hollingsworth PM, Twyford AD. DNA barcoding a taxonomically complex hemiparasitic genus reveals deep divergence between ploidy levels but lack of species-level resolution. AOB PLANTS 2018; 10:ply026. [PMID: 29765588 PMCID: PMC5941139 DOI: 10.1093/aobpla/ply026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/20/2018] [Indexed: 05/18/2023]
Abstract
DNA barcoding is emerging as a useful tool not only for species identification but also for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode data sets can provide insights into the mechanisms underlying the generation of species diversity. Here, we study evolutionary processes in taxonomically complex British Euphrasia (Orobanchaceae), a group with multiple ploidy levels, frequent self-fertilization, young species divergence and widespread hybridization. We use a phylogenetic approach to investigate the colonization history of British Euphrasia, followed by a DNA barcoding survey and population genetic analyses to reveal the causes of shared sequence variation. Phylogenetic analysis shows Euphrasia have colonized Britain from mainland Europe on multiple occasions. DNA barcoding reveals that no British Euphrasia species has a consistent diagnostic sequence profile, and instead, plastid haplotypes are either widespread across species, or are population specific. The partitioning of nuclear genetic variation suggests differences in ploidy act as a barrier to gene exchange, while the divergence between diploid and tetraploid ITS sequences supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, analyses of DNA barcoding data can reveal evolutionary patterns in taxonomically complex genera.
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Affiliation(s)
- Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, P.R. China
| | - Galina Gussarova
- Tromsø University Museum, UiT The Arctic University of Norway, Langnes, Tromsø, Norway
- CEES-Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
- Department of Botany, Faculty of Biology, St Petersburg State University, Universitetskaya nab., Russia
| | | | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, Carmarthenshire, UK
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, Ceredigion, UK
| | | | | | - Alex D Twyford
- University of Edinburgh, Institute of Evolutionary Biology, Edinburgh, UK
- Corresponding author’s e-mail address:
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Liu J, Milne RI, Möller M, Zhu GF, Ye LJ, Luo YH, Yang JB, Wambulwa MC, Wang CN, Li DZ, Gao LM. Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification. Mol Ecol Resour 2018; 18:1115-1131. [PMID: 29786943 DOI: 10.1111/1755-0998.12903] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/01/2018] [Accepted: 05/07/2018] [Indexed: 12/23/2022]
Abstract
Rapid and accurate identification of endangered species is a critical component of biosurveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or preprocessed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa. Here, we construct a comprehensive DNA barcode reference library and generate distribution maps using species distribution modelling (SDM), for all 15 Taxus species worldwide. We find that trnL-trnF is the ideal barcode for Taxus: It can distinguish all Taxus species and in combination with ITS identify hybrids. Among five analysis methods tested, NJ was the most effective. Among 4,151 individuals screened for trnL-trnF, 73 haplotypes were detected, all species-specific and some population private. Taxonomical, geographical and genetic dimensions of sampling strategy were all found to affect the comprehensiveness of the resulting DNA barcode library. Maps from SDM showed that most species had allopatric distributions, except T. mairei in the Sino-Himalayan region. Using the barcode library and distribution map data, two unknown forensic samples were identified to species (and in one case, population) level and another was determined as a putative interspecific hybrid. This integrated species identification system for Taxus can be used for biosurveillance, conservation management and to monitor and prosecute illegal trade. Similar identification systems are recommended for other IUCN- and CITES-listed taxa.
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Affiliation(s)
- Jie Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Guang-Fu Zhu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lin-Jiang Ye
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ya-Huang Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Moses C Wambulwa
- Biochemistry Department, South Eastern Kenya University, Kitui, Kenya
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, Department of Life Science, National Taiwan University, Taipei, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Yan M, Xiong Y, Liu R, Deng M, Song J. The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks. FRONTIERS IN PLANT SCIENCE 2018; 9:569. [PMID: 29868047 PMCID: PMC5952231 DOI: 10.3389/fpls.2018.00569] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 05/10/2023]
Abstract
The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia - Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiaojiao Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shangrao Normal University, Shangrao, China
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