101
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Ahmad W, Asaf S, Khan A, Al-Harrasi A, Al-Okaishi A, Khan AL. Complete chloroplast genome sequencing and comparative analysis of threatened dragon trees Dracaena serrulata and Dracaena cinnabari. Sci Rep 2022; 12:16787. [PMID: 36202844 PMCID: PMC9537188 DOI: 10.1038/s41598-022-20304-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Dracaena (Asparagaceae family) tree is famous for producing "dragon blood"—a bioactive red-colored resin. Despite its long history of use in traditional medicine, little knowledge exists on the genomic architecture, phylogenetic position, or evolution. Hence, in this study, we sequenced the whole chloroplast (cp) genomes of D. serrulata and D. cinnabari and performed comparative genomics of nine genomes of the genus Dracaena. The results showed that the genome sizes range from 155,055 (D. elliptica) to 155,449 (D. cochinchinensis). The cp genomes of D. serrulata and D. cinnabari encode 131 genes, each including 85 and 84 protein-coding genes, respectively. However, the D. hokouensis had the highest number of genes (133), with 85 protein coding genes. Similarly, about 80 and 82 repeats were identified in the cp genomes of D. serrulata and D. cinnabari, respectively, while the highest repeats (103) were detected in the cp genome of D. terniflora. The number of simple sequence repeats (SSRs) was 176 and 159 in D. serrulata and D. cinnabari cp genomes, respectively. Furthermore, the comparative analysis of complete cp genomes revealed high sequence similarity. However, some sequence divergences were observed in accD, matK, rpl16, rpoC2, and ycf1 genes and some intergenic spacers. The phylogenomic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, sister to the remaining Dracaena species sampled in this study, with high bootstrap values. In conclusion, this study provides valuable genetic information for studying the evolutionary relationships and population genetics of Dracaena, which is threatened in its conservation status.
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Affiliation(s)
- Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman.,Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman.
| | | | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA.
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102
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Docrat TF, Abdul NS, Marnewick JL. The phytotherapeutic potential of commercial South African medicinal plants: current knowledge and future prospects. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2022-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract
South Africa, a country considered affluent in nature, ranks third in global biodiversity and encompasses approximately 9% of higher plants on planet Earth. Many indigenous plants have been utilised as herbal medicine, proving successful in treating numerous ailments. From the common cold to pandemic maladies such as COVID-19 in the 21st century and the treatment of incurable diseases, South African inhabitants have found great promise in the healing properties of these plants. Phytomedicine is a rapidly evolving topic, with in-depth bioactive composition analysis, identifying therapeutic action mechanisms, and disease prevention. While we are now poised to take advantage of nature’s medicine cabinet with greater scientific vigour, it remains critical that these practises are done with caution. Overharvesting significantly impacts biodiversity and cultivation practices amidst the beautiful nature of these nutraceuticals. This book chapter focuses on the therapeutic potential of commonly used South African medicinal plants, their ethnopharmacological properties, and how we can conserve this treasure cove we call home for future generations.
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Affiliation(s)
- Taskeen F. Docrat
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology , Bellville , South Africa
| | - Naeem Sheik Abdul
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology , Bellville , South Africa
| | - Jeanine L. Marnewick
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology , Bellville , South Africa
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103
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Park YS, Kang JS, Park JY, Shim H, Yang HO, Kang JH, Yang TJ. Analysis of the complete plastomes and nuclear ribosomal DNAs from Euonymus hamiltonianus and its relatives sheds light on their diversity and evolution. PLoS One 2022; 17:e0275590. [PMID: 36197898 PMCID: PMC9534445 DOI: 10.1371/journal.pone.0275590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Euonymus hamiltonianus and its relatives (Celastraceae family) are used for ornamental and medicinal purposes. However, species identification in Euonymus is difficult due to their morphological diversity. Using plastid genome (plastome) data, we attempt to reveal phylogenetic relationship among Euonymus species and develop useful markers for molecular identification. We assembled the plastome and nuclear ribosomal DNA (nrDNA) sequences from five Euonymus lines collected from South Korea: three Euonymus hamiltonianus accessions, E. europaeus, and E. japonicus. We conducted an in-depth comparative analysis using ten plastomes, including other publicly available plastome data for this genus. The genome structures, gene contents, and gene orders were similar in all Euonymus plastomes in this study. Analysis of nucleotide diversity revealed six divergence hotspots in their plastomes. We identified 339 single nucleotide polymorphisms and 293 insertion or deletions among the four E. hamiltonianus plastomes, pointing to abundant diversity even within the same species. Among 77 commonly shared genes, 9 and 33 were identified as conserved genes in the genus Euonymus and E. hamiltonianus, respectively. Phylogenetic analysis based on plastome and nrDNA sequences revealed the overall consensus and relationships between plastomes and nrDNAs. Finally, we developed six barcoding markers and successfully applied them to 31 E. hamiltonianus lines collected from South Korea. Our findings provide the molecular basis for the classification and molecular taxonomic criteria for the genus Euonymus (at least in Korea), which should aid in more objective classification within this genus. Moreover, the newly developed markers will be useful for understanding the species delimitation of E. hamiltonianus and closely related species.
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Affiliation(s)
- Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Hyun Ok Yang
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Korea
| | | | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
- * E-mail:
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104
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González-Toral C, Cires E. Relevance of DNA preservation for future botany and ecology. Mol Ecol 2022; 31:5125-5131. [PMID: 36214196 DOI: 10.1111/mec.16652] [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: 04/12/2022] [Revised: 07/20/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
The use of molecular methods in plant systematics and taxonomy has increased during the last decades; however, the accessibility of curated genetic samples and their metadata is a bottleneck for DNA-based genetic studies in botany. Plant biodiversity DNA banks and DNA-friendly collections could be critical suppliers of curated genetic material for researchers in the current context of plant biodiversity loss. Here, we aimed to understand the potential of plant DNA banks and DNA-friendly collections to enhance the growth and openness of scientific knowledge. The preservation of genetic material should become part of a natural collection's process for the generation of extended specimens enabling the preservation of both the phenotype and genotype and contributing to the generation of data networks which cross-fertilize other fields. These curated collections are advantageous in endangered species research, detecting processes related to extinction, giving a genetic dimension to IUCN assessments or completing the Leipzig Catalogue of Vascular Plants. Therefore, DNA collections are fundamental in producing FAIR data, responsible research and innovation (RRI) and meeting the goals of international conservation programmes. The completion of natural collections is important for current research efforts and furthermore vital to support future research in an era of ongoing plant biodiversity loss.
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Affiliation(s)
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain.,Institute of Natural Resources and Territorial Planning (INDUROT), Mieres, Spain
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105
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Zhu S, Liu Q, Qiu S, Dai J, Gao X. DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances. Chin Med 2022; 17:112. [PMID: 36171596 PMCID: PMC9514984 DOI: 10.1186/s13020-022-00655-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.
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Affiliation(s)
- Shuang Zhu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Qiaozhen Liu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Simin Qiu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jiangpeng Dai
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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106
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Zhang ZR, Yang X, Li WY, Peng YQ, Gao J. Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions. FRONTIERS IN PLANT SCIENCE 2022; 13:965335. [PMID: 36186045 PMCID: PMC9521400 DOI: 10.3389/fpls.2022.965335] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.
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Affiliation(s)
- Zheng-Ren Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Wei-Ying Li
- Southwest Research Center for Landscape Architecture Engineering Technology, State Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yan-Qiong Peng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
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107
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Xiao T, He L, Yue L, Zhang Y, Lee SY. Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae). Front Genet 2022; 13:998575. [PMID: 36186481 PMCID: PMC9515656 DOI: 10.3389/fgene.2022.998575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Owing to its attractive flower shape and color, Renanthera (Orchidaceae), comprising about 19 species, has significant ornamental value as a houseplant, in floral design and in landscape gardens. Two species of Renanthera are categorized as endangered and critically endangered in China’s Red List and international trade in these orchids is currently strictly monitored by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). This paper reports on the de novo assembled and annotated plastome of four species of Renanthera; R. citrina, R. coccinea, R. imschootiana, and R. philippinensis. The length of the plastome sequences ranged from 144,673 bp (R. imschootiana) to 149,007 bp (R. coccinea) with GC content of 36.6–36.7%. The plastomes showed a typical quadripartite structure, including a large single-copy (84,241–86,404 bp), a small single-copy (11,468–12,167 bp), and a pair of inverted repeats (24,482–25,715 bp) regions. Of the 120 genes detected, 74 were protein coding, 38 were tRNA, and eight were rRNA genes. The plastome of Renanthera is rather conserved, but nucleotide variations that could distinguish them apart are noticeable—the total number of tandem repeats ranged from 62 (in R. imschootiana) to 74 (in R. citrina); while the number of long repeats ranged from 21 (in R. imschootiana and R. philippinensis) to 43 (in R. citrina). Three hypervariable regions (psbI-trnS-GCU, trnG-GCC, rpl32) were identified. Phylogenetic analyses based on the CDS using maximum likelihood (ML) and Bayesian inference (BI) revealed that Renanthera is closely related to Holcoglossum, Neofinetia, Pendulorchis, and Vanda. The relationship between the four species of Renanthera was fully resolved; a monophyletic clade was formed and R. coccinea was recorded as the first to diverge from the rest. The genetic data obtained from this study could serve as a useful resource for species identification in Renanthera as well as contribute to future research on the phylogenomics of Orchidaceae.
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Affiliation(s)
- Tao Xiao
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Liefen He
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Liangliang Yue
- Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, China
| | - Yonghong Zhang
- School of Life Sciences, Yunnan Normal University, Kunming, China
- *Correspondence: Yonghong Zhang, ; Shiou Yih Lee,
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, Nilai, Malaysia
- *Correspondence: Yonghong Zhang, ; Shiou Yih Lee,
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108
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Hao L, Xu W, Qi G, Xin T, Xu Z, Lei H, Song J. GAGE is a method for identification of plant species based on whole genome analysis and genome editing. Commun Biol 2022; 5:947. [PMID: 36088518 PMCID: PMC9464240 DOI: 10.1038/s42003-022-03894-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Whole genomes of plants should be ideal databases for their species identification, but unfortunately there was no such method before this exploration. Here we report a plant species identification method based on the whole Genome Analysis and Genome Editing (GAGE). GAGE searches for target sequences from the whole genome of the subject plant and specifically detects them by employing a CRISPR/Cas12a system. Similar to how Mendel chose Pisum sativum (pea), we selected Crocus sativus (saffron) to establish GAGE, in which we constructed a library containing all candidate target sequences. Taking a target sequence in the ITS2 region as an example, we confirmed the feasibility, specificity, and sensitivity of GAGE. Consequently, we succeeded in not only using GAGE to identify Cr. sativus and its adulterants, but also executing GAGE in the plants from different classes including angiosperms, gymnosperms, ferns, and lycophytes. This sensitive and rapid method is the first plant species identification method based on the whole genome and provides new insights into the application of the whole genome in species identification. A plant species identification method, GAGE, is reported that searches for target sequences from the whole genome of the subject plant and specifically detects them by employing a CRISPR/Cas12a system.
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109
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Wang J, Yan Z, Zhong P, Shen Z, Yang G, Ma L. Screening of universal DNA barcodes for identifying grass species of Gramineae. FRONTIERS IN PLANT SCIENCE 2022; 13:998863. [PMID: 36161013 PMCID: PMC9490308 DOI: 10.3389/fpls.2022.998863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
There is currently international interest in applying DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of four candidate plant DNA barcoding regions [rbcL, matK, trnL-F, and internal transcribed spacer (ITS)] in seven genera of Gramineae including Agropyron, Bromus, Elymus, Elytrigia, Festuca, Leymus, and Lolium. Fourteen accessions were analyzed, and matK and ITS showed the highest species, subspecies, and variety discriminatory power, each resolving 11 accessions. Species discrimination using rbcL and trnL-F was lower, resolving 7 and 8 accessions, respectively. Subspecies and variety discrimination using rbcL and trnL-F could not identify 4 accessions of Agropyron. A technical system can be established using the proposed DNA barcode to rapidly and reliably identify the seven genera of Gramineae. This study serves as a "useful reference" for identifying the genetic diversity of grass germplasm resources. DNA barcoding can be utilized to uncover the relatives of different species within the same family or between different families. It can also be used to determine the related groups of important herbage, turfgrass, and crops and provide crucial background information for discovering excellent genes and improving existing crop varieties.
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Affiliation(s)
- Jianli Wang
- Pratacultural Science Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhenfei Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Peng Zhong
- Branch of Animal Husbandry and Veterinary, Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Zhongbao Shen
- Pratacultural Science Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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110
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Dong S, Zhou M, Zhu J, Wang Q, Ge Y, Cheng R. The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination. BMC Genomics 2022; 23:620. [PMID: 36028808 PMCID: PMC9412808 DOI: 10.1186/s12864-022-08755-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins. RESULT This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124 bp of Jiangxi Province to 160,618 bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56-57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into four groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas. CONCLUSION Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family.
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Affiliation(s)
- Shujie Dong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Manjia Zhou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinxing Zhu
- Bureau of Agricultural and Rural Affairs of Suichang, Suichang, China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China. .,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China.
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111
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Authentication of Argan (Argania spinosa L.) Oil Using Novel DNA-Based Approaches: Detection of Olive and Soybean Oils as Potential Adulterants. Foods 2022; 11:foods11162498. [PMID: 36010499 PMCID: PMC9407626 DOI: 10.3390/foods11162498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/08/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Argan oil is a traditional product obtained from the fruits of the argan tree (Argania spinosa L.), which is endemic only to Morocco. It is commercialized worldwide as cosmetic and food-grade argan oil, attaining very high prices in the international market. Therefore, argan oil is very prone to adulteration with cheaper vegetable oils. The present work aims at developing novel real-time PCR approaches to detect olive and soybean oils as potential adulterants, as well as ascertain the presence of argan oil. The ITS region, matK and lectin genes were the targeted markers, allowing to detect argan, olive and soybean DNA down to 0.01 pg, 0.1 pg and 3.2 pg, respectively, with real-time PCR. Moreover, to propose practical quantitative methods, two calibrant models were developed using the normalized ΔCq method to estimate potential adulterations of argan oil with olive or soybean oils. The results allowed for the detection and quantification of olive and soybean oils within 50–1% and 25–1%, respectively, both in argan oil. Both approaches provided acceptable performance parameters and accurate determinations, as proven by their applicability to blind mixtures. Herein, new qualitative and quantitative PCR assays are proposed for the first time as reliable and high-throughput tools to authenticate and valorize argan oil.
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112
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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113
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Wang Y, Wang J, Chen Y, Liu S, Zhao Y, Chen N. Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10024. [PMID: 36011659 PMCID: PMC9408514 DOI: 10.3390/ijerph191610024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.
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Affiliation(s)
- Yichao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jing Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongfang Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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Javaid N, Ramzan M, Khan IA, Alahmadi TA, Datta R, Fahad S, Danish S. The chloroplast genome of Farsetia hamiltonii Royle, phylogenetic analysis, and comparative study with other members of Clade C of Brassicaceae. BMC PLANT BIOLOGY 2022; 22:384. [PMID: 35918648 PMCID: PMC9344719 DOI: 10.1186/s12870-022-03750-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/13/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Farsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades. RESULTS The chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species. CONCLUSION The entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.
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Affiliation(s)
- Nida Javaid
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Musarrat Ramzan
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi, Karachi, 75270 Pakistan
| | - Tahani Awad Alahmadi
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Medical City, PO Box-2925, Riyadh, 11461 Saudi Arabia
| | - Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska1, 61300 Brno, Czech Republic
| | - Shah Fahad
- Department of Agronomy, The University of Haripur, Khyber Pakhtunkhwa, Haripur, 22620 Pakistan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
| | - Subhan Danish
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60800 Punjab Pakistan
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Cui N, Chen W, Li X, Wang P. Comparative chloroplast genomes and phylogenetic analyses of Pinellia. Mol Biol Rep 2022; 49:7873-7885. [PMID: 35689783 PMCID: PMC9304046 DOI: 10.1007/s11033-022-07617-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/18/2022] [Indexed: 11/30/2022]
Abstract
Background Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear. Methods and results We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be. Conclusions The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia. Supplementary Information The online version of this article (10.1007/s11033-022-07617-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ning Cui
- Central Laboratory, Shandong Academy of Chinese Medicine, Ji'nan, China
| | - Weixu Chen
- Shang Yao Hua Yu (LinYi) Traditional Chinese Medicine Resources Co., Ltd, Linyi, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Ping Wang
- Central Laboratory, Shandong Academy of Chinese Medicine, Ji'nan, China.
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Yue J, Ni Y, Jiang M, Chen H, Chen P, Liu C. Characterization of Codonopsis pilosula subsp. tangshen plastome and comparative analysis of Codonopsis species. PLoS One 2022; 17:e0271813. [PMID: 35913971 PMCID: PMC9342729 DOI: 10.1371/journal.pone.0271813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
Codonopsis pilosula subsp. tangshen is one of the most important medicinal herbs used in traditional Chinese medicine. Correct identification of materials from C. pilosula subsp. tangshen is critical to ensure the efficacy and safety of the associated medicines. Traditional DNA molecular markers could distinguish Codonopsis species well, so we need to develop super or specific molecular markers. In this study, we reported the plastome of Codonopsis pilosula subsp. tangshen (Oliv.) D.Y. Hong conducted phylogenomic and comparative analyses in the Codonopsis genus for the first time. The entire length of the Codonopsis pilosula subsp. tangshen plastome was 170,672 bp. There were 108 genes in the plastome, including 76 protein-coding genes, 28 transfer RNA (tRNA), and four ribosomal RNA (rRNA) genes. Comparative analysis indicated that Codonopsis pilosula subsp. tangshen had an unusual large inversion in the large single-copy (LSC) region compared with the other three Codonopsis species. And there were two dispersed repeat sequences at both ends of the inverted regions, which might mediate the generation of this inversion. We found five hypervariable regions among the four Codonopsis species. PCR amplification and Sanger sequencing experiments demonstrated that two hypervariable regions could distinguish three medicinal Codonopsis species. Results obtained from this study will support taxonomic classification, discrimination, and molecular evolutionary studies of Codonopsis species.
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Affiliation(s)
- Jingwen Yue
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, P. R. China
| | - Yang Ni
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, P. R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Pinghua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, P. R. China
- * E-mail: (PHC); (CL)
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
- * E-mail: (PHC); (CL)
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Liu L, Zhang Y, Tumi L, Suni ML, Arakaki M, Burgess KS, Ge X. Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny. Ecol Evol 2022; 12:e9159. [PMID: 35919393 PMCID: PMC9336176 DOI: 10.1002/ece3.9159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/19/2022] [Accepted: 07/05/2022] [Indexed: 11/26/2022] Open
Abstract
The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%-37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein-coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69-78 tandem repeats, 45-60 SSRs (simple sequence repeats), and 8-22 repeat structures among 13 species. Four protein-coding genes were identified under positive site-specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.
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Affiliation(s)
- Lu Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yu‐Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- College of PharmacyShaanxi University of Chinese MedicineXi'anChina
| | - Liscely Tumi
- Facultad de Ciencias BiológicasUniversidad Nacional Mayor de San MarcosLimaPeru
| | - Mery L. Suni
- Facultad de Ciencias BiológicasUniversidad Nacional Mayor de San MarcosLimaPeru
| | - Mónica Arakaki
- Facultad de Ciencias BiológicasUniversidad Nacional Mayor de San MarcosLimaPeru
| | - Kevin S. Burgess
- Department of Biology, Columbus State UniversityUniversity System of GeorgiaColumbusGeorgiaUSA
| | - Xue‐Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation Biology, Core Botanical GardensChinese Academy of SciencesGuangzhouChina
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Ying Z, Awais M, Akter R, Xu F, Baik S, Jung D, Yang DC, Kwak GY, Wenying Y. Discrimination of Panax ginseng from counterfeits using single nucleotide polymorphism: A focused review. FRONTIERS IN PLANT SCIENCE 2022; 13:903306. [PMID: 35968150 PMCID: PMC9366256 DOI: 10.3389/fpls.2022.903306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/31/2022] [Indexed: 05/13/2023]
Abstract
Discrimination of plant species, cultivars, and landraces is challenging because plants have high phenotypic and genotypic resemblance. Panax ginseng is commonly referred to as Korean ginseng, which contains saponins with high efficacy on cells, and has been reported to be worth billions in agroeconomic value. Korean ginseng's increasing global agroeconomic value includes additional species and cultivars that are not Korean ginseng but have physical characteristics close to it. This almost unidentifiable physical characteristic of Korean ginseng-like species is discriminated via molecular markers. Single nucleotide polymorphism (SNP), found across the plant species in abundance, is a valuable tool in the molecular mapping of genes and distinguishing a plant species from adulterants. Differentiating the composition of genes in species is quite evident, but the varieties and landraces have fewer differences in addition to single nucleotide mismatch. Especially in the exon region, there exist both favorable and adverse effects on species. With the aforementioned ideas in discriminating ginseng based on molecular markers, SNP has proven reliable and convenient, with advanced markers available. This article provides the simplest cost-effective guidelines for experiments in a traditional laboratory setting to get hands-on SNP marker analysis. Hence, the current review provides detailed up-to-date information about the discrimination of Panax ginseng exclusively based on SNP adding with a straightforward method explained which can be followed to perform the analysis.
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Affiliation(s)
- Zheng Ying
- Weifang Engineering Vocational College, Qingzhou, China
| | - Muhammad Awais
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Reshmi Akter
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Fengjiao Xu
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Sul Baik
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Daehyo Jung
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Deok Chun Yang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Gi-Young Kwak
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - You Wenying
- Weifang Engineering Vocational College, Qingzhou, China
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119
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Cao DL, Zhang XJ, Xie SQ, Fan SJ, Qu XJ. Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica. BMC Genomics 2022; 23:540. [PMID: 35896957 PMCID: PMC9327190 DOI: 10.1186/s12864-022-08727-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Viola philippica Cav. is the only source plant of "Zi Hua Di Ding", which is a Traditional Chinese Medicine (TCM) that is utilized as an antifebrile and detoxicant agent for the treatment of acute pyogenic infections. Historically, many Viola species with violet flowers have been misused in "Zi Hua Di Ding". Viola have been recognized as a taxonomically difficult genera due to their highly similar morphological characteristics. Here, all common V. philippica adulterants were sampled. A total of 24 complete chloroplast (cp) genomes were analyzed, among these 5 cp genome sequences were downloaded from GenBank and 19 cp genomes, including 2 "Zi Hua Di Ding" purchased from a local TCM pharmacy, were newly sequenced. RESULTS The Viola cp genomes ranged from 156,483 bp to 158,940 bp in length. A total of 110 unique genes were annotated, including 76 protein-coding genes, 30 tRNAs, and four rRNAs. Sequence divergence analysis screening identified 16 highly diverged sequences; these could be used as markers for the identification of Viola species. The morphological, maximum likelihood and Bayesian inference trees of whole cp genome sequences and highly diverged sequences were divided into five monophyletic clades. The species in each of the five clades were identical in their positions within the morphological and cp genome tree. The shared morphological characters belonging to each clade was summarized. Interestingly, unique variable sites were found in ndhF, rpl22, and ycf1 of V. philippica, and these sites can be selected to distinguish V. philippica from samples all other Viola species, including its most closely related species. In addition, important morphological characteristics were proposed to assist the identification of V. philippica. We applied these methods to examine 2 "Zi Hua Di Ding" randomly purchased from the local TCM pharmacy, and this analysis revealed that the morphological and molecular characteristics were valid for the identification of V. philippica. CONCLUSIONS This study provides invaluable data for the improvement of species identification and germplasm of V. philippica that may facilitate the application of a super-barcode in TCM identification and enable future studies on phylogenetic evolution and safe medical applications.
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Affiliation(s)
- Dong-Ling Cao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China
| | - Xue-Jie Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China
| | - Shao-Qiu Xie
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China
| | - Shou-Jin Fan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China.
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China.
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Paula DP, Timbó RV, Togawa RC, Vogler AP, Andow DA. Quantitative prey species detection in predator guts across multiple trophic levels by mapping unassembled shotgun reads. Mol Ecol Resour 2022; 23:64-80. [DOI: 10.1111/1755-0998.13690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 06/11/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Débora P. Paula
- Embrapa Recursos Genéticos e Biotecnologia Brasília DF Brazil
| | - Renata V. Timbó
- Embrapa Recursos Genéticos e Biotecnologia Brasília DF Brazil
- Universidade de Brasília, Campus Universitário Darcy Ribeiro Brasília DF Brazil
| | | | - Alfried P. Vogler
- Imperial College London Ascot UK
- Department of Life Sciences Natural History Museum London UK
| | - David A. Andow
- Department of Entomology University of Minnesota St. Paul USA
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Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution. Genes (Basel) 2022; 13:genes13071279. [PMID: 35886061 PMCID: PMC9324613 DOI: 10.3390/genes13071279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 12/03/2022] Open
Abstract
With the development of molecular sequencing approaches, many taxonomic and phylogenetic problems of the genus Allium L. have been solved; however, the phylogenetic relationships of some subgenera or sections, such as section Bromatorrhiza, remain unresolved, which has greatly impeded our full understanding of the species relationships among the major clades of Allium. In this study, the complete chloroplast (cp) genomes of nine species in the Allium sect. Bromatorrhiza were determined using the Illumina paired-end sequencing, the NOVOPlasty de novo assembly strategy, and the PGA annotation method. The results showed that the cp genome exhibited high conservation and revealed a typical circular tetrad structure. Among the sect. Bromatorrhiza species, the gene content, SSRs, codon usage, and RNA editing site were similar. The genome structure and IR regions’ fluctuation were investigated while genes, CDSs, and non-coding regions were extracted for phylogeny reconstruction. Evolutionary rates (Ka/Ks values) were calculated, and positive selection analysis was further performed using the branch-site model. Five hypervariable regions were identified as candidate molecular markers for species authentication. A clear relationship among the sect. Bromatorrhiza species were detected based on concatenated genes and CDSs, respectively, which suggested that sect. Bromatorrhiza is monophyly. In addition, there were three genes with higher Ka/Ks values (rps2, ycf1, and ycf2), and four genes (rpoC2, atpF, atpI, and rpl14) were further revealed to own positive selected sites. These results provide new insights into the plastome component, phylogeny, and evolution of Allium species.
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Yu XQ, Jiang YZ, Folk RA, Zhao JL, Fu CN, Fang L, Peng H, Yang JB, Yang SX. Species discrimination in Schima (Theaceae): Next-generation super-barcodes meet evolutionary complexity. Mol Ecol Resour 2022; 22:3161-3175. [PMID: 35789203 DOI: 10.1111/1755-0998.13683] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022]
Abstract
Plastid genome and nrDNA arrays, proposed recently as "super barcodes", might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super barcodes. In this study, we generated multiple datasets comprising standard DNA barcodes (matK, rbcL, trnH-psbA, nrITS) and super-barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned datasets-the lowest estimated rate of super barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization, or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multi-locus nuclear markers for species discrimination in plant groups.
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Affiliation(s)
- Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | - Yin-Zi Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences.,College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, 39762, MS, United States
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | - Liang Fang
- College of Life Sciences, Jiujiang University, 332000, Jiujiang, Jiangxi, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Shi-Xiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
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123
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Wu X, Luo D, Zhang Y, Yang C, Crabbe MJC, Zhang T, Li G. Comparative Genomic and Phylogenetic Analysis of Chloroplast Genomes of Hawthorn (Crataegus spp.) in Southwest China. Front Genet 2022; 13:900357. [PMID: 35860470 PMCID: PMC9289535 DOI: 10.3389/fgene.2022.900357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
The hawthorns (Crataegus spp.) are widely distributed and famous for their edible and medicinal values. There are ∼18 species and seven varieties of hawthorn in China distributed throughout the country. We now report the chloroplast genome sequences from C. scabrifolia, C. chungtienensis and C. oresbia, from the southwest of China and compare them with the previously released six species in Crataegus and four species in Rosaceae. The chloroplast genome structure of Crataegus is typical and can be divided into four parts. The genome sizes are between 159,654 and 159,898bp. The three newly sequenced chloroplast genomes encode 132 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis of the chloroplast genomes revealed six divergent hotspot regions, including ndhA, rps16-trnQ-UUG, ndhF-rpl32, rps16-psbK, trnR-UCU-atpA and rpl32-trnL-UAG. According to the correlation and co-occurrence analysis of repeats with indels and SNPs, the relationship between them cannot be ignored. The phylogenetic tree constructed based on the complete chloroplast genome and intergenic region sequences indicated that C. scabrifolia has a different origin from C. chungtienensis and C. oresbia. We support the placement of C. hupehensis, C. cuneata, C. scabrifolia in C. subg. Crataegus and C. kansuensis, C. oresbia, C. kansuensis in C. subg. Sanguineae. In addition, based on the morphology, geographic distribution and phylogenetic relationships of C. chungtienensis and C. oresbia, we speculate that these two species may be the same species. In conclusion, this study has enriched the chloroplast genome resources of Crataegus and provided valuable information for the phylogeny and species identification of this genus.
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Affiliation(s)
- Xien Wu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Dengli Luo
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Yingmin Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Congwei Yang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Ticao Zhang, ; Guodong Li,
| | - Guodong Li
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Ticao Zhang, ; Guodong Li,
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124
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Travadi T, Sharma S, Pandit R, Nakrani M, Joshi C, Joshi M. A duplex PCR assay for authentication of Ocimum basilicum L. and Ocimum tenuiflorum L in Tulsi churna. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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125
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Noviana E, Indrayanto G, Rohman A. Advances in Fingerprint Analysis for Standardization and Quality Control of Herbal Medicines. Front Pharmacol 2022; 13:853023. [PMID: 35721184 PMCID: PMC9201489 DOI: 10.3389/fphar.2022.853023] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/26/2022] [Indexed: 01/01/2023] Open
Abstract
Herbal drugs or herbal medicines (HMs) have a long-standing history as natural remedies for preventing and curing diseases. HMs have garnered greater interest during the past decades due to their broad, synergistic actions on the physiological systems and relatively lower incidence of adverse events, compared to synthetic drugs. However, assuring reproducible quality, efficacy, and safety from herbal drugs remains a challenging task. HMs typically consist of many constituents whose presence and quantity may vary among different sources of materials. Fingerprint analysis has emerged as a very useful technique to assess the quality of herbal drug materials and formulations for establishing standardized herbal products. Rather than using a single or two marker(s), fingerprinting techniques take great consideration of the complexity of herbal drugs by evaluating the whole chemical profile and extracting a common pattern to be set as a criterion for assessing the individual material or formulation. In this review, we described and assessed various fingerprinting techniques reported to date, which are applicable to the standardization and quality control of HMs. We also evaluated the application of multivariate data analysis or chemometrics in assisting the analysis of the complex datasets from the determination of HMs. To ensure that these methods yield reliable results, we reviewed the validation status of the methods and provided perspectives on those. Finally, we concluded by highlighting major accomplishments and presenting a gap analysis between the existing techniques and what is needed to continue moving forward.
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Affiliation(s)
- Eka Noviana
- Departement of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Abdul Rohman
- Departement of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Center of Excellence, Institute for Halal Industry and Systems, Universitas Gadjah Mada, Yogyakarta, Indonesia
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126
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Karppinen K, Avetisyan A, Hykkerud AL, Jaakola L. A dPCR Method for Quantitative Authentication of Wild Lingonberry ( Vaccinium vitis-idaea) versus Cultivated American Cranberry ( V. macrocarpon). Foods 2022; 11:1476. [PMID: 35627046 PMCID: PMC9141823 DOI: 10.3390/foods11101476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023] Open
Abstract
Berries of the genus Vaccinium are highly valued health-beneficial superfoods, which are commonly subjected to adulteration and mixed with each other, or with other common berry species. A quantitative DNA-based method utilizing a chip-based digital polymerase chain reaction (dPCR) technique was developed for identifying and quantifying wild lingonberry (V. vitis-idaea) and cultivated American cranberry (V. macrocarpon). The dPCR method with species-specific primers for mini-barcoding was designed based on the indel regions found in the trnI-CAU-trnL-CAA locus in the chloroplast genome. The designed primers were able to amplify only target species, enabling to distinguish the two closely related species with good sensitivity. Our results illustrated the ability of the method to identify lingonberry and American cranberry DNA using PCR without the need for probes or further sequencing. The dPCR method could also quantify the DNA copy number in mixed samples. Based on this study, the method provides a basis for a simple, fast, and sensitive quantitative authentication analysis of lingonberry and American cranberry by dPCR. Moreover, it can also provide a platform for authentication analyses of other plant species as well by utilizing the indel regions of chloroplast genomes.
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Affiliation(s)
- Katja Karppinen
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
| | - Anna Avetisyan
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
| | - Anne Linn Hykkerud
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
| | - Laura Jaakola
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
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127
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Characterisation of the Complete Chloroplast Genomes of Seven Hyacinthus orientalis L. Cultivars: Insights into Cultivar Phylogeny. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To improve agricultural performance and obtain potential economic benefits, an understanding of phylogenetic relationships of Hyacinthus cultivars is needed. This study aims to revisit the phylogenetic relationships of Hyacinthus cultivars using complete chloroplast genomes. Nine chloroplast genomes were de novo sequenced, assembled and annotated from seven cultivars of Hyacinthus orientalis and two Scilloideae species including Bellevalia paradoxa and Scilla siberica. The chloroplast genomes of Hyacinthus cultivars ranged from 154,458 bp to 154,641 bp, while those of Bellevalia paradoxa and Scilla siberica were 154,020 bp and 154,943 bp, respectively. Each chloroplast genome was annotated with 133 genes, including 87 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Simple sequence repeats AAGC/CTTG and ACTAT/AGTAT were identified only in ‘Eros’, while AAATC/ATTTG were identified in all cultivars except ‘Eros’. Five haplotypes were identified based on 460 variable sites. Combined with six other previously published chloroplast genomes of Scilloideae, a sliding window analysis and a phylogenetic analysis were performed. Divergence hotspots ndhA and trnG-UGC were identified with a nucleotide diversity threshold at 0.04. The phylogenetic positions of Hyacinthus cultivars were different from the previous study using ISSR. Complete chloroplast genomes serve as new evidence in Hyacinthus cultivar phylogeny, contributing to cultivar identification, preservation and breeding.
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128
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Huo Z, Xu W, Guo H, Yang P, Zhang Q, Lu X, Wang L. The complete chloroplast genome of Persicaria perfoliata and comparative analysis with Four Medicinal Plants of Polygonaceae. Genome 2022; 65:377-389. [PMID: 35576612 DOI: 10.1139/gen-2021-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Polygonaceae is a large family of medicinal herbs that includes many species used as traditional Chinese medicine, such as Persicaria perfoliate. Here, we sequenced the complete cp genome of P. perfoliata using Illumina sequencing technology with the purpose to provide a method to facilitate accurate identification. After being annotated, the cp genome of P. perfoliata was compared with Fagopyrum tataricum, Persicaria chinensis, Fagopyrum dibotrys and Fallopia multiflora. The complete cp genome of P. perfoliata is 160,730 bp in length, containing a small single copy (SSC) region of 12,927 bp, a large single copy (LSC) region of 85,433 bp and a pair of inverted repeats (IR) regions of 62,370 bp. A total of 131 genes were annotated, including eight rRNA genes, 34 tRNA genes and 84 protein-coding genes. Forty-two simple sequence repeats and fifty-five repeat sequences were identified. Mutational hot spots analyses indicated that five genes (matK, ndhF, ccsA, cemA, rpl20) could be selected as candidates for molecular markers. Moreover, phylogenetic analysis showed that all the Polygonaceae species formed a monophyletic clade, and P. perfoliata showed the closest relationship with P. chinense. The study provides valuable molecular information to accurately identify P. perfoliata and assist in its development and application.
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Affiliation(s)
- Ziting Huo
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Wenbo Xu
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Huijun Guo
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Peng Yang
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Qianwen Zhang
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Xu Lu
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Long Wang
- China Pharmaceutical University, 56651, Nanjing, China;
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129
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Lee SY, Xu KW, Huang CY, Lee JH, Liao WB, Zhang YH, Fan Q. Molecular phylogenetic analyses based on the complete plastid genomes and nuclear sequences reveal Daphne (Thymelaeaceae) to be non-monophyletic as current circumscription. PLANT DIVERSITY 2022; 44:279-289. [PMID: 35769588 PMCID: PMC9209861 DOI: 10.1016/j.pld.2021.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 06/02/2023]
Abstract
The diverse members of the genus Daphne are prized for their fragrant flowers. Despite being promising ornamental plants in many countries, genetic information of Daphne is scarce. In this study, the plastomes of four species and one variety of Daphne were sequenced and analyzed. The plastomes were typical and contained a pair of inverted repeat (IR) regions that separated the large single-copy (LSC) region from the small single-copy (SSC) region. With a length ranging from 132,869 bp (D. genkwa) to 174,773 bp (D. championii), 106 to 141 genes were predicted. Comparative plastome analysis of the newly sequenced plastomes with four publicly available Daphne plastomes identified an expansion of the IRs, sequence variations, and mutational hotspots. Phylogenetic analyses indicated that the genus Daphne in its current circumscription is polyphyletic. Daphne genkwa was nested within the genus Wikstroemia, while D. championii was well resolved as sister to Edgeworthia. These findings concurred with results from our study that used nuclear ribosomal internal transcribed spacer sequence data. The conflicts on the molecular placement of D. championii and D. genkwa and the present taxonomic classification in Daphne suggest that a new intergeneric classification system of Daphneae warrants consideration.
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Affiliation(s)
- Shiou Yih Lee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
- Faculty of Health and Life Sciences, INTI International University, 71800, Nilai, Malaysia
| | - Ke-Wang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 219937, Nanjing, China
| | - Cui-Ying Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Wen-Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Yong-Hong Zhang
- School of Life Sciences, Yunnan Normal University, 650001, Kunming, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
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Tittarelli R, Gismondi A, Di Marco G, Mineo F, Vernich F, Russo C, Marsella LT, Canini A. Forensic Application of Genetic and Toxicological Analyses for the Identification and Characterization of the Opium Poppy ( Papaver somniferum L.). BIOLOGY 2022; 11:672. [PMID: 35625400 PMCID: PMC9138826 DOI: 10.3390/biology11050672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND A reliable and science-based taxonomic determination of Papaver somniferum L. (opium poppy), the illegal species of the genus Papaver, may have practical and legal implications for law enforcement. P. somniferum is a controlled plant because of its narcotic substances, such as morphine and codeine. As poppy plants have rather similar morphological features, both chemical and genetic analysis are required in order to achieve an accurate characterization of such species. The chemical structures of alkaloids are extremely variable even within the same species, which is why the genetic approach may lead to a more scientific Papaver sp. differentiation. The aim of our study was the taxonomic identification of poppy capsules seized by the Italian Police Forces being considered as potential P. somniferum derivatives. METHODS The alkaloids detected using gas chromatography/mass-spectrometry (GC/MS) were morphine, codeine, thebaine, noscapine, meconin, hydrocotarnine, and traces of papaverine. Further genetic analysis was carried out simultaneously using three plastid DNA barcoding regions (matK, trnH-psbA, and rbcL) for the samples' identification. RESULTS The Random Amplification of Polymorphic DNA (RAPD) method showed that the analysed samples were genetically identical. CONCLUSIONS The morphological, toxicological, and genetic profile of the samples revealed that they belonged to P. somniferum species. Furthermore, the alkaloid content of dried poppy capsules might be used to investigate and track their origin.
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Affiliation(s)
- Roberta Tittarelli
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Angelo Gismondi
- Laboratory of Botany, Department of Biology, Faculty of Mathematical, Physical and Natural Science, University Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.G.); (G.D.M.); (A.C.)
| | - Gabriele Di Marco
- Laboratory of Botany, Department of Biology, Faculty of Mathematical, Physical and Natural Science, University Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.G.); (G.D.M.); (A.C.)
| | - Federico Mineo
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Francesca Vernich
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Carmelo Russo
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Luigi Tonino Marsella
- Laboratory of Forensic Toxicology, Section of Legal and Forensic Medicine, Social Security and Forensic Toxicology, Department of Biomedicine and Prevention, Faculty of Medicine and Surgery, University Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (F.M.); (F.V.); (C.R.); (L.T.M.)
| | - Antonella Canini
- Laboratory of Botany, Department of Biology, Faculty of Mathematical, Physical and Natural Science, University Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.G.); (G.D.M.); (A.C.)
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Wong KH, Kong BLH, Siu TY, Wu HY, But GWC, Shaw P, Lau DTW. Complete chloroplast genomes of Asparagus aethiopicus L., A. densiflorus (Kunth) Jessop 'Myers', and A. cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congenerics. PLoS One 2022; 17:e0266376. [PMID: 35468142 PMCID: PMC9037925 DOI: 10.1371/journal.pone.0266376] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/19/2022] [Indexed: 11/21/2022] Open
Abstract
Asparagus species are widely used for medicinal, horticultural, and culinary purposes. Complete chloroplast DNA (cpDNA) genomes of three Asparagus specimens collected in Hong Kong-A. aethiopicus, A. densiflorus 'Myers', and A. cochinchinensis-were de novo assembled using Illumina sequencing. Their sizes ranged from 157,069 to 157,319 bp, with a total guanine-cytosine content of 37.5%. Structurally, a large single copy (84,598-85,350 bp) and a small single copy (18,677-18,685 bp) were separated by a pair of inverted repeats (26,518-26,573 bp). In total, 136 genes were annotated for A. aethiopicus and A. densiflorus 'Myers'; these included 90 mRNA, 38 tRNA, and 8 rRNA genes. Further, 132 genes, including 87 mRNA, 37 tRNA, and 8 rRNA genes, were annotated for A. cochinchinensis. For comparative and phylogenetic analysis, we included NCBI data for four congenerics, A. setaceus, A. racemosus, A. schoberioides, and A. officinalis. The gene content, order, and genome structure were relatively conserved among the genomes studied. There were similarities in simple sequence repeats in terms of repeat type, sequence complementarity, and cpDNA partition distribution. A. densiflorus 'Myers' had distinctive long sequence repeats in terms of their quantity, type, and length-interval frequency. Divergence hotspots, with nucleotide diversity (Pi) ≥ 0.015, were identified in five genomic regions: accD-psaI, ccsA, trnS-trnG, ycf1, and ndhC-trnV. Here, we summarise the historical changes in the generic subdivision of Asparagus. Our phylogenetic analysis, which also elucidates the nomenclatural complexity of A. aethiopicus and A. densiflorus 'Myers', further supports their close phylogenetic relationship. The findings are consistent with prior generic subdivisions, except for the placement of A. racemosus, which requires further study. These de novo assembled cpDNA genomes contribute valuable genomic resources and help to elucidate Asparagus taxonomy.
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Affiliation(s)
- Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Bobby Lim-Ho Kong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Tin-Yan Siu
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Grace Wing-Chiu But
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Pang‑Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - David Tai-Wai Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
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Wu HY, Wong KH, Kong BLH, Siu TY, But GWC, Tsang SSK, Lau DTW, Shaw PC. Comparative Analysis of Chloroplast Genomes of Dalbergia Species for Identification and Phylogenetic Analysis. PLANTS 2022; 11:plants11091109. [PMID: 35567110 PMCID: PMC9104903 DOI: 10.3390/plants11091109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
Dalbergia L.f. is a pantropical genus consisting of 269 species of trees, shrubs, and woody lianas. This genus is listed in CITES Appendices because of illegal logging and trafficking driven by the high economic value of its heartwood. Some species are also used medicinally. Species identification of Dalbergia timber and herbs is challenging but essential for CITES implementation. Molecular methods had been developed for some timber species, mostly from Madagascar and Southeast Asia, but medicinal species in south China were usually not included in those studies. Here, we sequenced and assembled the chloroplast genomes of five Dalbergia species native to Hong Kong, four of which are medicinal plants. Our aim is to find potential genetic markers for the identification of medicinal Dalbergia species based on divergence hotspots detected in chloroplast genomes after comparative and phylogenetic analysis. Dalbergia chloroplast genomes displayed the typical quadripartite structure, with the 50 kb inversion found in most Papilionoideae lineages. Their sizes and gene content are well conserved. Phylogenetic tree of Dalbergia chloroplast genomes showed an overall topology similar to that of ITS sequences. Four divergence hotspots (trnL(UAA)-trnT(UGU), ndhG-ndhI, ycf1a and ycf1b) were identified and candidate markers for identification of several Dalbergia species were suggested.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (H.-Y.W.); (B.L.-H.K.)
| | - Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (K.-H.W.); (T.-Y.S.); (D.T.-W.L.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
| | - Bobby Lim-Ho Kong
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (H.-Y.W.); (B.L.-H.K.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
| | - Tin-Yan Siu
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (K.-H.W.); (T.-Y.S.); (D.T.-W.L.)
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Grace Wing-Chiu But
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
| | - Stacey Shun-Kei Tsang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
| | - David Tai-Wai Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (K.-H.W.); (T.-Y.S.); (D.T.-W.L.)
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (H.-Y.W.); (B.L.-H.K.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (G.W.-C.B.); (S.S.-K.T.)
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Correspondence:
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Yang J, Zhang F, Ge Y, Yu W, Xue Q, Wang M, Wang H, Xue Q, Liu W, Niu Z, Ding X. Effects of geographic isolation on the Bulbophyllum chloroplast genomes. BMC PLANT BIOLOGY 2022; 22:201. [PMID: 35439926 PMCID: PMC9016995 DOI: 10.1186/s12870-022-03592-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/11/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Because chloroplast (cp) genome has more conserved structures than nuclear genome and mitochondrial genome, it is a useful tool in estimating the phylogenetic relationships of plants. With a series of researches for cp genomes, there have been comprehensive understandings about the cp genome features. The genus Bulbophyllum widely distributed in Asia, South America, Australia and other places. Therefore, it is an excellent type genus for studying the effects of geographic isolation. RESULTS In this study, the cp genomes of nine Bulbophyllum orchids were newly sequenced and assembled using the next-generation sequencing technology. Based on 19 Asian (AN) and eight South American (SA) Bulbophyllum orchids, the cp genome features of AN clade and SA clade were compared. Comparative analysis showed that there were considerable differences in overall cp genome features between two clades in three aspects, including basic cp genome features, SSC/IRB junctions (JSBs) and mutational hotspots. The phylogenetic analysis and divergence time estimation results showed that the AN clade has diverged from the SA clade in the late Oligocene (21.50-30.12 mya). After estimating the occurrence rates of the insertions and deletions (InDels), we found that the change trends of cp genome structures between two clades were different under geographic isolation. Finally, we compared selective pressures on cp genes and found that long-term geographic isolation made AN and SA Bulbophyllum cp genes evolved variably. CONCLUSION The results revealed that the overall structural characteristics of Bulbophyllum cp genomes diverged during the long-term geographic isolation, and the crassulacean acid metabolism (CAM) pathway may play an important role in the Bulbophyllum species evolution.
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Affiliation(s)
- Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Fuwei Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Yajie Ge
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Wenhui Yu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Qiqian Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Mengting Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Hongman Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China.
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China.
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Cao Q, Gao Q, Ma X, Zhang F, Xing R, Chi X, Chen S. Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau. BMC PLANT BIOLOGY 2022; 22:195. [PMID: 35413790 PMCID: PMC9004202 DOI: 10.1186/s12870-022-03577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/28/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND The genus Swertia is of great medicinal importance and one of the most taxonomically challenging taxa within Gentianaceae, largely due to the morphological similarities of species within this genus and with its closely related genera. Previous molecular studies confirmed its polyphyly but suffered from low phylogenetic resolutions because only limited sequence loci were used. Thus, we conducted the structural, gene evolutionary, and phylogenetic analyses of 11 newly obtained plastomes of Swertia. Our result greatly improved the phylogenetic resolutions in Swertia, shed new light on the plastome evolution and phylogenetic relationships of this genus. RESULTS The 11 Swertia plastomes together with the published seven species proved highly similar in overall size, structure, gene order, and content, but revealed some structural variations caused by the expansion and contraction of the IRb region into the LSC region, due to the heterogeneous length of the ψycf1. The gene rps16 was found to be in a state flux with pseudogenes or completely lost. Similar situation was also documented in other genera of Gentianaceae. This might imply loss of the gene in the common ancestor of Gentianaceae. The distribution plot of ENC vs. GC3 showed all these plastomes arranging very close in the Wright line with an expected ENC value (49-52%), suggesting the codon usage of Swertia was mainly constrained by a GC mutation bias. Most of the genes remained under the purifying selection, however, the cemA was identified under positive selection, possibly reflecting an adaptive response to low CO2 atmospheric conditions during the Late Miocene. Our phylogenomic analyses, based on 74 protein-coding genes (CDS), supported the polyphyly of Swertia with its close allies in the subtribe Swertiinae, presumably due to recent rapid radiation. The topology inferred from our phylogenetic analyses partly supported the current taxonomic treatment. Finally, several highly variable loci were identified, which can be used in future phylogenetic studies and accurate identification of medicinal genuineness of Swertia. CONCLUSIONS Our study confirmed the polyphyly of Swertia and demonstrated the power of plastome phylogenomics in improvement of phylogenetic resolution, thus contributing to a better understanding of the evolutionary history of Swertia.
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Affiliation(s)
- Qian Cao
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingbo Gao
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Xiaolei Ma
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Faqi Zhang
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Rui Xing
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Xiaofeng Chi
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Shilong Chen
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
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Ji Y, Yang J, Landis JB, Wang S, Jin L, Xie P, Liu H, Yang JB, Yi TS. Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:832034. [PMID: 35444671 PMCID: PMC9014178 DOI: 10.3389/fpls.2022.832034] [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: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.
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Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jin Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jacob B. Landis
- Section of Plant Biology and the L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Lei Jin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Pingxuan Xie
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, 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, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Shin SC, Song JH, Yoo YH, Lee JS, Kang SI, Kim HJ, Lee H, Kim HB. The complete chloroplast genome sequence of a medicinal citrus landrace, Citrus erythrosa Hort. ex Tanaka in Jeju Island, Korea. Mitochondrial DNA B Resour 2022; 7:580-582. [PMID: 35386626 PMCID: PMC8979535 DOI: 10.1080/23802359.2022.2057243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Citrus erythrosa (Dongjeongkyool in Korean) is a medicinal citrus landrace that grows in Korea. In this study, we characterized the complete chloroplast (Cp) genome (160,120 bp) of C. erythrosa. The Cp genome was consisted of 4 distinct regions: a large single copy (87,731 bp), a small single copy (18,393 bp), and a pair of inverted repeat regions (26,998 bp). The Cp genome encodes a total of 133 genes including 88 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic analysis reveals that C. erythrosa is a sister group to the clade of species including C. reticulata within the genus Citrus.
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Affiliation(s)
| | - Ji Hoon Song
- Jeju Institute of Korean Medicine, Jeju, Republic of Korea
| | - Yo-Han Yoo
- Korea Polar Research Institute, Incheon, Republic of Korea
| | - Joo-Sang Lee
- Jeju Institute of Korean Medicine, Jeju, Republic of Korea
| | - Seong-Il Kang
- Jeju Institute of Korean Medicine, Jeju, Republic of Korea
| | - Hee Jeong Kim
- Jeju Institute of Korean Medicine, Jeju, Republic of Korea
| | - Hyoungseok Lee
- Korea Polar Research Institute, Incheon, Republic of Korea
- Polar Science Department, University of Science & Technology, Incheon, Republic of Korea
| | - Ho Bang Kim
- Life Sciences Research Institute, Biomedic Co., Ltd., Bucheon, Republic of Korea
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Jiang S, Chen F, Qin P, Xie H, Peng G, Li Y, Guo X. The specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:837-848. [PMID: 35592487 PMCID: PMC9110604 DOI: 10.1007/s12298-022-01175-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 05/07/2023]
Abstract
UNLABELLED More than 600 species in over 40 genera have been identified in family Theaceae worldwide. The accurate identification of Theaceae plants can ensure the market economic order, and it plays a vital role in achieving the sustainable utilization of germplasm resources. DNA barcoding, one of the most potential species identification technologies at present, has advanced in the rapid, accurate and repetitive discrimination of species. In this study, matK + ndhF + ycf1 was observed as the optimal combined candidate gene sequence of DNA barcodes by analyzing genetic information of four single chloroplast DNA sequences, including matK, rbcL, ndhF and ycf1, as well as six combined gene sequences. Subsequently, the experiments were performed on phylogenetic analysis based on genetic distance to study the phylogenetic relationship of Theaceae plants and evaluate the species identification accuracy of matK + ndhF + ycf1. Lastly, the species-specific DNA barcodes were designed by searching the variable sites (one type of single nucleotide polymorphism sites) for the accurate identification of Camellia amplexicaulis, Franklinia alatamaha, Gordonia brandegeei and Stewartia micrantha. The previous methods of screening and testing candidate gene sequences were optimized, and innovation was made in the above methods. The process of making visual DNA barcodes was standardized. Besides, DNA barcoding technology increased the accuracy of species identification and DNA barcoding was analyzed in accordance with the theories of population genetics (e.g., neutral theory of molecular evolution). The results of the study will lay a basis for the identification and protection of Theaceae species and germplasm resources. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01175-7.
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Affiliation(s)
- Shuai Jiang
- College of Biology, Hunan University, Changsha, 410082 China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082 China
| | - Pai Qin
- College of Biology, Hunan University, Changsha, 410082 China
| | - Hai Xie
- College of Biology, Hunan University, Changsha, 410082 China
| | - Guo Peng
- College of Biology, Hunan University, Changsha, 410082 China
| | - Yongliang Li
- College of Biology, Hunan University, Changsha, 410082 China
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082 China
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Bosmali I, Lagiotis G, Haider N, Osathanunkul M, Biliaderis C, Madesis P. DNA-Based Identification of Eurasian Vicia Species Using Chloroplast and Nuclear DNA Barcodes. PLANTS 2022; 11:plants11070947. [PMID: 35406927 PMCID: PMC9003045 DOI: 10.3390/plants11070947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/19/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022]
Abstract
Many legume species of the Vicia L. genus (Fabaceae Lindl.) are key components of the Mediterranean diet and have an integral role in sustainable agriculture. Given the importance of the Vicia species for Eurasian culture, it is necessary to implement methodologies, such as DNA barcoding, that can enable the effective authentication and identification of species in the genus. In this study, we analysed the chloroplast trnL and rpoC1, as well as the nuclear ITS2 DNA barcoding regions, to identify 71 Vicia specimens of Eurasian descent. Both the trnL and ITS2 regions were highly effective in discriminating the analysed taxa, while the more conserved rpoC1 region could not identify all of the selected species due to high sequence conservation or non-annotated or absent rpoC1 species sequences in GenBank. A dendrographic representation of the generated trnL data showed sufficient clustering for most of the analysed taxa, although some topological discrepancies were observed. ITS2 and rpoC1 reconstructions were also used for resolving the topological discrepancies observed in the trnL tree. Our analysis suggests that a combination of DNA barcoding regions is essential for accurate species discrimination within the Vicia genus, while single-locus analyses do not provide the necessary resolution.
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Affiliation(s)
- Irene Bosmali
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, 57001 Thessaloniki, Greece; (I.B.); (G.L.)
- Laboratory of Food Chemistry and Biochemistry, Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Georgios Lagiotis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, 57001 Thessaloniki, Greece; (I.B.); (G.L.)
| | - Nadia Haider
- The Department of Molecular Biology and Biotechnology, Atomic Energy Commission (AEC), Damascus 6091, Syria;
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Costas Biliaderis
- Laboratory of Food Chemistry and Biochemistry, Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Panagiotis Madesis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, 57001 Thessaloniki, Greece; (I.B.); (G.L.)
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
- Correspondence:
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139
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Emaus MN, Cagliero C, Gostel MR, Johnson G, Anderson JL. Simple and efficient isolation of plant genomic DNA using magnetic ionic liquids. PLANT METHODS 2022; 18:37. [PMID: 35321738 PMCID: PMC8943943 DOI: 10.1186/s13007-022-00860-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/17/2022] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant DNA isolation and purification is a time-consuming and laborious process relative to epithelial and viral DNA sample preparation due to the cell wall. The lysis of plant cells to free intracellular DNA normally requires high temperatures, chemical surfactants, and mechanical separation of plant tissue prior to a DNA purification step. Traditional DNA purification methods also do not aid themselves towards fieldwork due to the numerous chemical and bulky equipment requirements. RESULTS In this study, intact plant tissue was coated by hydrophobic magnetic ionic liquids (MILs) and ionic liquids (ILs) and allowed to incubate under static conditions or dispersed in a suspension buffer to facilitate cell disruption and DNA extraction. The DNA-enriched MIL or IL was successfully integrated into the qPCR buffer without inhibiting the reaction. The two aforementioned advantages of ILs and MILs allow plant DNA sample preparation to occur in one minute or less without the aid of elevated temperatures or chemical surfactants that typically inhibit enzymatic amplification methods. MIL or IL-coated plant tissue could be successfully integrated into a qPCR assay without the need for custom enzymes or manual DNA isolation/purification steps that are required for conventional methods. CONCLUSIONS The limited amount of equipment, chemicals, and time required to disrupt plant cells while simultaneously extracting DNA using MILs makes the described procedure ideal for fieldwork and lab work in low resource environments.
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Affiliation(s)
- Miranda N. Emaus
- Department of Chemistry, Iowa State University, Ames, IA 50011 USA
| | - Cecilia Cagliero
- Dipartimento Di Scienza E Tecnologia del Farmaco, Università Degli Studi Di Torino, 10125 Turin, Italy
| | | | | | - Jared L. Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA 50011 USA
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Zhao C, Li K, Mou X, Zhu Y, Chen C, Zhang M, Wang Y, Zhou K, Sheng Y, Liu H, Bai Y, Li X, Zhou C, Deng D, Wu J, Wu HC, Bao R, Geng J. High-fidelity biosensing of dNTPs and nucleic acids by controllable subnanometer channel PaMscS. Biosens Bioelectron 2022; 200:113894. [PMID: 34973563 DOI: 10.1016/j.bios.2021.113894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 02/05/2023]
Abstract
Current tools for dNTP analysis mainly rely on expensive fluorescent labeling, mass spectrometry or electrochemistry. Single-molecule assay by protein nanopores with an internal diameter of ca. 1-3.6 nm provides a useful tool for dNTP sensing. However, the most commonly used protein nanopores require additional modifications to enable dNTP detection. In this study, the PaMscS channel (mechanosensitive channel of small conductance from Pseudomonas aeruginosa) embedded in the bilayer lipid membrane (BLM) of E. coli polar lipid extract was applied as a nanopore for single molecular sensing. Two mutants of PaMscS nanopores on the side portal region (PaMscS W130A and PaMscS K180R) were selected for direct dNTP or pyrophosphoric acid (PPi) detection without aptamer or protein modification. Notably, the PaMscS mutant pore can be adjusted by regulation of osmolarity differences, which is crucial for the optimal detection of specific molecules. In addition, we established a PaMscS-based diagnosis method for the rapid sensing of disease-associated nucleic acids by monitoring the consumption of dNTPs, with 86% specificity and 100% sensitivity among 22 clinical samples. This protein nanopore, without aptamer or modification, paves a new way for dNTPs, PPi direct sensing and nucleic acid detection with low cost but high versatility.
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Affiliation(s)
- Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Xingyu Mou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Yibo Zhu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; School of Pharmacy, North Sichuan Medical College, Nanchong, 637000, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yingying Sheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hao Liu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Yunjin Bai
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu, 610041, China
| | - Dong Deng
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jianping Wu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Rui Bao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
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Xu K, Lin C, Lee SY, Mao L, Meng K. Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships. BMC Genomics 2022; 23:203. [PMID: 35287585 PMCID: PMC8922745 DOI: 10.1186/s12864-022-08397-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships. RESULTS We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems. CONCLUSION Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.
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Affiliation(s)
- Kewang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 510275, China
| | - Chenxue Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 510275, China
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, 71800, Nilai, Malaysia
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 510275, China.
| | - Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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142
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Liu CK, Lei JQ, Jiang QP, Zhou SD, He XJ. The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus. BMC PLANT BIOLOGY 2022; 22:101. [PMID: 35255817 PMCID: PMC8900453 DOI: 10.1186/s12870-022-03488-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/02/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants. RESULTS In the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum. CONCLUSION The plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.
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Affiliation(s)
- Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jia-Qing Lei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Qiu-Ping Jiang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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143
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Zhang Y, Liu X, Zhang C, Xu C, Qin W, Shen G, Guo B. The complete chloroplast genome of Epimedium campanulatum Ogisu (Berberidaceae), a rare plant species endemic to China. Mitochondrial DNA B Resour 2022; 7:485-487. [PMID: 35311206 PMCID: PMC8928854 DOI: 10.1080/23802359.2021.2024771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Epimedium L. is an important medicinal herbaceous genus that belongs to the family Berberidaceae. Epimedium campanulatum Ogisu is a plant species only inhabited in the northwestern part of Sichuan province, China. Here, we reported the complete chloroplast genome sequence, assembly, and characterization of E. campanulatum. The chloroplast genome of E. campanulatum was 157,343 bp in length, and a total of 112 unique genes were identified. Phylogenetic results revealed that E. campanulatum formed a sister relationship with the cluster of Epimedium ecalcaratum, Epimedium davidii, and Epimedium chlorandrum. Our findings provided valuable data for future taxonomic and phylogenetic research within the genus Epimedium.
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Affiliation(s)
- Yixin Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Cheng Zhang
- Key Laboratory of Biodiversity Science and Ecological Engineering, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Weihan Qin
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
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144
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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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Amenu SG, Wei N, Wu L, Oyebanji O, Hu G, Zhou Y, Wang Q. Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution. BMC PLANT BIOLOGY 2022; 22:88. [PMID: 35219317 PMCID: PMC8881883 DOI: 10.1186/s12870-022-03480-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/15/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices. RESULTS All plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1, rps16-trnQ-UUG, and psbM-trnD. These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance. CONCLUSIONS Plastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.
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Affiliation(s)
- Sara Getachew Amenu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Lei Wu
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China
| | - Oyetola Oyebanji
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, People's Republic of China
- Department of Botany, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Guangwan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
| | - Yadong Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
| | - Qingfeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
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Cai Y, Gao Y, Zhang Z, Liu H, Wang Y, Ma Y, Li Y, Feng S, Wang H. Development and Application of a Cultivar-Specific Sequence-Characterized Amplified Region (SCAR) Marker for the Detection of Chrysanthemum morifolium Ramat. 'Daboju'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050604. [PMID: 35270074 PMCID: PMC8912837 DOI: 10.3390/plants11050604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 05/13/2023]
Abstract
Chrysanthemummorifolium Ramat. 'Daboju' is a C. morifolium cultivar with important ornamental and medicinal values, and is often used in the treatment of colds, blurred vision, dizziness, and itchy skin. As the morphological characteristics of C. morifolium 'Daboju' are very similar to those of other C. morifolium cultivars, they are often confused in practice. However, the medicinal value and practical use of C. morifolium depends on using the correct rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, morphologically similar C. × morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific DNA marker was developed with the aim of the rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, similar C. morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific 385-bp amplicon (named SCoT36-385), amplified only in C. morifolium 'Daboju' (and in all samples of this cultivar), was identified, cloned, and sequenced. Subsequently, a sequence-characterized amplified region (SCAR) marker (named DBJF/DBJR), generating a 360-bp amplicon, was developed from SCoT36-385 and tested for amplification in all 21 C. morifolium cultivars, ten C. morifolium 'Daboju' populations, and different simulated adulterations of 'Daboju' with other cultivars. The primers amplified the specific 360-bp-long DNA fragment in all the tested C. morifolium 'Daboju' samples but failed in the absence of 'Daboju'. The detection limit of the SCAR primer pair (DBJF/DBJR) was 100 pg of DNA extracted from C. morifolium 'Daboju'. Hence, this SCAR marker has a very high detection sensitivity, and can be used for accurate and rapid identification of C. morifolium 'Daboju'. It can play an important role in ensuring the quality of medicinal preparations and protecting C. morifolium 'Daboju' germplasm resources in breeding programs and in identifying lines generated from this cultivar.
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Affiliation(s)
- Yuchen Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Yadi Gao
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhenhao Zhang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Huijie Liu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yifan Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yuxin Ma
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yixin Li
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Shangguo Feng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
- Correspondence: (S.F.); (H.W.)
| | - Huizhong Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
- Correspondence: (S.F.); (H.W.)
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Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae). BIOMED RESEARCH INTERNATIONAL 2022; 2022:5364094. [PMID: 35252450 PMCID: PMC8893999 DOI: 10.1155/2022/5364094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/11/2022] [Indexed: 01/21/2023]
Abstract
The genus Styrax L. consists of approximately 130 species distributed in the Americas, eastern Asia, and the Mediterranean region. The phylogeny and evolutionary history of this genus are not clear. Knowledge of the phylogenetic relationships and the method for species identification will be critical for the evolution of this genus. In this study, we sequenced the chloroplast genome of 17 Styrax samples and added 17 additional chloroplast genome sequences from GenBank. The data were used to investigate chloroplast genome evolution, infer phylogenetic relationships, and access the species identification rate within Styrax. The Styrax chloroplast genome contains typical quadripartite structures, ranging from 157,641 bp to 159,333 bp. The chloroplast genome contains 114 unique genes. The P distance among the Styrax species ranged from 0.0003 to 0.00611. Seventeen small inversions and SSR sites were discovered in the Styrax chloroplast genome. By comparing with the chloroplast genome sequences, six mutation hotspots were identified, and the markers ycf1b and trnT-trnL were identified as the best Styrax-specific DNA barcodes. The specific barcodes and superbarcode exhibited higher discriminatory power than universal barcodes. Chloroplast phylogenomic results improved the resolution of the phylogenetic relationships of Styrax compared to previous analyses.
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Huang SS, Huang CH, Ko CY, Chen TY, Cheng YC, Chao J. An Ethnobotanical Study of Medicinal Plants in Kinmen. Front Pharmacol 2022; 12:681190. [PMID: 35222004 PMCID: PMC8864234 DOI: 10.3389/fphar.2021.681190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 12/08/2021] [Indexed: 01/04/2023] Open
Abstract
Kinmen is an outlying island that has the richest plant resources in Taiwan. The objective of this study was to record the methods that people in Kinmen use medicinal plants and to analyze the cultural characteristics of their use. Field investigations were carried out in various towns and villages in Kinmen, and 80 respondents were included in the survey. The search for respondents was conducted through local elderly people and medicinal plant groups. Semi-structured interviews were conducted with the local people to obtain their knowledge of medicinal plants and how they disseminate this information. Informed consent was obtained prior to the interviews, and the following was determined: plant use value (UV), frequency of citation (FC), and factor of informant consensus (Fic). These parameters were used to quantify the data and measure the agreement among the respondents on using plants to treat different diseases. Finally, the survey results were compared with the representative ethnobotanical literature in neighboring areas to evaluate the similarity between plant usage in Kinmen and neighboring areas as well as to determine whether there are new species or novel usages in the study area. In the Kinmen area, phytotherapy is generally used by elderly people with low educational attainments. According to the survey results, 83 medicinal plants belonging to 48 families were collected. These medicinal plants were mainly distributed in the Compositae, Lamiaceae, and Solanaceae families. Eighteen novel uses that have not been previously documented were found, four of which were related to newly recorded medicinal plant species in the Kinmen area. The results showed that 93.98 and 65.06% of the species collected in the present study were also recorded in literature from Taiwan and Fujian, respectively. This study showed that Kinmen’s ethnobotanical knowledge is closely related to the Catalogue of Medicinal Plant Resources in Taiwan, and local people indeed shared similar uses of medicinal species with people in Taiwan and Fujian (46.99%). The results from this study highlighted the importance of traditional medicine in the Kinmen area, where people have a specific understanding of using medicinal plants and communication with people in Taiwan and Fujian Province in China. It was found that Kinmen shares ethnobotanical knowledge with Taiwan and Fujian.
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Affiliation(s)
- Shyh-Shyun Huang
- School of Pharmacy, China Medical University, Taichung, Taiwan
- Department of Food Nutrition and Health Biotechnology, Asia University, Ministry of Health and Welfare, Taichung, Taiwan
| | - Chia-Hung Huang
- School of Pharmacy, China Medical University, Taichung, Taiwan
- Department of Pharmacy, Kinmen Hospital, Ministry of Health and Welfare, Kinmen, Taiwan
- Department of Nursing, National Quemoy University, Kinmen, Taiwan
| | - Chien-Yu Ko
- School of Pharmacy, China Medical University, Taichung, Taiwan
| | - Ting-Yang Chen
- School of Pharmacy, China Medical University, Taichung, Taiwan
| | - Yung-Chi Cheng
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Jung Chao
- Chinese Medicine Research Center, Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, Master Program for Food and Drug Safety, China Medical University, Taichung, Taiwan
- *Correspondence: Jung Chao,
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Chen J, Guo Y, Hu X, Zhou K. Comparison of the Chloroplast Genome Sequences of 13 Oil-Tea Camellia Samples and Identification of an Undetermined Oil-Tea Camellia Species From Hainan Province. FRONTIERS IN PLANT SCIENCE 2022; 12:798581. [PMID: 35197990 PMCID: PMC8860168 DOI: 10.3389/fpls.2021.798581] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/17/2021] [Indexed: 06/01/2023]
Abstract
The comparison of chloroplast genome (cpDNA) sequences among different plant species is an important source of plant molecular phylogenetic data. In this paper, the cpDNA sequences of 13 different oil-tea camellia samples were compared to identify an undetermined oil-tea camellia species from Hainan Province. The cpDNA of the samples was sequenced and resequenced, and divergence hotspots and simple sequence repeat (SSR) variations were analyzed. Bayesian inference (BI) and maximum-likelihood (ML) phylogenetic trees were constructed based on the full cpDNA sequences. The cpDNA sequences were 156512∼157089 bp in length and had the circular tetrad structure typical of angiosperms. The inverted repeats (IRs) of different species included varying contractions and expansions. The cpDNA sequences of the samples of the undetermined species of oil-tea camellia from Hainan Province and Camellia gauchowensis from Xuwen County were identical. In total, 136 genes were annotated, including 91 protein-coding genes (PCGs), 37 tRNA genes and 8 rRNA genes. The GC content of the cpDNA was 37.3%. The small single-copy (SSC)/IR boundary was rich in variation. Divergence hotspots were mainly located in the intergenic space (IGS) and coding sequences (CDSs), and there were obvious differences in divergence hotspots among species. The same divergence hotspots were found in Camellia vietnamensis, Camellia gauchowensis and the undetermined species of oil-tea camellia from Hainan Province. A total of 191∼198 SSR loci were detected. Most of the SSRs included A or T, and the distribution of SSRs in the cpDNA was uneven. Different species shared common SSRs and exhibited unique SSRs. Based on the full cpDNA sequences, the evolutionary relationships of different species of Camellia were well identified. The thirteen samples were classified into 2 clades and 6 subclades, and the different sections of Camellia clustered on the same branch in 2 clades and 2 subclades. Camellia vietnamensis was more closely related to the undetermined species of oil-tea camellia from Hainan Province and the sample of Camellia gauchowensis from Xuwen County than to the sample of Camellia gauchowensis from Luchuan County. Camellia osmantha was closely related to Camellia gauchowensis and Camellia vietnamensis. In conclusion, the cpDNA of different oil-tea camellia species has a conserved tetrad structure with certain length polymorphisms. SSRs are expected to be developed as "barcodes" or "identity cards" for species identification. SSR variations and other factors result in abundant divergence hotspots in the CDSs and IGS (one non-CDS region), indicating that full cpDNA sequences can be used for the species identification and phylogenetic analysis of Camellia. Accordingly, the undetermined species of oil-tea camellia from Hainan Province is likely Camellia vietnamensis, Camellia vietnamensis and Camellia gauchowensis may be the same species, and additional genetic evidence is needed to determine whether Camellia osmantha is a new independent species. The previous division of related sections of Camellia may need readjustment based on full cpDNA sequences.
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Affiliation(s)
- Jing Chen
- Engineering Research Center for Breeding of New Varieties of Tropical Crops, Ministry of Education, Haikou, China
- College of Horticulture, Hainan University, Haikou, China
| | - Yujian Guo
- Engineering Research Center for Breeding of New Varieties of Tropical Crops, Ministry of Education, Haikou, China
- College of Horticulture, Hainan University, Haikou, China
| | - Xinwen Hu
- Engineering Research Center for Breeding of New Varieties of Tropical Crops, Ministry of Education, Haikou, China
- College of Horticulture, Hainan University, Haikou, China
| | - Kaibing Zhou
- Engineering Research Center for Breeding of New Varieties of Tropical Crops, Ministry of Education, Haikou, China
- College of Horticulture, Hainan University, Haikou, China
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150
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ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea. DIVERSITY 2022. [DOI: 10.3390/d14020076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.
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