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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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2
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Bell KL, Turo KJ, Lowe A, Nota K, Keller A, Encinas‐Viso F, Parducci L, Richardson RT, Leggett RM, Brosi BJ, Burgess KS, Suyama Y, de Vere N. Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding. Mol Ecol 2023; 32:6345-6362. [PMID: 36086900 PMCID: PMC10947134 DOI: 10.1111/mec.16689] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.
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Affiliation(s)
- Karen L. Bell
- CSIRO Health & Biosecurity and CSIRO Land & WaterFloreatWAAustralia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Katherine J. Turo
- Department of Ecology, Evolution, and Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
| | | | - Kevin Nota
- Department of Ecology and GeneticsEvolutionary Biology Centre, Uppsala UniversityUppsalaSweden
| | - Alexander Keller
- Organismic and Cellular Networks, Faculty of BiologyBiocenter, Ludwig‐Maximilians‐Universität MünchenPlaneggGermany
| | - Francisco Encinas‐Viso
- Centre for Australian National Biodiversity ResearchCSIROBlack MountainAustralian Capital TerritoryAustralia
| | - Laura Parducci
- Department of Ecology and GeneticsEvolutionary Biology Centre, Uppsala UniversityUppsalaSweden
- Department of Environmental BiologySapienza University of RomeRomeItaly
| | - Rodney T. Richardson
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMarylandUSA
| | | | - Berry J. Brosi
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Kevin S. Burgess
- Department of BiologyCollege of Letters and Sciences, Columbus State University, University System of GeorgiaAtlantaGeorgiaUSA
| | - Yoshihisa Suyama
- Field Science CenterGraduate School of Agricultural Science, Tohoku UniversityOsakiMiyagiJapan
| | - Natasha de Vere
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R, Lawniczak MKN. Future of DNA-based insect monitoring. Trends Genet 2023:S0168-9525(23)00038-0. [PMID: 36907721 DOI: 10.1016/j.tig.2023.02.012] [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: 10/11/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).
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Affiliation(s)
- Physilia Y S Chua
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Adenauerallee 127, 53113 Bonn, Germany
| | - Cameron Ferguson
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Petra Korlevic
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leia Zhao
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Han W, Tang H, Wei L, Zhang E. The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases. Ecol Evol 2023; 13:e9849. [PMID: 36861023 PMCID: PMC9969238 DOI: 10.1002/ece3.9849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.
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Affiliation(s)
- Wu Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Hongqu Tang
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Lili Wei
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Enlou Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
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DNA Barcoding of Marine Mollusks Associated with Corallina officinalis Turfs in Southern Istria (Adriatic Sea). DIVERSITY 2021. [DOI: 10.3390/d13050196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Presence of mollusk assemblages was studied within red coralligenous algae Corallina officinalis L. along the southern Istrian coast. C. officinalis turfs can be considered a biodiversity reservoir, as they shelter numerous invertebrate species. The aim of this study was to identify mollusk species within these settlements using DNA barcoding as a method for detailed identification of mollusks. Nine locations and 18 localities with algal coverage range above 90% were chosen at four research areas. From 54 collected samples of C. officinalis turfs, a total of 46 mollusk species were identified. Molecular methods helped identify 16 gastropod, 14 bivalve and one polyplacophoran species. COI sequences for two bivalve species (Musculus cf. costulatus (Risso, 1826) and Gregariella semigranata (Reeve, 1858)) and seven gastropod species (Megastomia winfriedi Peñas & Rolán, 1999, Eatonina sp. Thiele, 1912, Eatonina cossurae (Calcara, 1841), Crisilla cf. maculata (Monterosato, 1869), Alvania cf. carinata (da Costa, 1778), Vitreolina antiflexa (Monterosato, 1884) and Odostomia plicata (Montagu, 1803)) represent new BINs in BOLD database. This study contributes to new findings related to the high biodiversity of mollusks associated with widespread C. officinalis settlements along the southern coastal area of Istria.
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Kolter A, Gemeinholzer B. Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases. Genome 2020; 64:265-298. [PMID: 32649839 DOI: 10.1139/gen-2019-0198] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The problem of low species-level identification rates in plants by DNA barcoding is exacerbated by the fact that reference databases are far from being comprehensive. We investigate the impact of increased sampling depth on identification success by analyzing the efficacy of established plant barcode marker sequences (rbcL, matK, trnL-trnF, psbA-trnH, ITS). Adding sequences of the same species to the reference database led to an increase in correct species assignment of +10.9% for rbcL and +19.0% for ITS. Simultaneously, erroneous identification dropped from ∼40% to ∼12.5%. Despite its evolutionary constraints, ITS showed the highest identification rate and identification gain by increased sampling effort, which makes it a very suitable marker in the planning phase of a barcode study. The limited sequence availability of trnL-trnF is problematic for an otherwise very promising plastid plant barcoding marker. Future developments in machine learning algorithms have the potential to give new impetus to plant barcoding, but are dependent on extensive reference databases. We expect that our results will be incorporated into future plans for the development of DNA barcoding reference databases and will lead to these being developed with greater depth and taxonomic coverage.
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Affiliation(s)
- Andreas Kolter
- Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany.,Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany
| | - Birgit Gemeinholzer
- Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany.,Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany
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Hao M, Jin Q, Meng G, Yang C, Yang S, Shi Z, Tang M, Liu S, Li Y, Zhang D, Su X, Shih C, Sun Y, Zhou X, Zhang AB. Regional assemblages shaped by historical and contemporary factors: Evidence from a species-rich insect group. Mol Ecol 2020; 29:2492-2510. [PMID: 32163643 DOI: 10.1111/mec.15412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/04/2020] [Accepted: 03/03/2020] [Indexed: 11/30/2022]
Abstract
Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7,788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multiscale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.
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Affiliation(s)
- Mengdi Hao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Qian Jin
- College of Life Sciences, Capital Normal University, Beijing, China.,Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, China
| | - Guanliang Meng
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Caiqing Yang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shenzhou Yang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Zhiyong Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Min Tang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yinan Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Dan Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xu Su
- Guizhou Provincial Center for Disease Control and Prevention, Guizhou, China
| | - Chungkun Shih
- College of Life Sciences, Capital Normal University, Beijing, China.,Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Yiran Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ai-Bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
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