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Liu J, Xu H, Wang Z, Li P, Yan Z, Bai M, Li J. Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini). INSECTS 2024; 15:508. [PMID: 39057241 PMCID: PMC11277550 DOI: 10.3390/insects15070508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024]
Abstract
To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.
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Affiliation(s)
- Jing Liu
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China; (J.L.); (H.X.); (Z.W.)
| | - Huixin Xu
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China; (J.L.); (H.X.); (Z.W.)
| | - Ziqing Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China; (J.L.); (H.X.); (Z.W.)
| | - Panpan Li
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zihan Yan
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050011, China;
| | - Ming Bai
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China; (J.L.); (H.X.); (Z.W.)
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Jing Li
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China; (J.L.); (H.X.); (Z.W.)
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Nath S, VanSlambrouck JT, Yao JW, Gullapalli A, Razi F, Lu Y. DNA barcoding of terrestrial invasive plant species in Southwest Michigan. PLANT DIRECT 2024; 8:e615. [PMID: 38895104 PMCID: PMC11185875 DOI: 10.1002/pld3.615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Because of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA-based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS, rbcL, matK, and trnH-psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR-and-sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared with rbcL and matK, ITS and trnH-psbA have better species discrimination rates (80.6% and 63.2%, respectively). When ITS and trnH-psbA are simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual-barcode approaches (e.g., ITS + trnH-psbA) might be the efficient and cost-effective method in DNA-based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species.
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Affiliation(s)
- Sneha Nath
- Department of Biological SciencesWestern Michigan UniversityKalamazooMichiganUSA
| | | | - Janelle W. Yao
- Kalamazoo Area Math and Science CenterKalamazooMichiganUSA
- Portage Central High SchoolPortageMichiganUSA
| | - Ashika Gullapalli
- Kalamazoo Area Math and Science CenterKalamazooMichiganUSA
- Portage Northern High SchoolPortageMichiganUSA
| | - Fayyaz Razi
- Kalamazoo Area Math and Science CenterKalamazooMichiganUSA
- Portage Central High SchoolPortageMichiganUSA
| | - Yan Lu
- Department of Biological SciencesWestern Michigan UniversityKalamazooMichiganUSA
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Sutula M, Kakanay A, Tussipkan D, Dzhumanov S, Manabayeva S. Phylogenetic Analysis of Rare and Endangered Tulipa Species ( Liliaceae) of Kazakhstan Based on Universal Barcoding Markers. BIOLOGY 2024; 13:365. [PMID: 38927245 PMCID: PMC11200791 DOI: 10.3390/biology13060365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024]
Abstract
In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.
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Affiliation(s)
- Maxim Sutula
- National Center for Biotechnology, Astana 010000, Kazakhstan; (M.S.); (A.K.); (D.T.)
| | - Ayan Kakanay
- National Center for Biotechnology, Astana 010000, Kazakhstan; (M.S.); (A.K.); (D.T.)
| | - Dilnur Tussipkan
- National Center for Biotechnology, Astana 010000, Kazakhstan; (M.S.); (A.K.); (D.T.)
| | | | - Shuga Manabayeva
- National Center for Biotechnology, Astana 010000, Kazakhstan; (M.S.); (A.K.); (D.T.)
- Faculty of Natural Sciences, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
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Wang Y, Zhao X, Chen Q, Yang J, Hu J, Jia D, Ma R. Complete Chloroplast Genome of Alternanthera sessilis and Comparative Analysis with Its Congeneric Invasive Weed Alternanthera philoxeroides. Genes (Basel) 2024; 15:544. [PMID: 38790173 PMCID: PMC11121667 DOI: 10.3390/genes15050544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Alternanthera sessilis is considered the closest relative to the invasive weed Alternanthera philoxeroides in China, making it an important native species for studying the invasive mechanisms and adaptations of A. philoxeroides. Chloroplasts play a crucial role in a plant's environmental adaptation, with their genomes being pivotal in the evolution and adaptation of both invasive and related species. However, the chloroplast genome of A. sessilis has remained unknown until now. In this study, we sequenced and assembled the complete chloroplast genome of A. sessilis using high-throughput sequencing. The A. sessilis chloroplast genome is 151,935 base pairs long, comprising two inverted repeat regions, a large single copy region, and a small single copy region. This chloroplast genome contains 128 genes, including 8 rRNA-coding genes, 37 tRNA-coding genes, 4 pseudogenes, and 83 protein-coding genes. When compared to the chloroplast genome of the invasive weed A. philoxeroides and other Amaranthaceae species, we observed significant variations in the ccsA, ycf1, and ycf2 regions in the A. sessilis chloroplast genome. Moreover, two genes, ccsA and accD, were found to be undergoing rapid evolution due to positive selection pressure. The phylogenetic trees were constructed for the Amaranthaceae family, estimating the time of independent species formation between A. philoxeroides and A. sessilis to be approximately 3.5186-8.8242 million years ago. These findings provide a foundation for understanding the population variation within invasive species among the Alternanthera genus.
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Affiliation(s)
- Yuanxin Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Xueying Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Qianhui Chen
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Jun Yang
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Jun Hu
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Dong Jia
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-Quality and Effciency in Loess Plateau, Taigu 030801, China
| | - Ruiyan Ma
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taiyuan 030031, China
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Lonare N, Patil G, Waghmare S, Bhor R, Hardikar H, Tembe S. DNA Barcoding of Invasive Terrestrial Plant Species in India. Mol Biotechnol 2024:10.1007/s12033-024-01102-z. [PMID: 38430432 DOI: 10.1007/s12033-024-01102-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
Invasive plants are known to cause biodiversity loss and pose a major risk to human health and environment. Identification of invasive plants and distinguishing them from native species has been relied on morphological examination. Stringent requirement of floral characters and decreasing number of expert taxonomists are making conventional morphology-based identification system tedious and resource-intensive. DNA barcoding may help in quick identification of invasive species if distinct sequence divergence pattern at various taxonomic levels is observed. The present work evaluates the utility of four molecular markers; rbcL, matK, their combination (rbcL + matK), and psbA-trnH for identification of 37 invasive plant species from India and also in distinguishing them from 97 native species. A psbA-trnH locus was found to be of restricted utility in this work as it was represented by the members of a single family. A hierarchical increase in K2P mean divergence across different taxonomic levels was found to be the maximum for matK alone followed by rbcL + matK and rbcL alone, respectively. NJ clustering analysis, however, confirmed the suitability of combined locus (rbcL + matK) over individual rbcL and matK as the DNA barcode. RbcL showed the lowest resolution power among the three markers studied. MatK exhibited much better performance compared to rbcL alone in identifying most of the species accurately although it failed to show monophyly of genus Dinebra. Two families; Asteraceae and Poaceae, remained polyphyletic in the trees constructed by all three markers. Combined locus (rbcL + matK) was found to be the most suitable marker as it raised the resolution power of both the markers and could identify more than 90% of genera correctly. Phylogenetic tree constructed by Maximum-Parsimony method using combined locus as a molecular marker exhibited the best resolution, thus, supporting the significance of two-locus combination of rbcL + matK for barcoding invasive plant species from India. Present study contributes to the global barcode data of invasive plant species by adding fifty-one new sequences to it. Effective barcoding of additional number of native as well as invasive plant species from India is possible using this dual locus if it is combined with one or more new molecular plastid markers. Expansion of barcode database with a focus on barcode performance optimisation to improve discrimination ability at species level can be undertaken in future.
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Affiliation(s)
- Nayan Lonare
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Gayatri Patil
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Suprriya Waghmare
- IMT Technologies Pvt. Ltd, Kondhwa Khurd, Pune, Maharashtra, 411048, India
| | - Reshma Bhor
- IMT Technologies Pvt. Ltd, Kondhwa Khurd, Pune, Maharashtra, 411048, India
| | - Hrishikesh Hardikar
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Sanket Tembe
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India.
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Whitley BS, Li Z, Jones L, de Vere N. Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants. Methods Mol Biol 2024; 2744:445-473. [PMID: 38683335 DOI: 10.1007/978-1-0716-3581-0_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Plant DNA barcoding has a multitude of applications ranging from species detection and biomonitoring to investigating ecological networks and checking food quality. The ability to accurately identify species, using DNA barcoding, depends on the quality and comprehensiveness of the reference library that is used. This chapter describes how to create plant reference libraries using the rbcL, matK, and ITS2 DNA barcode regions. It covers the creation of species lists, the collection of specimens from the field and herbarium, DNA extraction, PCR amplification, and DNA sequencing. This methodology gives special attention to using samples from herbaria, as they represent important collections of easily accessible, taxonomically verified plant material.
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Affiliation(s)
- Brandon S Whitley
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Zhao Li
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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Fu QL, Mo ZQ, Xiang XG, Milne RI, Jacquemyn H, Burgess KS, Sun YN, Yan H, Qiu L, Yang BY, Tan SL. Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae). BMC PLANT BIOLOGY 2023; 23:645. [PMID: 38097946 PMCID: PMC10722739 DOI: 10.1186/s12870-023-04663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND The genus Triplostegia contains two recognized species, T. glandulifera and T. grandiflora, but its phylogenetic position and species delimitation remain controversial. In this study, we assembled plastid genomes and nuclear ribosomal DNA (nrDNA) cistrons sampled from 22 wild Triplostegia individuals, each from a separate population, and examined these with 11 recently published Triplostegia plastomes. Morphological traits were measured from herbarium specimens and wild material, and ecological niche models were constructed. RESULTS Triplostegia is a monophyletic genus within the subfamily Dipsacoideae comprising three monophyletic species, T. glandulifera, T. grandiflora, and an unrecognized species Triplostegia sp. A, which occupies much higher altitude than the other two. The new species had previously been misidentified as T. glandulifera, but differs in taproot, leaf, and other characters. Triplotegia is an old genus, with stem age 39.96 Ma, and within it T. glandulifera diverged 7.94 Ma. Triplostegia grandiflora and sp. A diverged 1.05 Ma, perhaps in response to Quaternary climate fluctuations. Niche overlap between Triplostegia species was positively correlated with their phylogenetic relatedness. CONCLUSIONS Our results provide new insights into the species delimitation of Triplostegia, and indicate that a taxonomic revision of Triplostegia is needed. We also identified that either rpoB-trnC or ycf1 could serve as a DNA barcode for Triplostegia.
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Affiliation(s)
- Qing-Li Fu
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Hans Jacquemyn
- KU Leuven, Department of Biology, Plant Conservation and Population Biology, B-3001, Leuven, Belgium
| | - Kevin S Burgess
- College of Letters and Sciences, Columbus State University, University System of Georgia, Columbus, GA, 31907-5645, USA
| | - Ya-Nan Sun
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Hua Yan
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Li Qiu
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Bo-Yun Yang
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Shao-Lin Tan
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China.
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Liu DK, Zhou CY, Tu XD, Zhao Z, Chen JL, Gao XY, Xu SW, Zeng MY, Ma L, Ahmad S, Li MH, Lan S, Liu ZJ. Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes. BMC Genomics 2023; 24:749. [PMID: 38057701 DOI: 10.1186/s12864-023-09847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation. RESULTS We are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233 bp to 145,463 bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnNGUU-rpl32 > rpoB-trnCGCA > psbK-psbI > psaC-rps15 > trnEUUC-trnTGGU > accD-psaI) and five coding sequences (ycf1 > rps15 > matK > psbK > ccsA) were selected as potential barcodes based on nucleotide diversity and species discrimination analysis, which suggested that the potential barcode ycf1 was most suitable for species discrimination. A total of 47-56 SSRs and 11-14 long repeats (> 20 bp) were identified in Chiloschista plastomes, and they were mostly located in the large single copy intergenic region. Phylogenetic analysis indicated that Chiloschista was monophyletic. It was clustered with Phalaenopsis and formed the basic clade of the subtribe Aeridinae with a moderate support value. The results also showed that seven Chiloschista species were divided into three major clades with full support. CONCLUSION This study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.
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Affiliation(s)
- Ding-Kun Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cheng-Yuan Zhou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiong-De Tu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhuang Zhao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jin-Liao Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu-Yong Gao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shao-Wei Xu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng-Yao Zeng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liang Ma
- Fujian Health College, Fuzhou, 350101, Fujian, China
| | - Sagheer Ahmad
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ming-He Li
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wang G, Bai X, Ren Y, Su Y, Han J. Development of nucleotide signatures for common poisonous organisms provides a new strategy for food poisoning diagnosis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 265:115529. [PMID: 37776823 DOI: 10.1016/j.ecoenv.2023.115529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
DNA barcoding is widely used in toxic species authentication, but due to serious DNA degradation of forensic materials, the application of full-length barcode sequences in food poisoning diagnosis is greatly limited. Nucleotide signature, a shorter specific molecular marker, derived from traditional DNA barcoding has been proposed as an emerging tool of toxic species detection in deeply processed materials. In this study, to resolve the frequent food poisoning accidents with unknown origin, we envisioned developing a nucleotide signature data set of common poisonous organisms and combining high-throughput sequencing (HTS) to reveal the poisoning cause. Ninety-three individuals and 1093 DNA barcode sequences of twelve common poisonous plants, fish, mushrooms and their related species were collected. Through sequence alignment and screening, the nucleotide signatures were respectively developed and validated as their specific molecular markers. The sequence length varied from 19 bp to 38 bp. These fragments were conserved within the same species or genera, and the specificity between related species has been also demonstrated. To further evaluate the application potential of nucleotide signature in forensic diagnosis, simulated forensic specimens (SFS) containing different poisonous ingredients were sequenced by HTS with PCR-free libraries. As a result, the nucleotide signature was successfully captured from original HTS data without assembly and annotation, accompanied by a high detection sensitivity of 0.1 ng/µl in mixture system. Therefore, this method was suitable for the assay of forensic materials with serious DNA degradation. The present study undoubtedly provides a new perspective and strong support for the detection of toxic ingredients and the diagnosis of food poisoning.
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Affiliation(s)
- Gang Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xuanjiao Bai
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Ying Ren
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yuying Su
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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10
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Banerjee P, Stewart KA, Dey G, Antognazza CM, Sharma RK, Maity JP, Saha S, Doi H, de Vere N, Chan MWY, Lin PY, Chao HC, Chen CY. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AOB PLANTS 2022; 14:plac031. [PMID: 35990516 PMCID: PMC9389569 DOI: 10.1093/aobpla/plac031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Kathryn A Stewart
- Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gobinda Dey
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Caterina M Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Santanu Saha
- Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K
| | - Michael W Y Chan
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pin-Yun Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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11
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Matiz-Ceron L, Reyes A, Anzola J. Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier. FRONTIERS IN PLANT SCIENCE 2022; 12:782663. [PMID: 35185949 PMCID: PMC8850773 DOI: 10.3389/fpls.2021.782663] [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: 09/24/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.
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Affiliation(s)
- Luisa Matiz-Ceron
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Juan Anzola
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
- Department of Engineering and Natural Sciences, Universidad Central, Bogotá, Colombia
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12
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Abstract
Growing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2, matK, rbcL, trnH-psbA and their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matK exhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.
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13
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Mao X, Xie W, Li X, Shi S, Guo Z. Establishing community-wide DNA barcode references for conserving mangrove forests in China. BMC PLANT BIOLOGY 2021; 21:571. [PMID: 34863107 PMCID: PMC8642986 DOI: 10.1186/s12870-021-03349-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. DNA barcoding technology may help protect mangrove ecosystems by providing rapid species identification. RESULTS To investigate this potential, 898 plant specimens were collected from 33 major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity, and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. CONCLUSION We suggest using ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.
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Affiliation(s)
- Xiaomeng Mao
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wei Xie
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xinnian Li
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
- Forevergen Biosciences Center, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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14
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Hu JL, Ci XQ, Liu ZF, Dormontt EE, Conran JG, Lowe AJ, Li J. Assessing candidate DNA barcodes for Chinese and internationally traded timber species. Mol Ecol Resour 2021; 22:1478-1492. [PMID: 34752673 DOI: 10.1111/1755-0998.13546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/22/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.
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Affiliation(s)
- Jian-Lin Hu
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Zhi-Fang Liu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Eleanor E Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - John G Conran
- Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and Sprigg Geobiology Centre (SGC), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew J Lowe
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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15
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Yang B, Zhang Z, Yang C, Wang Y, Orr MC, Hongbin W, Zhang AB. Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks. Syst Biol 2021; 71:690-705. [PMID: 34524452 DOI: 10.1093/sysbio/syab076] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 09/08/2021] [Indexed: 11/14/2022] Open
Abstract
Integrative taxonomy is central to modern taxonomy and systematic biology, including behaviour, niche preference, distribution, morphological analysis and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network (MMNet)) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently-available alternative methods when tested with 10 independent datasets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species) and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy (>98%) in four datasets including closely related species from the same genus. The average accuracy of two modest sub-genomic (single nucleotide polymorphism) datasets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image versus gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multi-modal information for integrative taxonomy, such as image, audio, video, 3D scanning and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring and conservation of biodiversity.
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Affiliation(s)
- Bing Yang
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
| | - Zhenxin Zhang
- The Key Laboratory of 3D Information Acquisition and Application, MOE, Capital Normal University, Beijing 100048, People's Republic of China.,Beijing Laboratory of Water Resources Security, Capital Normal University, Beijing 100048, People's Republic of China.,Base of the State Key Laboratory of Urban Environmental Process and Digital, Capital Normal University, Beijing 100048, People's Republic of China
| | - Caiqing Yang
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
| | - Ying Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
| | - Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Wang Hongbin
- Museum of Forest Biodiversity, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, People's Republic of China
| | - Ai-Bing Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
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16
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Liu Y, Xu C, Sun Y, Chen X, Dong W, Yang X, Zhou S. Method for quick DNA barcode reference library construction. Ecol Evol 2021; 11:11627-11638. [PMID: 34522329 PMCID: PMC8427591 DOI: 10.1002/ece3.7788] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
DNA barcoding has become one of the most important techniques in plant species identification. Successful application of this technology is dependent on the availability of reference database of high species coverage. Unfortunately, there are experimental and data processing challenges to construct such a library within a short time. Here, we present our solutions to these challenges. We sequenced six conventional DNA barcode fragments (ITS1, ITS2, matK1, matK2, rbcL1, and rbcL2) of 380 flowering plants on next-generation sequencing (NGS) platforms (Illumina Hiseq 2500 and Ion Torrent S5) and the Sanger sequencing platform. After comparing the sequencing depths, read lengths, base qualities, and base accuracies, we conclude that Illumina Hiseq2500 PE250 run is suitable for conventional DNA barcoding. We developed a new "Cotu" method to create consensus sequences from NGS reads for longer output sequences and more reliable bases than the other three methods. Step-by-step instructions to our method are provided. By using high-throughput machines (PCR and NGS), labeling PCR, and the Cotu method, it is possible to significantly reduce the cost and labor investments for DNA barcoding. A regional or even global DNA barcoding reference library with high species coverage is likely to be constructed in a few years.
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Affiliation(s)
- Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Yuzhe Sun
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Xun Chen
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- College of Landscape ArchitectureNortheast Forestry UniversityHarbinChina
| | - Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- Laboratory of Systematic Evolution and Biogeography of Woody PlantsSchool of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Xueying Yang
- National Engineering Laboratory for Forensic ScienceKey Laboratory of Forensic GeneticsInstitute of Forensic ScienceMinistry of Public SecurityBeijingChina
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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17
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Sooriyapathirana SDSS, Ranaweera LT, Jayarathne HSM, Gayathree THI, Rathnayake PGRG, Karunarathne SI, Thilakarathne SMNK, Salih R, Weebadde CK, Weebadde CP. Photosynthetic Phenomics of Field- and Greenhouse-Grown Amaranths vs. Sensory and Species Delimits. PLANT PHENOMICS (WASHINGTON, D.C.) 2021; 2021:2539380. [PMID: 33615238 PMCID: PMC7888303 DOI: 10.34133/2021/2539380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/24/2020] [Indexed: 12/01/2022]
Abstract
Consumers hesitate to purchase field-grown shoot-tops of amaranths in Sri Lanka, citing the low-cleanliness making growers focus on greenhouse farming. However, the photosynthetic and growth variations in relation to the organoleptic preference of the greenhouse-grown amaranths in comparison to field-grown counterparts have not been studied. Also, the species delimits of the amaranths in Sri Lanka have not been identified, limiting our ability to interpret species-specific production characteristics. Thus, we assessed the common types of amaranths under greenhouse and field conditions. The photosynthesis was measured using a MultispeQ device of the PhotosynQ phenomic platform, which records chlorophyll fluorescence-based parameters. The shoot-tops were harvested and prepared as dishes according to the typical recipe for amaranths in Sri Lanka. The dishes were subjected to an organoleptic assessment for the parameters color, aroma, bitterness, texture, and overall taste. The differences in plant and the shoot-top biomass were also assessed. The markers atpB-rbcL, matk-trnT, and ITS were used to define the species delimits. The field-grown and greenhouse-grown amaranths exhibited species/cultivar-specific photosynthetic variations. The texture and overall taste of the dishes were different among greenhouse and field-grown material. The tasters preferred the texture and the overall taste of the greenhouse-grown shoot-tops. The greenhouse-grown plants also yielded higher shoot-top harvests compared to field-grown counterparts. Out of the tested markers, ITS defines the delimits of amaranth species. The higher organoleptic preference, the appreciable yield levels, unique photosynthetic patterns of the greenhouse-grown amaranths, and species definitions provide the much-needed platform for clean shoot-top production guaranteeing the highest end-user trust.
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Affiliation(s)
- S. D. S. S. Sooriyapathirana
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka
- PhotosynQ Inc., 325 E Grand River Avenue, Suite 331, East Lansing, MI 48823, USA
| | - L. T. Ranaweera
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka
| | - H. S. M. Jayarathne
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka
| | - T. H. I. Gayathree
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka
| | - P. G. R. G. Rathnayake
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka
| | - S. I. Karunarathne
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka
| | - S. M. N. K. Thilakarathne
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka
| | - R. Salih
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400 Peradeniya, Sri Lanka
| | - C. K. Weebadde
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing 48824, USA
| | - C. P. Weebadde
- PhotosynQ Inc., 325 E Grand River Avenue, Suite 331, East Lansing, MI 48823, USA
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18
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Le DT, Zhang YQ, Xu Y, Guo LX, Ruan ZP, Burgess KS, Ge XJ. The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens. PLoS One 2020; 15:e0235569. [PMID: 32735584 PMCID: PMC7394517 DOI: 10.1371/journal.pone.0235569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/17/2020] [Indexed: 12/29/2022] Open
Abstract
The palm family (Arecaceae) is of high ecological and economic value, yet identification in the family remains a challenge for both taxonomists and horticulturalists. The family consists of approximately 2600 species across 181 genera and DNA barcoding may be a useful tool for species identification within the group. However, there have been few systematic evaluations of DNA barcodes for the palm family. In the present study, five DNA barcodes (rbcL, matK, trnH-psbA, ITS, ITS2) were evaluated for species identification ability across 669 samples representing 314 species and 100 genera in the Arecaceae, employing four analytical methods. The ITS gene region was found to not be a suitable barcode for the palm family, due in part, to low recovery rates and paralogous gene copies. Among the four analyses used, species resolution for ITS2 was much higher than that achieved with the plastid barcodes alone (rbcL, matK, trnH-psbA), and the barcode combination ITS2 + matK + rbcL gave the highest resolution among all single barcodes and their combinations, followed by ITS2 + matK. Among 669 palm samples analyzed, 110 samples (16.3%) were found to be misidentified. The 2992 DNA barcode sequences generated in this study greatly enriches the existing identification toolbox available to plant taxonomists that are interested in researching genetic relationships among palm taxa as well as for horticulturalists that need to confirm palm collections for botanical garden curation and horticultural applications. Our results indicate that the use of the ITS2 DNA barcode gene region provides a useful and cost-effective tool to confirm the identity of taxa in the Palm family.
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Affiliation(s)
- Duc-Thanh Le
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Li-Xiu Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Kevin S. Burgess
- Department of Biology, Columbus State University, University System of Georgia, Columbus, Georgia, United States of America
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Alsos IG, Lavergne S, Merkel MKF, Boleda M, Lammers Y, Alberti A, Pouchon C, Denoeud F, Pitelkova I, Pușcaș M, Roquet C, Hurdu BI, Thuiller W, Zimmermann NE, Hollingsworth PM, Coissac E. The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material. PLANTS (BASEL, SWITZERLAND) 2020; 9:E432. [PMID: 32244605 PMCID: PMC7238428 DOI: 10.3390/plants9040432] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Sebastien Lavergne
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | - Marti Boleda
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - Youri Lammers
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Charles Pouchon
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Iva Pitelkova
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Mihai Pușcaș
- A. Borza Botanical Garden and Faculty of Biology and Geology, Babeș-Bolyai University, 400015 Cluj-Napoca, Romania;
| | - Cristina Roquet
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, ES-08193 Bellaterra, Spain
| | - Bogdan-Iuliu Hurdu
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015 Cluj-Napoca, Romania;
| | - Wilfried Thuiller
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | | | - Eric Coissac
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
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Li Q, Deng J, Chen C, Zeng L, Lin X, Cheng Z, Qiao G, Huang X. DNA Barcoding Subtropical Aphids and Implications for Population Differentiation. INSECTS 2019; 11:E11. [PMID: 31877643 PMCID: PMC7022676 DOI: 10.3390/insects11010011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 11/16/2022]
Abstract
DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, representing 75 genera, and 13 subfamilies, to build the first comprehensive DNA barcode library for subtropical aphids. We examined the utility of DNA barcodes in identifying aphid species and population differentiation and evaluated the ability of different species delimitation methods (automatic barcode gap discovery (ABGD), generalized mixed Yule-coalescent (GMYC), and Bayesian Poisson tree processes (bPTP)). We found that most aphid species demonstrated barcode gaps and that a threshold value of 2% genetic distance is suitable for distinguishing most species. Our results indicated that ten morphospecies may have species divergence related to factors such as host plant or geography. By using two pest species Aphis spiraecola and A. gossypii as examples, we also discussed the effect of the sampling scale of host plants on the results and reliability of DNA barcoding of phytophagous insects. This DNA barcode library will be valuable for future studies and applications.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Jun Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Cui Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Linda Zeng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Xiaolan Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Zhentao Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
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Mosa KA, Gairola S, Jamdade R, El-Keblawy A, Al Shaer KI, Al Harthi EK, Shabana HA, Mahmoud T. The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora. FRONTIERS IN PLANT SCIENCE 2019; 9:1929. [PMID: 30719028 PMCID: PMC6348273 DOI: 10.3389/fpls.2018.01929] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.
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Affiliation(s)
- Kareem A. Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Sanjay Gairola
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, Sharjah, United Arab Emirates
| | - Rahul Jamdade
- Plant Biotechnology Laboratory, Sharjah Research Academy, Sharjah, United Arab Emirates
| | - Ali El-Keblawy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Eman Khalid Al Harthi
- Plant Biotechnology Laboratory, Sharjah Research Academy, Sharjah, United Arab Emirates
| | - Hatem A. Shabana
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, Sharjah, United Arab Emirates
| | - Tamer Mahmoud
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, Sharjah, United Arab Emirates
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Liu L, Guo Z, Zhong C, Shi S. DNA barcoding reveals insect diversity in the mangrove ecosystems of Hainan Island, China. Genome 2018; 61:797-806. [PMID: 30398899 DOI: 10.1139/gen-2018-0062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Insect diversity is an indicator of environmental conditions. Frequent outbreaks of mangrove pests have threatened the fragile mangrove ecosystem in China and the sustainable utilization of mangrove resources. The understanding of mangrove pests, as well as a fundamental knowledge of insect diversity, in mangrove forests in China has been hindered by the difficulty of morphological species delimitation because captured insect specimens are either larvae or incompletely preserved adults. DNA barcoding technology uses only a small amount of DNA to conduct species identification. Taking advantage of this, we investigated the entomofauna of mangrove forests on Hainan Island by using a barcode combining cytochrome c oxidase subunit I (COI) and cytochrome-b (Cytb). We collected 627 specimens at six localities around the island, which were identified as 219 insect species belonging to 11 orders and 72 families. Lepidoptera, Coleoptera, and Hymenoptera are the most species-rich and abundant taxa. We also identified 13 mangrove pests, 5 parasitoids, and 12 species of predators.
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Affiliation(s)
- Lu Liu
- a State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zixiao Guo
- a State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Cairong Zhong
- b Hainan Dongzhai Harbor National Nature Reserve, Haikou, Hainan, China
| | - Suhua Shi
- a State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Dormontt EE, van Dijk KJ, Bell KL, Biffin E, Breed MF, Byrne M, Caddy-Retalic S, Encinas-Viso F, Nevill PG, Shapcott A, Young JM, Waycott M, Lowe AJ. Advancing DNA Barcoding and Metabarcoding Applications for Plants Requires Systematic Analysis of Herbarium Collections—An Australian Perspective. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00134] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Campanaro A, Tommasi N, Guzzetti L, Galimberti A, Bruni I, Labra M. DNA barcoding to promote social awareness and identity of neglected, underutilized plant species having valuable nutritional properties. Food Res Int 2018; 115:1-9. [PMID: 30599919 DOI: 10.1016/j.foodres.2018.07.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/18/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022]
Abstract
It is estimated that about 7000 plant species and a large number of cultivars and varieties have been cultivated for consumption in human history. However, <0.5% of these currently provide the majority of human food energy needs worldwide (e.g., rice, wheat, maize, and potato). Global issues such as climate change, diffusion of pests, and resistance to agrochemical treatments are posing great concern about the sustainable cultivation of these major staples, especially in equatorial and tropical countries, such as Sub Saharan Africa. In addition, most of these regions contain malnutrition and micronutrient deficiencies, and the sum of such problems create serious implications at social, political, and economic levels. A possible solution relies on the exploitation of plant biodiversity and particularly on the so-called NUS (Neglected and Underutilized Species). These plants are traditionally grown in their centres of origin and continue to be maintained by sociocultural preferences, however they remain inadequately documented and neglected by formal research and conservation programs. Although they are important in terms of micronutrients and the ability to grow in harsh conditions, these species are falling into disuse due to agronomic, genetic, economic, and cultural reasons. To promote and spread their cultivation at the global scale, along with knowledge on their suitability for human nutrition, reliable identification systems are necessary to guarantee adequate authenticity along the entire supply chain and distribution network. A precise identification of the different species and their varieties is fundamental both to retrieve information on their origin and authenticate the raw materials (i.e., seeds, leaves and fruit) and related processed products that can be distributed at the local or global scale. DNA-based techniques can help achieve this mission. In particular, the DNA barcoding approach has gained a role of primary importance due to its universality and versatility. Here, we discuss the advantages in using DNA barcoding for the identification of some of the most representative NUS species, as well as their traceability and conservation of cultural practices around them.
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Affiliation(s)
- Ausilia Campanaro
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Nicola Tommasi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Lorenzo Guzzetti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Andrea Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Ilaria Bruni
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy.
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Gong L, Qiu XH, Huang J, Xu W, Bai JQ, Zhang J, Su H, Xu CM, Huang ZH. Constructing a DNA barcode reference library for southern herbs in China: A resource for authentication of southern Chinese medicine. PLoS One 2018; 13:e0201240. [PMID: 30044868 PMCID: PMC6059470 DOI: 10.1371/journal.pone.0201240] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022] Open
Abstract
Southern Chinese Medicine (SCM) is an important sect of Traditional Chinese Medicine (TCM) with its own special cultural style. Species identification is essential for TCM quality control because authentic herbs are possibly substituted with adulterants that would threaten the health of the public or even cause death. Here, we provided the first local reference DNA barcode library based on the second internal transcribed spacer (ITS2) for the molecular identification of SCM. A total of 1512 specimens of southern herbs representing 359 species were collected under the instructions and identification of taxonomic experts. Genomic DNA was extracted, and the PCR reaction proceeded according to standard procedures. After Sanger sequencing, sequence assembling and annotation, a reliable ITS2 barcode library with 1276 sequences from 309 species of Southern herbs was constructed. The PCR efficiency of the whole samples was 84.39%. Characteristics of the ITS2 barcode were analyzed, including sequence lengths and GC contents in different taxa. Neighbor-joining trees based on Kimura 2-Parameter (K2P) genetic distances showed a 67.56% successful rate of species identification with ITS2 barcode. In addition, 96.57% of species could be successfully identified at the genus level by the BLAST method. Eleven plant species were discovered to be cryptic. In addition, we found that there is an incorrect sequence existing in the public database, making a reliable local DNA barcode reference more meaningful. ITS2 barcodes exhibit advantages in TCM identification. This DNA barcode reference library could be used in Southern Chinese Medicine quality control, thus contributing to protecting public health.
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Affiliation(s)
- Lu Gong
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Xiao Hui Qiu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Juan Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Wen Xu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Jun Qi Bai
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Jing Zhang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - He Su
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Chu Mei Xu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Zhi Hai Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
- * E-mail:
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