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Kang JS, Giang VNL, Park HS, Park YS, Cho W, Nguyen VB, Shim H, Waminal NE, Park JY, Kim HH, Yang TJ. Evolution of the Araliaceae family involved rapid diversification of the Asian Palmate group and Hydrocotyle specific mutational pressure. Sci Rep 2023; 13:22325. [PMID: 38102332 PMCID: PMC10724125 DOI: 10.1038/s41598-023-49830-7] [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: 04/04/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
The Araliaceae contain many valuable species in medicinal and industrial aspects. We performed intensive phylogenomics using the plastid genome (plastome) and 45S nuclear ribosomal DNA sequences. A total of 66 plastome sequences were used, 13 of which were newly assembled in this study, 12 from new sequences, and one from existing data. While Araliaceae plastomes showed conserved genome structure, phylogenetic reconstructions based on four different plastome datasets revealed phylogenetic discordance within the Asian Palmate group. The divergence time estimation revealed that splits in two Araliaceae subfamilies and the clades exhibiting phylogenetic discordances in the Asian Palmate group occurred at two climatic optima, suggesting that global warming events triggered species divergence, particularly the rapid diversification of the Asian Palmate group during the Middle Miocene. Nucleotide substitution analyses indicated that the Hydrocotyloideae plastomes have undergone accelerated AT-biased mutations (C-to-T transitions) compared with the Aralioideae plastomes, and the acceleration may occur in their mitochondrial and nuclear genomes as well. This implies that members of the genus Hydrocotyle, the only aquatic plants in the Araliaceae, have experienced a distinct evolutionary history from the other species. We also discussed the intercontinental disjunction in the genus Panax and proposed a hypothesis to complement the previously proposed hypothesis. Our results provide the evolutionary trajectory of Araliaceae and advance our current understanding of the evolution of Araliaceae species.
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Affiliation(s)
- Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Vo Ngoc Linh Giang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, South Korea
| | - Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Woohyeon Cho
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Van Binh Nguyen
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Biology, Dalat University, Dalat, 670000, Vietnam
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Nomar Espinosa Waminal
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Gatersleben, Germany
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea.
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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2
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Yan R, Gu L, Qu L, Wang X, Hu G. New Insights into Phylogenetic Relationship of Hydrocotyle (Araliaceae) Based on Plastid Genomes. Int J Mol Sci 2023; 24:16629. [PMID: 38068952 PMCID: PMC10706649 DOI: 10.3390/ijms242316629] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of Hydrocotyle need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of Hydrocotyle and performed comparative plastid genomic analyses with four previously published Hydrocotyle plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of Hydrocotyle exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958-84,792 bp), a small single-copy (SSC) region (18,585-18,768 bp), and a pair of inverted repeats (IRs) (25,058-25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of Hydrocotyle plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, and ndhF-rpl32) and two coding genes (rpl16 and ycf1). Three protein-coding genes (atpE, rpl16, and ycf2) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of Hydrocotyle from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of Hydrocotyle. The diagnostic characteristics currently used in Hydrocotyle may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.
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Affiliation(s)
- Rongrong Yan
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Li Gu
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Lu Qu
- Institute of Medicinal Plant Development Yunnan Branch, Chinese Academy of Medical Sciences, Jinghong 666100, China;
| | - Xiaoyu Wang
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Guoxiong Hu
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
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3
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Chen Z, Liu Q, Xiao Y, Zhou G, Yu P, Bai J, Huang H, Gong Y. Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships. J Appl Genet 2023; 64:419-429. [PMID: 37380816 DOI: 10.1007/s13353-023-00767-7] [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: 03/28/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and evolutionary studies. In this study, we utilized Illumina NovaSeq 6000 to sequence the DNA of Camellia sinensis L. cultivar 'Zhuyeqi', followed by the assembly of its chloroplast genome using SPAdes v3.10.1, with subsequent analysis of its features and phylogenetic placement. The results showed that the cp genome of 'Zhuyeqi' was 157,072 bp, with a large single-copy region (LSC, 86,628 bp), a small single-copy region (SSC,18,282 bp), and two inverted repeat regions (IR, 26,081 bp). The total AT and GC contents of the cp genome of 'Zhuyeqi' were observed to be 62.21% and 37.29%, respectively. The cp genome encoded 135 unique genes, including 90 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. Moreover, 31 codons and 247 simple sequence repeats (SSRs) were identified. The cp genomes of 'Zhuyeqi' were found to be relatively conserved, with conservation observed in the IR region, which showed no evidence of inversions or rearrangements. The five regions with the largest variations were identified, with four regions (rps12, rps19, rps16, and rpl33) located in the LSC region and one divergent region (trnI-GAU) in the IR region. Phylogenetic analysis revealed that Camellia sinensis (KJ996106.1) was closely related to 'Zhuyeqi', indicating a close phylogenetic relationship between these two species. These findings could provide important genetic information for further research into breeding of tea tree, phylogeny, and evolution of Camellia sinensis.
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Affiliation(s)
- Zhiyin Chen
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Qing Liu
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Ying Xiao
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Guihua Zhou
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Penghui Yu
- Tea Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jing Bai
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Hua Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, People's Republic of China.
| | - Yihui Gong
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China.
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Jin DP, Sim S, Park JW, Choi JE, Yoon J, Lim CE, Kim MH. Identification of the Plant Family Caryophyllaceae in Korea Using DNA Barcoding. PLANTS (BASEL, SWITZERLAND) 2023; 12:2060. [PMID: 37653977 PMCID: PMC10222892 DOI: 10.3390/plants12102060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 09/02/2023]
Abstract
Caryophyllaceae is a large angiosperm family, with many species being utilized as ornamental or medicinal plants in Korea, in addition to several endangered species that are managed by the government. In this study, we used DNA barcoding for the accurate identification of Korean Caryophyllaceae. A total of 78 taxa (n = 215) were sequenced based on three chloroplast regions (rbcL, matK, and psbA-trnH) and nuclear ribosomal internal transcribed spacers (ITS). In the neighbor-joining tree, a higher accuracy of identification was generally observed when using ITS (>73%) rather than chloroplast regions (<62%). The highest resolution was found for rbcL + ITS (77.6%), although resolution varied according to the genus. Among the genera that included two and more species, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified. However, the species of five other genera (Cerastium, Gypsophila, Dianthus, Silene, and Spergularia) showed relatively low resolutions (0-61.1%). In the cases of Cerastium, Dianthus, and Silene, ambiguous taxonomic relationships among unidentified species may have been a factor contributing to such low resolutions. However, in contrast to these results, Gypsophila and Spergularia have been identified well in previous studies. Our findings indicate the need of taxonomic reconsideration in Korea.
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Affiliation(s)
- Dong-Pil Jin
- Urban Biodiversity Research Division, Sejong National Arboretum, Korean Arboretum and Gardens Institute, Sejong 30106, Republic of Korea
| | - Sunhee Sim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Jong-Won Park
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-Eun Choi
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Jiwon Yoon
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Chae Eun Lim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Min-Ha Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
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5
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Vu TTT, Vu LTK, Nguyen QH, Pham KV, Nguyen DT, Nguyen LTN, Chu MH. Cytotoxic effects of steroidal glycosides isolated from the Paris vietnamensis plant on cancer cell lines and against bacterial strains. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1676168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Thuy Thi Thu Vu
- Department of Genetics and Modern Biology, Thainguyen University of Education, Thainguyen University, Vietnam
| | - Lien Thi Kim Vu
- Laboratory of Applied Nanotechnology, Institute of Theoretical and Applied Research, Duy Tan University, Hanoi, Vietnam
| | - Quan Huu Nguyen
- Department of Genetics and Modern Biology, Thainguyen University of Education, Thainguyen University, Vietnam
| | - Khang Van Pham
- Department of Organic Chemistry, Thainguyen University of Education, Thainguyen University, Vietnam
| | - Dung Tien Nguyen
- Department of Medicinal Plants, Center for Research and Technology Transfer, Institute of Regional Research and Development, Hanoi, Vietnam
| | - Lan Thi Ngoc Nguyen
- Department of Genetics and Modern Biology, Thainguyen University of Education, Thainguyen University, Vietnam
| | - Mau Hoang Chu
- Department of Genetics and Modern Biology, Thainguyen University of Education, Thainguyen University, Vietnam
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6
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Perkins AJ. Molecular phylogenetics and species delimitation in annual species of Hydrocotyle (Araliaceae) from South Western Australia. Mol Phylogenet Evol 2019; 134:129-141. [PMID: 30771512 DOI: 10.1016/j.ympev.2019.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 10/27/2022]
Abstract
Hydrocotyle L. is a cosmopolitan genus, with approximately 130 species, of mostly perennial herbs in the family Araliaceae. The genus includes around 95 perennial and 35 annual species, with all annual species endemic to Australia. In this study, I used sequences of a nDNA marker (ETS) and two cpDNA markers (psbA-trnH and trnL-trnF) to reconstruct phylogenetic relationships among the annual species of Hydrocotyle. The final sampling included 21 species of Hydrocotyle and seven outgroup taxa. The phylogenetic analyses of the combined molecular dataset (i.e., ETS, psbA-trnH and trnL-trnF) recovered three major clades within Hydrocotyle, defined by annual or perennial life histories, and the presence/absence of floral bracts. The topology reconstructed here indicates that there is insufficient molecular evidence for the formal recognition of two putative new species, Hydrocotyle sp. Hamelinensis and Hydrocotyle sp. Puberula, previously identified on the basis of morphology. More specifically, H. sp. Hamelinensis is conspecific with H. tetragonocarpa Bunge, while H. sp. Puberula is conspecific with H. scutellifera Benth. Morphological studies of H. tetragonocarpa revealed that this species is andromonoecious and has heterocarpic schizocarps. Fertile plants of H. tetragonocarpa bear fruit that are either ovoid and wingless or broadly obcordate and winged. A detailed re-examination of the schizocarp surfaces of H. scutellifera indicated that these schizocarps are either glabrous or papillate, with neither of these two character states co-varying with any other vegetative or reproductive traits. The phylogeny of the annual Hydrocotyle recovered a paraphyletic Hydrocotyle, with Neosciadium glochidiatum (Benth.) Domin nested within the genus. This study is the first to reconstruct a molecular phylogeny of Hydrocotyle using samples of both annual and perennial taxa. The findings from this study provide a phylogenetic framework for future systematic and taxonomic research within the genus.
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Affiliation(s)
- Andrew J Perkins
- Western Australian Herbarium, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Western Australia 6983, Australia.
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7
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Yan M, Xiong Y, Liu R, Deng M, Song J. The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks. FRONTIERS IN PLANT SCIENCE 2018; 9:569. [PMID: 29868047 PMCID: PMC5952231 DOI: 10.3389/fpls.2018.00569] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 05/10/2023]
Abstract
The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia - Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiaojiao Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shangrao Normal University, Shangrao, China
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8
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Krawczyk K, Nobis M, Myszczyński K, Klichowska E, Sawicki J. Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa). Sci Rep 2018; 8:1924. [PMID: 29386579 PMCID: PMC5792575 DOI: 10.1038/s41598-018-20399-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/17/2018] [Indexed: 02/03/2023] Open
Abstract
Present study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search of the most variable and the most discriminative loci within Stipa. The results showed that the problem with selecting a good barcode locus for feather grasses lies in the very low level of genetic diversity within its plastome. None of the single chloroplast loci is polymorphic enough to play a role of a barcode or a phylogenetic marker for Stipa. The biggest number of taxa was successfully identified by the analysis of 600 bp long DNA fragment comprising a part of rbcL gene, the complete rbcL-rpl23 spacer and a part of rpl23 gene. The effectiveness of multi-locus barcode composed of six best-performing loci for Stipa (ndhH, rpl23, ndhF-rpl32, rpl32-ccsA, psbK-psbI and petA-psbJ) didn't reach 70% of analyzed taxa. The analysis of complete plastome sequences as a super-barcode for Stipa although much more effective, still didn't allow for discrimination of all the analyzed taxa of feather grasses.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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9
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Kuzmina ML, Braukmann TWA, Fazekas AJ, Graham SW, Dewaard SL, Rodrigues A, Bennett BA, Dickinson TA, Saarela JM, Catling PM, Newmaster SG, Percy DM, Fenneman E, Lauron-Moreau A, Ford B, Gillespie L, Subramanyam R, Whitton J, Jennings L, Metsger D, Warne CP, Brown A, Sears E, Dewaard JR, Zakharov EV, Hebert PDN. Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700079. [PMID: 29299394 PMCID: PMC5749818 DOI: 10.3732/apps.1700079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/26/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. METHODS Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery. RESULTS Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae). DISCUSSION Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.
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Affiliation(s)
- Maria L. Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Thomas W. A. Braukmann
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Aron J. Fazekas
- The Arboretum, University of Guelph, 50 Stone Road East, Ontario N1G 2W1, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Stephanie L. Dewaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Anuar Rodrigues
- Office of the Vice-Principal Academic and Dean, University of Toronto, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Bruce A. Bennett
- Yukon Conservation Data Centre (CDC), Whitehorse, Yukon Territory Y1A 2C6, Canada
| | - Timothy A. Dickinson
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum (ROM), 100 Queens Park, Toronto, Ontario M5S2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S, Canada
| | - Jeffery M. Saarela
- Beaty Centre for Species Discovery and National Herbarium of Canada (CAN), Botany Section, Research and Collections, National Heritage Campus of the Canadian Museum of Nature, Gatineau, Québec J9J 3N7, Canada
| | - Paul M. Catling
- The Agriculture and Agri-Food Canada Collection of Vascular Plants (DAO), 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Steven G. Newmaster
- BIO Herbarium (OAC), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Diana M. Percy
- Natural History Museum, Cromwell Road, Kensington, London SW75BD, United Kingdom
| | - Erin Fenneman
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Aurélien Lauron-Moreau
- Institut de recherche en biologie végétale, Université de Montréal, 2900 Edouard Montpetit Boulevard, Montréal, Québec H3T 1J4, Canada
| | - Bruce Ford
- University of Manitoba Vascular Plant Herbarium (WIN), Department of Biological Sciences, University of Manitoba, 66 Chancellors Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Lynn Gillespie
- Beaty Centre for Species Discovery and National Herbarium of Canada (CAN), Botany Section, Research and Collections, National Heritage Campus of the Canadian Museum of Nature, Gatineau, Québec J9J 3N7, Canada
| | - Ragupathy Subramanyam
- BIO Herbarium (OAC), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Jeannette Whitton
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Linda Jennings
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Deborah Metsger
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum (ROM), 100 Queens Park, Toronto, Ontario M5S2C6, Canada
| | - Connor P. Warne
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Allison Brown
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Elizabeth Sears
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Jeremy R. Dewaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
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Xu SZ, Li ZY, Jin XH. DNA barcoding of invasive plants in China: A resource for identifying invasive plants. Mol Ecol Resour 2017; 18:128-136. [PMID: 28865184 DOI: 10.1111/1755-0998.12715] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 01/05/2023]
Abstract
Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China. In this study, five common single markers (ITS, ITS2, matK, rbcL and trnH-psbA) were evaluated using 634 species (including 469 invasive plant species in China, 10 new records to China, 16 potentially invasive plant species around the world but not introduced into China yet and 139 plant species native to China) based on three different methods. Our results indicated that ITS2 displayed largest intra- and interspecific divergence (1.72% and 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH-psbA provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates, respectively. The combination of ITS + matK performed best and provided 91.03% discriminatory power, followed by ITS2 + matK (85.78%). For identifying unknown individuals, ITS + matK had 100% correct identification rate based on our database, followed by ITS/ITS2 (both 93.33%) and ITS2 + matK (91.67%). Thus, we propose ITS/ITS2 + matK as the most suitable barcode for invasive plants in China. This study also demonstrated that DNA barcoding is an efficient tool for identifying invasive species.
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Affiliation(s)
- Song-Zhi Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhen-Yu Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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11
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Patoka J, Bláha M, Kalous L, Vrabec V, Buřič M, Kouba A. Potential pest transfer mediated by international ornamental plant trade. Sci Rep 2016; 6:25896. [PMID: 27221025 PMCID: PMC4879528 DOI: 10.1038/srep25896] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/22/2016] [Indexed: 11/20/2022] Open
Abstract
In recent years, the keeping of ornamental freshwater animals and plants in garden ponds has been growing in popularity. Water hyacinth (Eichhornia crassipes) is one of the preferred macrophytes seasonally imported mainly from South-eastern Asia throughout the world. This constitutes a secondary introduction inasmuch as the species is native to South America. Although many assemblages of aquatic invertebrates have been described as associated with this plant in the wild, there has been no research focused on their potential introduction via the international plant trade. We examined 216 specimens of water hyacinths imported for ornamental purposes from Indonesia into the Czech Republic. Numerous meio- and macroinvertebrates belonging to at least 39 species were captured. On the total number of individuals, the highest prevalence was of Tubulinea and Rotifera. Most of these were still alive and vital, including a caterpillar of the Indo–Australian invasive moth Spodoptera litura. Water hyacinths are usually placed into outdoor ponds immediately after import, which facilitates the release of non-target alien species. The present paper aims to draw attention to “hitchhikers” associated with the ornamental trade.
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Affiliation(s)
- Jiří Patoka
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Martin Bláha
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Lukáš Kalous
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Vladimír Vrabec
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Miloš Buřič
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Antonín Kouba
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
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12
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Huang XC, Ci XQ, Conran JG, Li J. Application of DNA Barcodes in Asian Tropical Trees--A Case Study from Xishuangbanna Nature Reserve, Southwest China. PLoS One 2015; 10:e0129295. [PMID: 26121045 PMCID: PMC4509572 DOI: 10.1371/journal.pone.0129295] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/27/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world. METHODOLOGY AND PRINCIPAL FINDINGS A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH-psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH-psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6-58.1%) and genus (72.8-76.2%) identification. With trnH-psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7-28.5% and 31.6-35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas. CONCLUSIONS/SIGNIFICANCE Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH-psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.
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Affiliation(s)
- Xiao-cui Huang
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiu-qin Ci
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - John G. Conran
- Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, Benham Bldg DX, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Jie Li
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
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13
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Abstract
DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.
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Affiliation(s)
- Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, Carmarthenshire, SA32 8HG, UK,
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Same barcode, different biology: differential patterns of infectivity, specificity and pathogenicity in two almost identical parasite strains. Int J Parasitol 2014; 44:543-9. [PMID: 24874264 DOI: 10.1016/j.ijpara.2014.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 11/23/2022]
Abstract
Two Norwegian isolates of the monogenean Gyrodactylus salaris Malmberg, 1957 with identical cytochrome c oxidase subunit I barcodes from different hosts, show highly divergent biological and behavioural characteristics. The Lierelva parasite strain, typically infecting Atlantic salmon, Salmo salar L., grew exponentially on Atlantic salmon, but the Pålsbufjorden parasite strain, commonly infecting Arctic charr, Salvelinus alpinus L., grew slowly on both hosts and was non-pathogenic to Atlantic salmon. Both parasite strains reproduced successfully on Arctic charr, but the Atlantic salmon-infecting Lierelva strain grew faster on both hosts. Experiments with isolated worms revealed differences in reproductive rates which may account for the observed population differences. Atlantic salmon parasites consistently gave birth at an earlier age than the Arctic charr parasites, with the differential increasing from 1 day for the first birth up to 2-4 days for the third birth. Arctic charr-infecting parasites were more active on Atlantic salmon than salmon parasites on Arctic charr, a behavioural strategy leading to enhanced G. salaris mortality. Sequencing of 10 kb of nuclear genomic markers revealed only four single nucleotide polymorphisms, confirming that isolates of G. salaris with differences in fitness traits influencing establishment, fecundity and behaviour may be remarkably similar at a molecular level. The framework for reporting and control of G. salaris requires re-appraisal in light of the discovery of variants with such divergent biology.
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15
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Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S. Plant DNA barcoding: from gene to genome. Biol Rev Camb Philos Soc 2014; 90:157-66. [DOI: 10.1111/brv.12104] [Citation(s) in RCA: 438] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 02/05/2014] [Accepted: 02/27/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Xiwen Li
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Yang Yang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland; Brisbane Queensland 4072 Australia
| | - Maurizio Rossetto
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust; Mrs Macquaries Road Sydney New South Wales 2000 Australia
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences; Beijing 100700 China
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16
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Horst JL, Kimball S, Becerra JX, Noge K, Venable DL. Documenting the early stages of invasion of Matthiola parvifloraand predicting its spread in North America. SOUTHWEST NAT 2014. [DOI: 10.1894/f07-fmo-13.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Saarela JM, Sokoloff PC, Gillespie LJ, Consaul LL, Bull RD. DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. PLoS One 2013; 8:e77982. [PMID: 24348895 PMCID: PMC3865322 DOI: 10.1371/journal.pone.0077982] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/08/2013] [Indexed: 01/16/2023] Open
Abstract
Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.
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Affiliation(s)
- Jeffery M. Saarela
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Paul C. Sokoloff
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Lynn J. Gillespie
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Laurie L. Consaul
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Roger D. Bull
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
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18
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Tripathi AM, Tyagi A, Kumar A, Singh A, Singh S, Chaudhary LB, Roy S. The internal transcribed spacer (ITS) region and trnH-psbA [corrected] are suitable candidate loci for DNA barcoding of tropical tree species of India. PLoS One 2013; 8:e57934. [PMID: 23460915 PMCID: PMC3584017 DOI: 10.1371/journal.pone.0057934] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 01/29/2013] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND DNA barcoding as a tool for species identification has been successful in animals and other organisms, including certain groups of plants. The exploration of this new tool for species identification, particularly in tree species, is very scanty from biodiversity-rich countries like India. rbcL and matK are standard barcode loci while ITS, and trnH-psbA are considered as supplementary loci for plants. METHODOLOGY AND PRINCIPAL FINDINGS Plant barcode loci, namely, rbcL, matK, ITS, trnH-psbA, and the recently proposed ITS2, were tested for their efficacy as barcode loci using 300 accessions of tropical tree species. We tested these loci for PCR, sequencing success, and species discrimination ability using three methods. rbcL was the best locus as far as PCR and sequencing success rate were concerned, but not for the species discrimination ability of tropical tree species. ITS and trnH-psbA were the second best loci in PCR and sequencing success, respectively. The species discrimination ability of ITS ranged from 24.4 percent to 74.3 percent and that of trnH-psbA was 25.6 percent to 67.7 percent, depending upon the data set and the method used. matK provided the least PCR success, followed by ITS2 (59. 0%). Species resolution by ITS2 and rbcL ranged from 9.0 percent to 48.7 percent and 13.2 percent to 43.6 percent, respectively. Further, we observed that the NCBI nucleotide database is poorly represented by the sequences of barcode loci studied here for tree species. CONCLUSION Although a conservative approach of a success rate of 60-70 percent by both ITS and trnH-psbA may not be considered as highly successful but would certainly help in large-scale biodiversity inventorization, particularly for tropical tree species, considering the standard success rate of plant DNA barcode program reported so far. The recommended matK and rbcL primers combination may not work in tropical tree species as barcode markers.
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Affiliation(s)
- Abhinandan Mani Tripathi
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Antariksh Tyagi
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Anoop Kumar
- Plant Diversity, Systematic and Herbarium Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Akanksha Singh
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Shivani Singh
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Lal Babu Chaudhary
- Plant Diversity, Systematic and Herbarium Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Sribash Roy
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
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Ghahramanzadeh R, Esselink G, Kodde LP, Duistermaat H, van Valkenburg JLCH, Marashi SH, Smulders MJM, van de Wiel CCM. Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding. Mol Ecol Resour 2012; 13:21-31. [PMID: 23039943 DOI: 10.1111/1755-0998.12020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/08/2012] [Accepted: 08/16/2012] [Indexed: 11/29/2022]
Abstract
Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH-psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics.
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Affiliation(s)
- R Ghahramanzadeh
- Wageningen UR Plant Breeding, Wageningen, NL-6700 AA, The Netherlands
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20
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Biological invasions in soil: DNA barcoding as a monitoring tool in a multiple taxa survey targeting European earthworms and springtails in North America. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0338-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bafeel SO, Arif IA, Bakir MA, Al Homaidan AA, Al Farhan AH, Khan HA. DNA barcoding of arid wild plants using rbcL gene sequences. GENETICS AND MOLECULAR RESEARCH 2012; 11:1934-41. [PMID: 22869548 DOI: 10.4238/2012.july.19.12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life (CBOL) plant working group needs to be evaluated for a wide range of plant species. We therefore tested the potential of the rbcL marker for the identification of wild plants belonging to diverse families of arid regions. Maximum likelihood tree analysis was performed to evaluate the discriminatory power of the rbcL gene. Our findings showed that using rbcL gene sequences enabled identification of the majority of the samples (92%) to genus level and only 17% to species level.
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Affiliation(s)
- S O Bafeel
- Department of Biology, College of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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22
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de Vere N, Rich TCG, Ford CR, Trinder SA, Long C, Moore CW, Satterthwaite D, Davies H, Allainguillaume J, Ronca S, Tatarinova T, Garbett H, Walker K, Wilkinson MJ. DNA barcoding the native flowering plants and conifers of Wales. PLoS One 2012; 7:e37945. [PMID: 22701588 PMCID: PMC3368937 DOI: 10.1371/journal.pone.0037945] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 04/26/2012] [Indexed: 11/19/2022] Open
Abstract
We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.
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Affiliation(s)
- Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, United Kingdom.
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Arca M, Hinsinger DD, Cruaud C, Tillier A, Bousquet J, Frascaria-Lacoste N. Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus. PLoS One 2012; 7:e34089. [PMID: 22479532 PMCID: PMC3313964 DOI: 10.1371/journal.pone.0034089] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/21/2012] [Indexed: 02/01/2023] Open
Abstract
The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA "universal" barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed.
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Affiliation(s)
- Mariangela Arca
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
| | - Damien Daniel Hinsinger
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt, Université Laval, Québec, Québec, Canada
| | | | - Annie Tillier
- Département systématique et évolution and Service de systématique moléculaire, Muséum national d'histoire naturelle, Paris, France
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt, Université Laval, Québec, Québec, Canada
| | - Nathalie Frascaria-Lacoste
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
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Schroeder H, Hoeltken AM, Fladung M. Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:374-81. [PMID: 21973311 DOI: 10.1111/j.1438-8677.2011.00502.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Within the genus Populus several species belonging to different sections are cross-compatible. Hence, high numbers of interspecies hybrids occur naturally and, additionally, have been artificially produced in huge breeding programmes during the last 100 years. Therefore, determination of a single poplar species, used for the production of 'multi-species hybrids' is often difficult, and represents a great challenge for the use of molecular markers in species identification. Within this study, over 20 chloroplast regions, both intergenic spacers and coding regions, have been tested for their ability to differentiate different poplar species using 23 already published barcoding primer combinations and 17 newly designed primer combinations. About half of the published barcoding primers yielded amplification products, whereas the new primers designed on the basis of the total sequenced cpDNA genome of Populus trichocarpa Torr. & Gray yielded much higher amplification success. Intergenic spacers were found to be more variable than coding regions within the genus Populus. The highest discrimination power of Populus species was found in the combination of two intergenic spacers (trnG-psbK, psbK-psbl) and the coding region rpoC. In barcoding projects, the coding regions matK and rbcL are often recommended, but within the genus Populus they only show moderate variability and are not efficient in species discrimination.
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Affiliation(s)
- H Schroeder
- Johann Heinrich von Thünen Institute, Institute for Forest Genetics, Grosshansdorf, Germany.
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25
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Xiang XG, Hu H, Wang W, Jin XH. DNA barcoding of the recently evolved genus Holcoglossum (Orchidaceae: Aeridinae): a test of DNA barcode candidates. Mol Ecol Resour 2011; 11:1012-21. [PMID: 21722327 DOI: 10.1111/j.1755-0998.2011.03044.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Orchidaceae is one of the largest families of flowering plants. Many species of orchid are endangered, and all species are included in Conventions on International Trade of Endangered Species of Fauna and Flora (CITES) I and II, but it is very difficult to identify orchid species, even those with fertile parts. The genus Holcoglossum (Orchidaceae: Aeridinae) has long been problematic in taxonomy. It consists of both long-evolved and radiated species and is an excellent case to use for testing DNA barcodes for Orchidaceae. We investigated the power of a subset of proposed plant barcoding loci [rbcL, matK, atpF-atpH, psbK-psbI, trnH-psbA and internal transcribed spacer (ITS)] to discriminate between species in this genus. Our results showed that all these DNA regions, except psbK-psbI and atpF-atpH, can be amplified easily from Holcoglossum and sequenced with established primers. The DNA regions matK and ITS had the highest variability. Among the six loci, matK resolved eight of the 12 Holcoglossum species and had the highest discriminatory ability. However, the combination of matK and ITS showed a greater ability to identify species than matK alone. Single or combined DNA markers discriminated between Holcoglossum species distributed in tropical areas effectively, but had less ability to identify radiated species from the temperate Hengduan Mountains of China. In the study, matK proved to be a useful DNA barcode for the genus Holcoglossum; however, complementary DNA regions are still required to accelerate the investigation and preservation of radiated species of orchid.
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Affiliation(s)
- Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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26
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Hollingsworth PM, Graham SW, Little DP. Choosing and using a plant DNA barcode. PLoS One 2011; 6:e19254. [PMID: 21637336 PMCID: PMC3102656 DOI: 10.1371/journal.pone.0019254] [Citation(s) in RCA: 580] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 03/24/2011] [Indexed: 12/02/2022] Open
Abstract
The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.
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Affiliation(s)
- Peter M Hollingsworth
- Genetics and Conservation Section, Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom.
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27
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de Groot GA, During HJ, Maas JW, Schneider H, Vogel JC, Erkens RHJ. Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective. PLoS One 2011; 6:e16371. [PMID: 21298108 PMCID: PMC3027654 DOI: 10.1371/journal.pone.0016371] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 12/20/2010] [Indexed: 11/30/2022] Open
Abstract
Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes—while playing an essential role in fern colonization and reproduction—generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNA-identifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distance-based analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a whole range of questions previously unaddressed in fern gametophyte ecology.
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Affiliation(s)
- G Arjen de Groot
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
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Ran JH, Wang PP, Zhao HJ, Wang XQ. A test of seven candidate barcode regions from the plastome in Picea (Pinaceae). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:1109-26. [PMID: 21106009 DOI: 10.1111/j.1744-7909.2010.00995.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
DNA barcoding, as a tool for species discrimination, has been used efficiently in animals, algae and fungi, but there are still debates on which DNA region(s) can be used as the standard barcode(s) for land plants. Gymnosperms, especially conifers, are important components of forests, and there is an urgent need for them to be identified through DNA barcoding because of their high frequency of collection in the field. However, the feasibility of DNA barcoding in gymnosperms has not been examined based on a dense species sampling. Here we selected seven candidate DNA barcodes from the plastome (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbA-trnH, and psbK-psbI) to evaluate their suitability in Picea (spruce). The results showed that none of them or their different combinations has sufficient resolution for spruce species, although matK+rbcL might be used as a two-locus barcode. The low efficiency of these candidate barcodes in Picea might be caused by the paternal inheritance of the chloroplast genome, long generation time, recent radiation, and frequent inter-specific hybridization aided by wind pollination. Some of these factors could also be responsible for the difficulties in barcoding other plant groups. Furthermore, the potential of the nuclear LEAFY gene as a land plant barcode was discussed.
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Affiliation(s)
- Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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