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Tnah LH, Lee SL, Lee CT, Ng KKS, Ng CH, Zawiah N. DNA barcode identification of cultivated and wild tropical fruit species. 3 Biotech 2024; 14:7. [PMID: 38074292 PMCID: PMC10703749 DOI: 10.1007/s13205-023-03848-w] [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: 01/25/2023] [Accepted: 11/08/2023] [Indexed: 01/19/2024] Open
Abstract
With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03848-w.
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Affiliation(s)
- Lee Hong Tnah
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Soon Leong Lee
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Chai Ting Lee
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Kevin Kit Siong Ng
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Chin Hong Ng
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Ngah Zawiah
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
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Zhan J, Zheng Y, Xia Q, Wang J, Liu S, Yang Z. Diversity investigation by application of DNA barcoding: A case study of lepidopteran insects in Xinjiang wild fruit forests, China. Ecol Evol 2022; 12:e8678. [PMID: 35309745 PMCID: PMC8901863 DOI: 10.1002/ece3.8678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/23/2022] [Accepted: 02/06/2022] [Indexed: 11/10/2022] Open
Abstract
To investigate the species diversity of lepidopteran insects in Xinjiang wild fruit forests, establish insect community monitoring systems, and determine the local species pool, we test the applicability of DNA barcoding based on cytochrome c oxidase subunit I (COI) gene for accurate and rapid identification of insect species. From 2017 to 2019, a total of 212 samples with ambiguous morphological identification were selected for DNA barcoding analysis. Five sequence‐based methods for species delimitation (ABGD, BINs, GMYC, jMOTU, and bPTP) were conducted for comparison to traditional morphology‐based identification. In total, 2,422 samples were recorded, representing 143 species of 110 genera in 17 families in Lepidoptera. The diversity analysis showed that the richness indices for Noctuidae was the highest (54 species), and for Pterophoridae, Cossidae, Limacodidae, Lasiocampidae, Pieridae, and Lycaenidae were the lowest (all with 1 species). The Shannon–Wiener species diversity index (H′) and Pielou's evenness (J′) of lepidopteran insects first increased and then decreased across these 3 years, while the Simpson diversity index showed a trend of subtracted then added. For molecular‐based identification, 67 lepidopteran species within 61 genera in 14 families were identified through DNA barcoding. Neighbor‐joining (NJ) analysis showed that conspecific individuals were clustered together and formed monophyletic groups with a high support value, except for Lacanobia contigua (Denis & Schiffermüller, 1775) (Noctuidae: Hadeninae). Sixty‐seven morphospecies were classified into various numbers of MOTUs based on ABGD, BINs, GMYC, jMOTU, and bPTP (70, 96, 2, 71, and 71, respectively). In Xinjiang wild fruit forests, the family with the largest number of species is Noctuidae, followed by Geometridae, Crambidae, and the remaining families. The highest Shannon diversity index is observed for the family Noctuidae. Our results indicate that the distance‐based methods (ABGD and jMOTU) and character‐based method (bPTP) outperform GMYC. BINs is inclined to overestimate species diversity compared to other methods.
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Affiliation(s)
- Jinyu Zhan
- Key Laboratory of Plant Protection Resources and Pest Management Ministry of Education Northwest A&F University Yangling China
- Entomological Museum College of Plant Protection Northwest A&F University Yangling China
| | - Yufeng Zheng
- Key Laboratory of Plant Protection Resources and Pest Management Ministry of Education Northwest A&F University Yangling China
- Entomological Museum College of Plant Protection Northwest A&F University Yangling China
| | - Qing Xia
- Key Laboratory of Plant Protection Resources and Pest Management Ministry of Education Northwest A&F University Yangling China
- Entomological Museum College of Plant Protection Northwest A&F University Yangling China
| | - Jin Wang
- Key Laboratory of Plant Protection Resources and Pest Management Ministry of Education Northwest A&F University Yangling China
- Entomological Museum College of Plant Protection Northwest A&F University Yangling China
| | - Sibo Liu
- Key Laboratory of Plant Protection Resources and Pest Management Ministry of Education Northwest A&F University Yangling China
- Entomological Museum College of Plant Protection Northwest A&F University Yangling China
| | - Zhaofu Yang
- Key Laboratory of Plant Protection Resources and Pest Management Ministry of Education Northwest A&F University Yangling China
- Entomological Museum College of Plant Protection Northwest A&F University Yangling China
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EL-Banhawy A, Acedo C, Qari S, Elkordy A. Molecular Identification and Phylogenetic Placement of Rosa arabica Crép. (Rosaceae), a Critically Endangered Plant Species. Life (Basel) 2020; 10:life10120335. [PMID: 33317197 PMCID: PMC7763824 DOI: 10.3390/life10120335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/25/2020] [Accepted: 12/07/2020] [Indexed: 11/21/2022] Open
Abstract
The Egyptian narrowly endemic and critically endangered plant species Rosa arabica Crép. was studied employing a taxonomic and molecular approach. Morphological investigations, distance analysis, and phylogenetic reconstruction revealed that R. arabica is a distinct species with great affinity to R. canina and differentiated from R. rubiginosa. Molecular identification based on the sequences of multiple markers single or in combination ITS, matK, rbcL, and trnL-F succeeded in identifying R. arabica at genus and species levels. We evaluated the potential of each marker and a combination of the nuclear ITS -Internal Transcribed Spacer- with one of the plastid markers, matK, rbcL, or trnL-F, to accurately identify Rosa species. All of them were successful in identifying R. arabica. Classification based on DNA sequences shows that R. arabica is placed within section Caninae in a clade comprising R. canina and R. rubiginosa. Moreover, R. arabica is closely related to other European Rosa species. In conclusion, our results indicate that the four DNA markers can provide species resolution in the context of the genus Rosa and relatives, aiming to characterize morphology and genetic diversity in the ecological and economically important genus Rosa.
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Affiliation(s)
- Ahmed EL-Banhawy
- Botany Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (A.E.-B.); (S.Q.)
| | - Carmen Acedo
- Biodiversity and Environment Management Department, Faculty of Biological and Environmental Sciences, University of León, 24071 León, Spain; (C.A.); (A.E.)
| | - Sameer Qari
- Biology Department, Aljumum University College, Umm Al-Qura University, Makkah 21421, Saudi Arabia
- Correspondence: (A.E.-B.); (S.Q.)
| | - Ahmed Elkordy
- Biodiversity and Environment Management Department, Faculty of Biological and Environmental Sciences, University of León, 24071 León, Spain; (C.A.); (A.E.)
- Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
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Contreras R, van den Brink L, Burgos B, González M, Gacitúa S. Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9060744. [PMID: 32545703 PMCID: PMC7355918 DOI: 10.3390/plants9060744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/31/2020] [Accepted: 06/11/2020] [Indexed: 05/25/2023]
Abstract
The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.
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Affiliation(s)
- Roberto Contreras
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Av. Copayapu 485, 1530000 Copiapó, Chile
| | - Liesbeth van den Brink
- Department of Evolution and Ecology, Plant Ecology Group, Universität Tübingen, 72076 Tübingen, Germany;
| | - Boris Burgos
- Corporación Nacional Forestal (CONAF), Región de Atacama, Juan Martínez 55, 1530000 Copiapó, Chile;
| | - Marlene González
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
| | - Sandra Gacitúa
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
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Osathanunkul M. Bar-HRM for authenticating soursop (Annona muricata) tea. Sci Rep 2018; 8:12666. [PMID: 30139965 PMCID: PMC6107521 DOI: 10.1038/s41598-018-31127-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/23/2018] [Indexed: 11/08/2022] Open
Abstract
Drinking soursop (Annona muricata) tea has become popular in Thailand due to recent findings about the medicinal properties of soursop tea regarding anti-cancer in particular. Consequently, numerous A. muricata tea products were found to be sold on markets and relatively expensive. It is almost impossible to identify the plant species component in the tea bag or powder products using traditional methods which are based on morphological characters. Therefore, a main objective of this study is to develop a molecular method called Bar-HRM (DNA barcoding coupled with High Resolution Melting) for authenticating A. muricata products. Three chloroplast regions including matK, rbcL and trnL were selected for in silico analyses. The findings show that rbcL is the most suitable region to be used for species identification in HRM analysis. Eleven A. muricata herbal products were purchased and tested with rbcL primers. Results from melting profile indicated that three out of eleven tested products were adulterated with other Annona species. It is believed that the Annona products are adulterated to increase the quantity and to make more profit. Notably, all of the tested products purchased from local producers were found to contain herbal species that differ from the species indicated by the seller.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand.
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Next generation crop improvement program: Progress and prospect in tea ( Camellia sinensis (L.) O. Kuntze). ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aasci.2018.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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van Zonneveld M, Loo J, Maselli S, Madrid JJ, Echeverria JL. Bridging molecular genetics and participatory research: how access and benefit-sharing stimulate interdisciplinary research for tropical biology and conservation. Biotropica 2018. [DOI: 10.1111/btp.12515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Judy Loo
- Bioversity International, HQ; Rome Italy
| | - Silvana Maselli
- University del Valle en Guatemala (UVG); Ciudad de Guatemala Guatemala
| | - Julio Javier Madrid
- The Association of Community Forestry Organizations in the Petén (ACOFOP); Santa Elena Guatemala
| | - José Luis Echeverria
- National Council of Protected Areas (CONAP); Oficina Técnica de Biodiversidad; Ciudad de Guatemala Guatemala
- ABS National Focal Point; Ciudad de Guatemala Guatemala
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Hosein FN, Austin N, Maharaj S, Johnson W, Rostant L, Ramdass AC, Rampersad SN. Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad. Ecol Evol 2017; 7:7311-7333. [PMID: 28944019 PMCID: PMC5606854 DOI: 10.1002/ece3.3220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 05/17/2017] [Accepted: 06/12/2017] [Indexed: 02/06/2023] Open
Abstract
The islands of the Caribbean are considered to be a "biodiversity hotspot." Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology-based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the ability of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad was assessed using three DNA barcodes (matK, rbcL, and rpoC1). Herbarium identifications were previously made for all species under study. matK, rbcL, and rpoC1 markers were successful in amplifying target regions for seven of the 14 species. rpoC1 sequences required extensive editing and were unusable. rbcL primers resulted in cleanest reads, however, matK appeared to be superior to rbcL based on a number of parameters assessed including level of DNA polymorphism in the sequences, genetic distance, reference library coverage based on BLASTN statistics, direct sequence comparisons within "best match" and "best close match" criteria, and finally, degree of clustering with moderate to strong bootstrap support (>60%) in neighbor-joining tree-based comparisons. The performance of both markers seemed to be species-specific based on the parameters examined. Overall, the Trinidad sequences were accurately identified to the genus level for all endemic plant species successfully amplified and sequenced using both matK and rbcL markers. DNA barcoding can contribute to taxonomic and biodiversity research and will complement efforts to select taxa for various molecular ecology and population genetics studies.
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Affiliation(s)
- Fazeeda N. Hosein
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Nigel Austin
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Shobha Maharaj
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Winston Johnson
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Luke Rostant
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Amanda C. Ramdass
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Sephra N. Rampersad
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
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Yu N, Wei YL, Zhang X, Zhu N, Wang YL, Zhu Y, Zhang HP, Li FM, Yang L, Sun JQ, Sun AD. Barcode ITS2: a useful tool for identifying Trachelospermum jasminoides and a good monitor for medicine market. Sci Rep 2017; 7:5037. [PMID: 28698616 PMCID: PMC5506054 DOI: 10.1038/s41598-017-04674-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/18/2017] [Indexed: 01/31/2023] Open
Abstract
Trachelospermum jasminoides is commonly used in traditional Chinese medicine. However, the use of the plant's local alternatives is frequent, causing potential clinical problems. The T. jasminoides sold in the medicine market is commonly dried and sliced, making traditional identification methods difficult. In this study, the ITS2 region was evaluated on 127 sequences representing T. jasminoides and its local alternatives according to PCR and sequencing rates, intra- and inter-specific divergences, secondary structure, and discrimination capacity. Results indicated the 100% success rates of PCR and sequencing and the obvious presence of a barcoding gap. Results of BLAST 1, nearest distance and neighbor-joining tree methods showed that barcode ITS2 could successfully identify all the texted samples. The secondary structures of the ITS2 region provided another dimensionality for species identification. Two-dimensional images were obtained for better and easier identification. Previous studies on DNA barcoding concentrated more on the same family, genus, or species. However, an ideal barcode should be variable enough to identify closely related species. Meanwhile, the barcodes should also be conservative in identifying distantly related species. This study highlights the application of barcode ITS2 in solving practical problems in the distantly related local alternatives of medical plants.
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Affiliation(s)
- Ning Yu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yu-Long Wei
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Xin Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Ning Zhu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yan-Li Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yue Zhu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Hai-Ping Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Fen-Mei Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Lan Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Jia-Qi Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Ai-Dong Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China.
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11
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Sequencing and
De Novo
Assembly of the Complete Chloroplast Genome of the Peruvian Carrot (
Arracacia xanthorrhiza
Bancroft). GENOME ANNOUNCEMENTS 2017; 5:5/7/e01519-16. [PMID: 28209812 PMCID: PMC5313604 DOI: 10.1128/genomea.01519-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Arracacia xanthorrhiza is an important secondary food crop in South America and Puerto Rico. The lack of crop protection and improvement strategies leads to infections damaging the storage roots. Here, we report the annotated complete chloroplast genome sequence of A. xanthorrhiza as a step toward developing genomic resources for this crop.
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Shaik RS, Zhu X, Clements DR, Weston LA. Understanding invasion history and predicting invasive niches using genetic sequencing technology in Australia: case studies from Cucurbitaceae and Boraginaceae. CONSERVATION PHYSIOLOGY 2016; 4:cow030. [PMID: 27766152 PMCID: PMC5069847 DOI: 10.1093/conphys/cow030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 05/07/2023]
Abstract
Part of the challenge in dealing with invasive plant species is that they seldom represent a uniform, static entity. Often, an accurate understanding of the history of plant introduction and knowledge of the real levels of genetic diversity present in species and populations of importance is lacking. Currently, the role of genetic diversity in promoting the successful establishment of invasive plants is not well defined. Genetic profiling of invasive plants should enhance our understanding of the dynamics of colonization in the invaded range. Recent advances in DNA sequencing technology have greatly facilitated the rapid and complete assessment of plant population genetics. Here, we apply our current understanding of the genetics and ecophysiology of plant invasions to recent work on Australian plant invaders from the Cucurbitaceae and Boraginaceae. The Cucurbitaceae study showed that both prickly paddy melon (Cucumis myriocarpus) and camel melon (Citrullus lanatus) were represented by only a single genotype in Australia, implying that each was probably introduced as a single introduction event. In contrast, a third invasive melon, Citrullus colocynthis, possessed a moderate level of genetic diversity in Australia and was potentially introduced to the continent at least twice. The Boraginaceae study demonstrated the value of comparing two similar congeneric species; one, Echium plantagineum, is highly invasive and genetically diverse, whereas the other, Echium vulgare, exhibits less genetic diversity and occupies a more limited ecological niche. Sequence analysis provided precise identification of invasive plant species, as well as information on genetic diversity and phylogeographic history. Improved sequencing technologies will continue to allow greater resolution of genetic relationships among invasive plant populations, thereby potentially improving our ability to predict the impact of these relationships upon future spread and better manage invaders possessing potentially diverse biotypes and exhibiting diverse breeding systems, life histories and invasion histories.
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Affiliation(s)
- Razia S. Shaik
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Xiaocheng Zhu
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - David R. Clements
- Department of Biology, Trinity Western University, Langley, BC, CanadaV2Y 1Y1
| | - Leslie A. Weston
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
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Feng S, Jiang M, Shi Y, Jiao K, Shen C, Lu J, Ying Q, Wang H. Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study. FRONTIERS IN PLANT SCIENCE 2016; 7:1047. [PMID: 27486467 PMCID: PMC4949264 DOI: 10.3389/fpls.2016.01047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/04/2016] [Indexed: 05/15/2023]
Abstract
Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources.
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Affiliation(s)
- Shangguo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Mengying Jiang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yujun Shi
- School of Foreign Languages, Zhejiang Gongshang UniversityHangzhou, China
| | - Kaili Jiao
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Chenjia Shen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Qicai Ying
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
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