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Chen S, Yin X, Han J, Sun W, Yao H, Song J, Li X. DNA barcoding in herbal medicine: Retrospective and prospective. J Pharm Anal 2023; 13:431-441. [PMID: 37305789 PMCID: PMC10257146 DOI: 10.1016/j.jpha.2023.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/07/2023] [Accepted: 03/25/2023] [Indexed: 06/13/2023] Open
Abstract
DNA barcoding has been widely used for herb identification in recent decades, enabling safety and innovation in the field of herbal medicine. In this article, we summarize recent progress in DNA barcoding for herbal medicine to provide ideas for the further development and application of this technology. Most importantly, the standard DNA barcode has been extended in two ways. First, while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples, super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic levels. Second, mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials. In addition, some molecular techniques, such as high-throughput sequencing and isothermal amplification, are combined with DNA barcodes for species identification, which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding era. Furthermore, standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference sequences for species identification, which increases the accuracy and credibility of species discrimination based on DNA barcodes. In summary, DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.
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Affiliation(s)
- Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xianmei Yin
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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Genetic differentiation of a critically endangered population of the limpet Patella candei candei d’Orbigny, 1840, in the Canary Islands. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01456-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe adoption of measures to protect the viability of threatened populations should be supported by empirical data identifying appropriate conservation units and management strategies. The global population of the majorera limpet, P. candei candei d’Orbigny, 1840, is restricted to the Macaronesian islands in the NE Atlantic, including near-to-extinct and healthy populations in Fuerteventura and Selvagens, respectively. The taxonomic position, genetic diversity and intra- and interspecific relationships of these populations are unclear, which is hindering the implementation of a recovery plan for the overexploited majorera limpet on Fuerteventura. In this study, ddRAD-based genome scanning was used to overcome the limitations of mitochondrial DNA-based analysis. As a result, P. candei candei was genetically differentiated from the closely related P. candei crenata for the first time. Moreover, genetic differentiation was detected between P. candei candei samples from Selvagens and Fuerteventura, indicating that translocations from the healthy Selvagens source population are inadvisable. In conclusion, the majorera limpet requires population-specific management focused on the preservation of exceptional genetic diversity with which to face future environmental challenges.
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Fassio G, Bouchet P, Oliverio M, Strong EE. Re-evaluating the case for poecilogony in the gastropod Planaxis sulcatus (Cerithioidea, Planaxidae). BMC Ecol Evol 2022; 22:13. [PMID: 35130841 PMCID: PMC8822645 DOI: 10.1186/s12862-022-01961-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022] Open
Abstract
Background Planaxis sulcatus has been touted as a textbook example of poecilogony, with members of this wide-ranging Indo-Pacific marine gastropod said to produce free-swimming veligers as well as brooded juveniles. A recent paper by Wiggering et al. (BMC Evol Biol 20:76, 2020) assessed a mitochondrial gene phylogeny based on partial COI and 16S rRNA sequences for 31 individuals supplemented by observations from the brood pouch of 64 mostly unsequenced individuals. ABGD and bGYMC supported three reciprocally monophyletic clades, with two distributed in the Indo-Pacific, and one restricted to the northern Indian Ocean and Red Sea. Given an apparent lack of correlation between clade membership and morphological differentiation or mode of development, the reported 3.08% maximum K2P model-corrected genetic divergence in COI among all specimens was concluded to represent population structuring. Hence, the hypothesis that phylogenetic structure is evidence of cryptic species was rejected and P. sulcatus was concluded to represent a case of geographic poecilogony. Results Our goal was to reassess the case for poecilogony in Planaxis sulcatus with a larger molecular dataset and expanded geographic coverage. We sequenced an additional 55 individuals and included published and unpublished sequence data from other sources, including from Wiggering et al. Our dataset comprised 108 individuals (88 COI, 81 16S rRNA) and included nine countries unrepresented in the previous study. The expanded molecular dataset yielded a maximum K2P model-corrected genetic divergence among all sequenced specimens of 12.09%. The value of 3.08% erroneously reported by Wiggering et al. is the prior maximal distance value that yields a single-species partition in ABGD, and not the maximum K2P intraspecific divergence that can be calculated for the dataset. The bGMYC analysis recognized between two and six subdivisions, while the best-scoring ASAP partitions recognized two, four, or five subdivisions, not all of which were robustly supported in Bayesian and maximum likelihood phylogenetic analyses of the concatenated and single gene datasets. These hypotheses yielded maximum intra-clade genetic distances in COI of 2.56–6.19%, which are more consistent with hypothesized species-level thresholds for marine caenogastropods. Conclusions Based on our analyses of a more comprehensive dataset, we conclude that the evidence marshalled by Wiggering et al. in support of Planaxis sulcatus comprising a single widespread, highly variable species with geographic poecilogony is unconvincing and requires further investigation in an integrative taxonomic framework. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01961-7.
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Dincă V, Dapporto L, Somervuo P, Vodă R, Cuvelier S, Gascoigne-Pees M, Huemer P, Mutanen M, Hebert PDN, Vila R. High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity. Commun Biol 2021; 4:315. [PMID: 33750912 PMCID: PMC7943782 DOI: 10.1038/s42003-021-01834-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 02/11/2021] [Indexed: 11/09/2022] Open
Abstract
The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we captured 62% of the total haplotype diversity and show that most species possess a few very common haplotypes and many rare ones. Specimens in the dataset have an average 95.3% probability of being correctly identified. Mitochondrial diversity displayed elevated haplotype richness in southern European refugia, establishing the generality of this key biogeographic pattern for an entire taxonomic group. Fifteen percent of the species are involved in barcode sharing, but two thirds of these cases may reflect the need for further taxonomic research. This dataset provides a unique resource for conservation and for studying evolutionary processes, cryptic species, phylogeography, and ecology.
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Affiliation(s)
- Vlad Dincă
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu, 90014, Oulu, Finland.
- Institut de Biologia Evolutiva (CSIC-UPF), 03008, Barcelona, Spain.
| | - Leonardo Dapporto
- ZEN lab, Dipartimento di Biologia, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, FI-00014, Helsinki, Finland
| | | | - Sylvain Cuvelier
- VVE Workgroup Butterflies, Diamantstraat 4, 8900, Ieper, Belgium
| | | | - Peter Huemer
- Naturwissenschaftliche Sammlungen, Sammlungs- und Forschungszentrum, Tiroler Landesmuseen, 6060, Hall in Tirol, Austria
| | - Marko Mutanen
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu, 90014, Oulu, Finland
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), 03008, Barcelona, Spain
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Kannan A, Rama Rao S, Ratnayeke S, Yow YY. The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata. PeerJ 2020; 8:e8755. [PMID: 32274263 PMCID: PMC7127494 DOI: 10.7717/peerj.8755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/16/2020] [Indexed: 12/05/2022] Open
Abstract
Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as ‘barcodes’ to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06–6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.
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Affiliation(s)
- Adrian Kannan
- Department of Biological Sciences, School of Science & Technology, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Suganiya Rama Rao
- Department of Biological Sciences, School of Science & Technology, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Shyamala Ratnayeke
- Department of Biological Sciences, School of Science & Technology, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Yoon-Yen Yow
- Department of Biological Sciences, School of Science & Technology, Sunway University, Selangor Darul Ehsan, Malaysia
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He T, Jiao L, Wiedenhoeft AC, Yin Y. Machine learning approaches outperform distance- and tree-based methods for DNA barcoding of Pterocarpus wood. PLANTA 2019; 249:1617-1625. [PMID: 30825008 DOI: 10.1007/s00425-019-03116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/20/2019] [Indexed: 05/10/2023]
Abstract
Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal logging and associated trade, and the development of reliable and efficient analytical methods is essential for its extensive application in the trade of wood and in the forensics of natural materials more broadly. In this study, 120 DNA sequences of four barcodes (ITS2, matK, ndhF-rpl32, and rbcL) generated in our previous study and 85 downloaded from National Center for Biotechnology Information (NCBI) were collected to establish a reference data set for six commercial Pterocarpus woods. MLAs (BLOG, BP-neural network, SMO and J48) were compared with distance- (TaxonDNA) and tree-based (NJ tree) methods based on identification accuracy and cost-effectiveness across these six species, and also were applied to discriminate the CITES-listed species Pterocarpus santalinus from its anatomically similar species P. tinctorius for forensic identification. MLAs provided higher identification accuracy (30.8-100%) than distance- (15.1-97.4%) and tree-based methods (11.1-87.5%), with SMO performing the best among the machine learning classifiers. The two-locus combination ITS2 + matK when using SMO classifier exhibited the highest resolution (100%) with the fewest barcodes for discriminating the six Pterocarpus species. The CITES-listed species P. santalinus was discriminated successfully from P. tinctorius using MLAs with a single barcode, ndhF-rpl32. This study shows that MLAs provided higher identification accuracy and cost-effectiveness for forensic application over other analytical methods in DNA barcoding of Pterocarpus wood.
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Affiliation(s)
- Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and National Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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Neiber MT, Glaubrecht M. Unparalleled disjunction or unexpected relationships? Molecular phylogeny and biogeography of Melanopsidae (Caenogastropoda: Cerithioidea), with the description of a new family and a new genus from the ancient continent Zealandia. Cladistics 2018; 35:401-425. [DOI: 10.1111/cla.12361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2018] [Indexed: 11/27/2022] Open
Affiliation(s)
- Marco T. Neiber
- Department of Animal Diversity Center of Natural History (CeNak) Zoological Museum Universität Hamburg Martin‐Luther‐King‐Platz 3 D‐20146 Hamburg Germany
| | - Matthias Glaubrecht
- Department of Animal Diversity Center of Natural History (CeNak) Zoological Museum Universität Hamburg Martin‐Luther‐King‐Platz 3 D‐20146 Hamburg Germany
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The Octocorals of Dongsha Atoll (South China Sea): An Iterative Approach to Species Identification Using Classical Taxonomy and Molecular Barcodes. Zool Stud 2018; 57:e50. [PMID: 31966290 DOI: 10.6620/zs.2018.57-50] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/16/2018] [Indexed: 01/04/2023]
Abstract
Yehuda Benayahu, Leendert Pieter van Ofwegen, Chang-feng Dai, Ming-Shiou Jeng, Keryea Soong, Alex Shlagman, Samuel W. Du, Prudence Hong, Nimrah H. Imam, Alice Chung, Tiana Wu, and Catherine S. McFadden (2018) Surveys of octocorals from Dongsha Atoll, Taiwan were conducted during 2011, 2013 and 2015 by SCUBA at a depth range of 6-25 m. The collections yielded ~540 specimens, encompassing the variety of taxa occurring in the explored sites; estimates of their abundances were also recorded. Dongsha features a highly diverse octocoral fauna, and octocorals are the dominant benthic organisms in the surveyed reef sites, often covering the majority of the hard substratum. Specimens were identified to the genus and species levels based on an iterative approach that integrates classical taxonomy with character-based molecular barcodes. A total of 51 nominal species representing 20 genera belonging to seven families were recorded, plus ~30 colonies that could only be assigned to a genus. Members of the family Alcyoniidae were the most abundant and diverse taxa, with 27 nominal species plus at least one potentially new, undescribed species of Sinularia, and 5-7 species each of Cladiella, Lobophytum and Sarcophyton. Problems with the taxonomic identification and phylogenetic relationships of species in these genera are discussed. The peculiarity of the Dongsha octocoral species composition is noted, and the composition is also compared to the other Taiwanese reef systems.
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Gong S, Ding Y, Wang Y, Jiang G, Zhu C. Advances in DNA Barcoding of Toxic Marine Organisms. Int J Mol Sci 2018; 19:E2931. [PMID: 30261656 PMCID: PMC6213214 DOI: 10.3390/ijms19102931] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/28/2018] [Accepted: 09/20/2018] [Indexed: 01/10/2023] Open
Abstract
There are more than 200,000 marine species worldwide. These include many important economic species, such as large yellow croaker, ribbonfish, tuna, and salmon, but also many potentially toxic species, such as blue-green algae, diatoms, cnidarians, ctenophores, Nassarius spp., and pufferfish. However, some edible and toxic species may look similar, and the correct identification of marine species is thus a major issue. The failure of traditional classification methods in certain species has promoted the use of DNA barcoding, which uses short, standard DNA fragments to assist with species identification. In this review, we summarize recent advances in DNA barcoding of toxic marine species such as jellyfish and pufferfish, using genes including cytochrome oxidase I gene (COI), cytochrome b gene (cytb), 16S rDNA, internal transcribed spacer (ITS), and Ribulose-1,5-bisphosphate carboxylase oxygenase gene (rbcL). We also discuss the application of this technique for improving the identification of marine species. The use of DNA barcoding can benefit the studies of biological diversity, biogeography, food safety, and the detection of both invasive and new species. However, the technique has limitations, particularly for the analysis of complex objects and the selection of standard DNA barcodes. The development of high-throughput methods may offer solutions to some of these issues.
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Affiliation(s)
- Shaohua Gong
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Yanfei Ding
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Yi Wang
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Guangze Jiang
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Cheng Zhu
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
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Harasewych MG. Tropidofusus ypotethys: a new genus and new species of Columbariidae (Mollusca: Gastropoda: Turbinelloidea). MOLLUSCAN RESEARCH 2018. [DOI: 10.1080/13235818.2018.1484265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- M. G. Harasewych
- Department of Invertebrate Zoology, MRC-163, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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Regional genetic diversity for NNV grouper viruses across the Indo-Asian region - implications for selecting virus resistance in farmed groupers. Sci Rep 2017; 7:10658. [PMID: 28878324 PMCID: PMC5587679 DOI: 10.1038/s41598-017-11263-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/22/2017] [Indexed: 11/22/2022] Open
Abstract
Grouper aquaculture around Asia is impacted by the nervous necrosis virus (NNV) and, in response, host resistance to this infection is being considered as a trait for selection. However efficient selection may be confounded if there are different genetic strains of NNV within and between regions and over years. This study uses statistical approaches and assessment of “characteristic attributes” (i.e. nucleotide positions that discriminate among strains) to assess whether published and new NNV RNA2 cds sequences show genetic differentiation over geography, host species and years. Rather clear evidence was found for regional strains of NNV. Interestingly, most of the geographic defining “characteristic attributes” were in codon position three, and not translated into differences for the protein capsid (i.e. they were synonymous variations), suggesting that while NNV strains were geographically isolated and had diverged in different regions for RNA sequences, selection had largely conserved the protein sequences among regions. The apparent selection constraint on the capsid protein may mitigate the risk that despite geographic subdivision, NNV strain variability will confound genetic selection for host resistance. The existence of regional Asian NNV strains may suggest that hatcheries are at risk from NNV not only from imported material but also from endemic reservoirs.
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A phylogeny of Southern Hemisphere whelks (Gastropoda: Buccinulidae) and concordance with the fossil record. Mol Phylogenet Evol 2017; 114:367-381. [PMID: 28669812 DOI: 10.1016/j.ympev.2017.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/31/2017] [Accepted: 06/26/2017] [Indexed: 11/24/2022]
Abstract
Under current marine snail taxonomy, the majority of whelks from the Southern Hemisphere (Buccinulidae) are hypothesised to represent a monophyletic clade that has evolved independently from Northern Hemisphere taxa (Buccinidae). Phylogenetic analysis of mitochondrial genomic and nuclear ribosomal DNA sequence data indicates that Southern Hemisphere taxa are not monophyletic, and results suggest that dispersal across the equator has occurred in both directions. New Zealand buccinulid whelks, noted for their high endemic diversity, are also found to not be monophyletic. Using independent fossil calibrations, estimated genetic divergence dates show remarkable concordance with the fossil record of the Penion and Kelletia. The divergence dates and the geographic distribution of the genera through time implies that some benthic marine snails are capable of dispersal over long distances, despite varied developmental strategies. Phylogenetic results also indicate that one species, P. benthicolus belongs in Antarctoneptunea.
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Molecular phylogeny and biogeography of the land snail family Hygromiidae (Gastropoda: Helicoidea). Mol Phylogenet Evol 2017; 111:169-184. [DOI: 10.1016/j.ympev.2017.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 03/28/2017] [Accepted: 04/03/2017] [Indexed: 11/18/2022]
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Chakraborty M, Dhar B, Ghosh SK. Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes. Mol Ecol Resour 2017; 17:1359-1370. [PMID: 28332322 DOI: 10.1111/1755-0998.12671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/26/2017] [Accepted: 03/07/2017] [Indexed: 11/29/2022]
Abstract
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification.
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Affiliation(s)
- Mohua Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Bishal Dhar
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar, Assam, India.,University of Kalyani, Kalyani, West Bengal, India
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Yang J, Vázquez L, Chen X, Li H, Zhang H, Liu Z, Zhao G. Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks ( Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes. FRONTIERS IN PLANT SCIENCE 2017; 8:816. [PMID: 28579999 PMCID: PMC5437370 DOI: 10.3389/fpls.2017.00816] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/01/2017] [Indexed: 05/04/2023]
Abstract
Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species (Quercus rubra and Castanea mollissima) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in Quercus subgenus Quercus, a diverse species group without sufficient molecular differentiation. With the comparison, nine and 14 plastid markers were selected as barcoding and phylogeographic candidates for the Chinese oaks. Five (psbA-trnH, matK-trnK, ycf3-trnS, matK, and ycf1) of the nine plastid candidate barcodes, with the addition of newly designed ITS and a single-copy nuclear gene (SAP), were then tested on 35 Chinese oak species employing four different barcoding approaches (genetic distance-, BLAST-, character-, and tree-based methods). The four methods showed different species identification powers with character-based method performing the best. Of the seven barcodes tested, a barcoding gap was absent in all of them across the Chinese oaks, while ITS and psbA-trnH provided the highest species resolution (30.30%) with the character- and BLAST-based methods, respectively. The six-marker combination (psbA-trnH + matK-trnK + matK + ycf1 + ITS + SAP) showed the best species resolution (84.85%) using the character-based method for barcoding the Chinese oaks. The barcoding results provided additional implications for taxonomy of the Chinese oaks in subg. Quercus, basically identifying three major infrageneric clades of the Chinese oaks (corresponding to Groups Quercus, Cerris, and Ilex) referenced to previous phylogenetic classification of Quercus. While the morphology-based allocations proposed for the Chinese oaks in subg. Quercus were challenged. A low variation rate of the chloroplast genome, and complex speciation patterns involving incomplete lineage sorting, interspecific hybridization and introgression, possibly have negative impacts on the species assignment and phylogeny of oak species.
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Affiliation(s)
- Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Lucía Vázquez
- Biology Department, University of Illinois at SpringfieldSpringfield, IL, United States
| | - Xiaodan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Huimin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Hao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Zhanlin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
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Sun S, Li Q, Kong L, Yu H, Zheng X, Yu R, Dai L, Sun Y, Chen J, Liu J, Ni L, Feng Y, Yu Z, Zou S, Lin J. DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs. Sci Rep 2016; 6:33367. [PMID: 27640675 PMCID: PMC5027561 DOI: 10.1038/srep33367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/25/2016] [Indexed: 11/26/2022] Open
Abstract
This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes.
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Affiliation(s)
- Shao’e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ruihai Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lina Dai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yan Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Chen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lehai Ni
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yanwei Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhenzhen Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shanmei Zou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jiping Lin
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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18
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Falade MO, Opene AJ, Benson O. DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria. F1000Res 2016; 5:1268. [PMID: 27990256 PMCID: PMC5133684 DOI: 10.12688/f1000research.7895.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/20/2022] Open
Abstract
DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5' region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodonmelanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.
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Affiliation(s)
- Mofolusho O. Falade
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Anthony J. Opene
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Otarigho Benson
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
- Department of Biological Science, Edo University, Iyamho, Edo State, Nigeria
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Zou S, Li Q. Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:327-335. [PMID: 26899167 DOI: 10.1007/s10126-016-9692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
With the global biodiversity crisis, DNA barcoding aims for fast species identification and cryptic species diversity revelation. For more than 10 years, large amounts of DNA barcode data have been accumulating in publicly available databases, most of which were conducted by distance or tree-building methods that have often been argued, especially for cryptic species revelation. In this context, overlooked cryptic diversity may exist in the available barcoding data. The character-based DNA barcoding, however, has a good chance for detecting the overlooked cryptic diversity. In this study, marine mollusk was as the ideal case for detecting the overlooked potential cryptic species from existing cytochrome c oxidase I (COI) sequences with character-based DNA barcode. A total of 1081 COI sequences of mollusks, belonging to 176 species of 25 families of Gastropoda, Cephalopoda, and Lamellibranchia, were conducted by character analysis. As a whole, the character-based barcoding results were consistent with previous distance and tree-building analysis for species discrimination. More importantly, quite a number of species analyzed were divided into distinct clades with unique diagnostical characters. Based on the concept of cryptic species revelation of character-based barcoding, these species divided into separate taxonomic groups might be potential cryptic species. The detection of the overlooked potential cryptic diversity proves that the character-based barcoding mode possesses more advantages of revealing cryptic biodiversity. With the development of DNA barcoding, making the best use of barcoding data is worthy of our attention for species conservation.
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Affiliation(s)
- Shanmei Zou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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Zou S, Fei C, Song J, Bao Y, He M, Wang C. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta). PLoS One 2016; 11:e0153833. [PMID: 27092945 PMCID: PMC4841637 DOI: 10.1371/journal.pone.0153833] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/13/2016] [Indexed: 01/19/2023] Open
Abstract
Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.
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Affiliation(s)
- Shanmei Zou
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Cong Fei
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiameng Song
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yachao Bao
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Meilin He
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Changhai Wang
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
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21
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DNA barcoding of genus Metapenaeopsis (Decapoda: Penaeidae) and molecular phylogeny inferred from mitochondrial and nuclear DNA sequences. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Kumar PS, Kumar DS, Umamaheswari S. A perspective on toxicology of Conus venom peptides. ASIAN PAC J TROP MED 2015; 8:337-51. [PMID: 26003592 DOI: 10.1016/s1995-7645(14)60342-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The evolutionarily unique and ecologically diverse family Conidae presents fundamental opportunities for marine pharmacology research and drug discovery. The focus of this investigation is to summarize the worldwide distribution of Conus and their species diversity with special reference to the Indian coast. In addition, this study will contribute to understanding the structural properties of conotoxin and therapeutic application of Conus venom peptides. Cone snails can inject a mix of various conotoxins and these venoms are their major weapon for prey capture, and may also have other biological purposes, and some of these conotoxins fatal to humans. Conus venoms contain a remarkable diversity of pharmacologically active small peptides; their targets are an iron channel and receptors in the neuromuscular system. Interspecific divergence is pronounced in venom peptide genes, which is generally attributed to their species specific biotic interactions. There is a notable interspecific divergence observed in venom peptide genes, which can be justified as of biotic interactions that stipulate species peculiar habitat and ecology of cone snails. There are several conopeptides used in clinical trials and one peptide (Ziconotide) has received FDA approval for treatment of pain. This perspective provides a comprehensive overview of the distribution of cone shells and focus on the molecular approach in documenting their taxonomy and diversity with special reference to geographic distribution of Indian cone snails, structure and properties of conopeptide and their pharmacological targets and future directions.
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Affiliation(s)
| | - Dhanabalan Senthil Kumar
- Department of Zoology, Kandaswami Kandar College, Paramathi Velur-638 182, Namakkal, Tamil Nadu, India
| | - Sundaresan Umamaheswari
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchurapalli, Tamil Nadu 620024, India
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23
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Zielske S, Haase M. Molecular phylogeny and a modified approach of character-based barcoding refining the taxonomy of New Caledonian freshwater gastropods (Caenogastropoda, Truncatelloidea, Tateidae). Mol Phylogenet Evol 2015; 89:171-81. [PMID: 25929789 DOI: 10.1016/j.ympev.2015.04.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/11/2015] [Accepted: 04/21/2015] [Indexed: 11/26/2022]
Abstract
The islands of New Caledonia represent one of the world's biodiversity hotspots with many endemic species including freshwater gastropods of the family Tateidae. A phylogenetic analysis based on the mitochondrial COI and 16S rRNA and the nuclear ITS2 genes revealed two cryptic genera, Crosseana gen. n. and Novacaledonia gen. n. In order to provide character-based diagnoses we modified a DNA barcoding approach identifying strings of pairwise diagnostic characters, i.e. alignment positions, at which two genera are alternatively fixed for different nucleotides. The combination or string of all pairwise diagnostic characters was unique for each genus. Inconsistent mitochondrial and nuclear topologies suggest that Hemistomia cockerelli Haase and Bouchet, 1998 and H. fabrorum Haase and Bouchet, 1998, two morphologically well-defined species, hybridize. The age of the most recent common ancestor of the New Caledonian radiation of Tateidae was estimated at 24.6±9.5 MY. These findings are in line with the notion that New Caledonia is rather a Darwinian island that was colonized after an extended phase of submergence - in case of the tateids probably from Australia - despite being a fragment of Gondwanaland.
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Affiliation(s)
- Susan Zielske
- Vogelwarte, Zoological Institute and Museum, Greifswald University, Soldmannstr. 23, 17489 Greifswald, Germany.
| | - Martin Haase
- Vogelwarte, Zoological Institute and Museum, Greifswald University, Soldmannstr. 23, 17489 Greifswald, Germany.
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24
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Gutiérrez EE, Pine RH. No need to replace an "anomalous" primate (Primates) with an "anomalous" bear (Carnivora, Ursidae). Zookeys 2015; 487:141-54. [PMID: 25829853 PMCID: PMC4366689 DOI: 10.3897/zookeys.487.9176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/13/2015] [Indexed: 11/18/2022] Open
Abstract
By means of mitochondrial 12S rRNA sequencing of putative "yeti", "bigfoot", and other "anomalous primate" hair samples, a recent study concluded that two samples, presented as from the Himalayas, do not belong to an "anomalous primate", but to an unknown, anomalous type of ursid. That is, that they match 12S rRNA sequences of a fossil Polar Bear (Ursusmaritimus), but neither of modern Polar Bears, nor of Brown Bears (Ursusarctos), the closest relative of Polar Bears, and one that occurs today in the Himalayas. We have undertaken direct comparison of sequences; replication of the original comparative study; inference of phylogenetic relationships of the two samples with respect to those from all extant species of Ursidae (except for the Giant Panda, Ailuropodamelanoleuca) and two extinct Pleistocene species; and application of a non-tree-based population aggregation approach for species diagnosis and identification. Our results demonstrate that the very short fragment of the 12S rRNA gene sequenced by Sykes et al. is not sufficiently informative to support the hypotheses provided by these authors with respect to the taxonomic identity of the individuals from which these sequences were obtained. We have concluded that there is no reason to believe that the two samples came from anything other than Brown Bears. These analyses afforded an opportunity to test the monophyly of morphologically defined species and to comment on both their phylogenetic relationships and future efforts necessary to advance our understanding of ursid systematics.
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Affiliation(s)
- Eliécer E. Gutiérrez
- Division of Mammals, National Museum of Natural History, NHB 390, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington DC 20013-7012, USA
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Ronald H. Pine
- Biodiversity Institute & Natural History Museum, University of Kansas, Lawrence, KS 66045 USA
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Yu Z, Li Q, Kong L, Yu H. Utility of DNA barcoding for Tellinoidea: a comparison of distance, coalescent and character-based methods on multiple genes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:55-65. [PMID: 25107691 DOI: 10.1007/s10126-014-9596-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/18/2014] [Indexed: 06/03/2023]
Abstract
DNA barcoding has become a promising tool for rapid species identification using a short fragment of mitochondrial gene. Currently, an increasing number of analytical methods are available to assign DNA barcodes to taxa. The methods can be broadly divided into three main categories: (i) distance-based methods (the classical approach and the automatic barcode gap discovery (ABGD) approach), (ii) coalescent-based methods (the monophyly-based method and the general mixed Yule coalescent (GMYC) model) and (iii) the character-based method (CAOS). This study is set out to evaluate the availability of each method in barcoding Tellinoidea on the cytomchrome c oxidase subunit I (COI) and the 16 small-subunit ribosomal DNA (16S rDNA) genes. As a result, the character-based method was found to be the best in all cases, especially on a genus level. For distance-based methods, the elaborate one gained a success equal or greater than the basic one. The traditional coalescent-based method nicely delimited all of the tellinoideans on a species level. The GMYC model, which is the most radical, clearly inflated the number of species units by 34.6 % for COI gene and by 58.8 % for 16S gene. Thus, we conclude that CAOS better approximates a real barcode, and suggest the use of the ABGD method and the monophyly-based method for primary partitions. Additionally, COI gene may be more suitable as a standard barcode marker than 16S gene, particularly for tree-based methods.
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Affiliation(s)
- Zhenzhen Yu
- The Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, 266003, China
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26
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An K, Cao H, Wang X, Chen H. The subgenusAshima(Diptera, Drosophildae,Phortica) from China, with DNA barcoding and descriptions of three new species. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.968235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Yu Z, Li Q, Kong L. New insight into the phylogeny of Sinonovacula (Bivalvia: Solecurtidae) revealed by comprehensive DNA barcoding analyses of two mitochondrial genes. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1554-7. [PMID: 25186335 DOI: 10.3109/19401736.2014.953135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The present study was undertaken to clarify the genetic relationships of Sinonovacula through comprehensive DNA barcoding analyses of COI and 16S rRNA genes. For both genes, the K2P distances between individuals of Sinonovacula and individuals of other genera belonging to Tellinoidea were much bigger than those between Sinonovacula and genera of Solenoidea. On the Bayesian tree of combined data, Sinonovacula and Cultellus formed a well supports monophylic clade. An extremely high matching rate of CAs between Sinonovacula and the reference family Cultellidae was found. Thus, we suggest transferring Sinonovacula from Solecurtidae to Cultellidae, as a sister group of Cultellus.
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Affiliation(s)
- Zhenzhen Yu
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
| | - Qi Li
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
| | - Lingfeng Kong
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
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28
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Yu H, Kong L, Li Q. Evaluation of the efficacy of twelve mitochondrial protein-coding genes as barcodes for mollusk DNA barcoding. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1336-9. [PMID: 25109631 DOI: 10.3109/19401736.2014.945579] [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] [Indexed: 11/13/2022]
Abstract
In this study, we evaluated the efficacy of 12 mitochondrial protein-coding genes from 238 mitochondrial genomes of 140 molluscan species as potential DNA barcodes for mollusks. Three barcoding methods (distance, monophyly and character-based methods) were used in species identification. The species recovery rates based on genetic distances for the 12 genes ranged from 70.83 to 83.33%. There were no significant differences in intra- or interspecific variability among the 12 genes. The monophyly and character-based methods provided higher resolution than the distance-based method in species delimitation. Especially in closely related taxa, the character-based method showed some advantages. The results suggested that besides the standard COI barcode, other 11 mitochondrial protein-coding genes could also be potentially used as a molecular diagnostic for molluscan species discrimination. Our results also showed that the combination of mitochondrial genes did not enhance the efficacy for species identification and a single mitochondrial gene would be fully competent.
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Affiliation(s)
- Hong Yu
- a The Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
| | - Lingfeng Kong
- a The Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
| | - Qi Li
- a The Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
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29
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Jaén-Molina R, Marrero-Rodríguez Á, Reyes-Betancort JA, Santos-Guerra A, Naranjo-Suárez J, Caujapé-Castells J. Molecular taxonomic identification in the absence of a ‘barcoding gap’: a test with the endemic flora of the Canarian oceanic hotspot. Mol Ecol Resour 2014; 15:42-56. [DOI: 10.1111/1755-0998.12292] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 05/22/2014] [Accepted: 06/04/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Ruth Jaén-Molina
- Jardín Botánico Canario “Viera y Clavijo”-Unidad Asociada CSIC; Cabildo de Gran Canaria; Apartado de correos 14 de Tafira Alta 35017 Las Palmas de Gran Canaria Spain
- Fundación Canaria Amurga Maspalomas; Avda. Tirajana 39, II 6 35100 San Bartolomé de Tirajana Spain
| | - Águedo Marrero-Rodríguez
- Jardín Botánico Canario “Viera y Clavijo”-Unidad Asociada CSIC; Cabildo de Gran Canaria; Apartado de correos 14 de Tafira Alta 35017 Las Palmas de Gran Canaria Spain
| | - J. Alfredo Reyes-Betancort
- Unidad de Botánica Aplicada; Jardín de Aclimatación de La Orotava (ICIA); c/Retama 2 38400 Puerto de la Cruz, Tenerife Spain
| | - Arnoldo Santos-Guerra
- Unidad de Botánica Aplicada; Jardín de Aclimatación de La Orotava (ICIA); c/Retama 2 38400 Puerto de la Cruz, Tenerife Spain
| | - José Naranjo-Suárez
- Jardín Botánico Canario “Viera y Clavijo”-Unidad Asociada CSIC; Cabildo de Gran Canaria; Apartado de correos 14 de Tafira Alta 35017 Las Palmas de Gran Canaria Spain
| | - Juli Caujapé-Castells
- Jardín Botánico Canario “Viera y Clavijo”-Unidad Asociada CSIC; Cabildo de Gran Canaria; Apartado de correos 14 de Tafira Alta 35017 Las Palmas de Gran Canaria Spain
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30
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Wong WH, Tay YC, Puniamoorthy J, Balke M, Cranston PS, Meier R. 'Direct PCR' optimization yields a rapid, cost-effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction. Mol Ecol Resour 2014; 14:1271-80. [PMID: 24816169 DOI: 10.1111/1755-0998.12275] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/05/2014] [Accepted: 05/05/2014] [Indexed: 02/04/2023]
Abstract
Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately, obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short cut to DNA barcoding, that is, a nondestructive PCR method that skips DNA extraction ('direct PCR') and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of nonbiting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g. details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (i) tissue quantity, (ii) body part, (iii) primer pair and (iv) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g. Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands.
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Affiliation(s)
- Wing Hing Wong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
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31
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The Cochlostoma (Holcopoma) westerlundi group in Italy (Caenogastropoda: Cochlostomatidae). Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0372-x] [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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32
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Layton KK, Martel AL, Hebert PDN. Patterns of DNA barcode variation in Canadian marine molluscs. PLoS One 2014; 9:e95003. [PMID: 24743320 PMCID: PMC3990619 DOI: 10.1371/journal.pone.0095003] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/21/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. METHODOLOGY/PRINCIPAL FINDINGS This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%), and showed a significant positive correlation with nearest neighbour distances. CONCLUSIONS/SIGNIFICANCE DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.
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Affiliation(s)
- Kara K.S. Layton
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - André L. Martel
- Research and Collections (Zoology), Canadian Museum of Nature, Gatineau, Quebec, Canada
| | - Paul DN. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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33
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Fan L, Hui JHL, Yu ZG, Chu KH. VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding. Mol Ecol Resour 2014; 14:871-81. [PMID: 24479510 DOI: 10.1111/1755-0998.12235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 12/17/2022]
Abstract
Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.
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Affiliation(s)
- Long Fan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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34
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Malekzadeh-Viayeh R, Pak-Tarmani R, Rostamkhani N, Fontaneto D. Diversity of the rotiferBrachionus plicatilisspecies complex (Rotifera: Monogononta) in Iran through integrative taxonomy. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12106] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - Nasim Rostamkhani
- Department of Biology; Faculty of Sciences; Urmia University; Urmia Iran
| | - Diego Fontaneto
- National Research Council; Institute of Ecosystem Study; I-28922 Verbania Pallanza Italy
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35
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Peters H, O'Leary BC, Hawkins JP, Carpenter KE, Roberts CM. Conus: first comprehensive conservation red list assessment of a marine gastropod mollusc genus. PLoS One 2013; 8:e83353. [PMID: 24376693 PMCID: PMC3871662 DOI: 10.1371/journal.pone.0083353] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/01/2013] [Indexed: 11/18/2022] Open
Abstract
Marine molluscs represent an estimated 23% of all extant marine taxa, but research into their conservation status has so far failed to reflect this importance, with minimal inclusion on the authoritative Red List of the International Union for the Conservation of Nature (IUCN). We assessed the status of all 632 valid species of the tropical marine gastropod mollusc, Conus (cone snails), using Red List standards and procedures to lay the groundwork for future decadal monitoring, one of the first fully comprehensive global assessments of a marine taxon. Three-quarters (75.6%) of species were not currently considered at risk of extinction owing to their wide distribution and perceived abundance. However, 6.5% were considered threatened with extinction with a further 4.1% near threatened. Data deficiency prevented 13.8% of species from being categorised although they also possess characteristics that signal concern. Where hotspots of endemism occur, most notably in the Eastern Atlantic, 42.9% of the 98 species from that biogeographical region were classified as threatened or near threatened with extinction. All 14 species included in the highest categories of Critically Endangered and Endangered are endemic to either Cape Verde or Senegal, with each of the three Critically Endangered species restricted to single islands in Cape Verde. Threats to all these species are driven by habitat loss and anthropogenic disturbance, in particular from urban pollution, tourism and coastal development. Our findings show that levels of extinction risk to which cone snails are exposed are of a similar magnitude to those seen in many fully assessed terrestrial taxa. The widely held view that marine species are less at risk is not upheld.
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Affiliation(s)
- Howard Peters
- Environment Department, University of York, York, United Kingdom
| | - Bethan C O'Leary
- Environment Department, University of York, York, United Kingdom
| | - Julie P Hawkins
- Environment Department, University of York, York, United Kingdom
| | - Kent E Carpenter
- International Union for Conservation of Nature, Global Marine Species Assessment, Biological Sciences, Old Dominion University, Norfolk, Virginia, United States Of America
| | - Callum M Roberts
- Environment Department, University of York, York, United Kingdom
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36
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Cheng R, Zheng X, Ma Y, Li Q. The complete mitochondrial genomes of two octopods Cistopus chinensis and Cistopus taiwanicus: revealing the phylogenetic position of the genus Cistopus within the order Octopoda. PLoS One 2013; 8:e84216. [PMID: 24358345 PMCID: PMC3866134 DOI: 10.1371/journal.pone.0084216] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/13/2013] [Indexed: 11/23/2022] Open
Abstract
In the present study, we determined the complete mitochondrial DNA (mtDNA) sequences of two species of Cistopus, namely C. chinensis and C. taiwanicus, and conducted a comparative mt genome analysis across the class Cephalopoda. The mtDNA length of C. chinensis and C. taiwanicus are 15706 and 15793 nucleotides with an AT content of 76.21% and 76.5%, respectively. The sequence identity of mtDNA between C. chinensis and C. taiwanicus was 88%, suggesting a close relationship. Compared with C. taiwanicus and other octopods, C. chinensis encoded two additional tRNA genes, showing a novel gene arrangement. In addition, an unusual 23 poly (A) signal structure is found in the ATP8 coding region of C. chinensis. The entire genome and each protein coding gene of the two Cistopus species displayed notable levels of AT and GC skews. Based on sliding window analysis among Octopodiformes, ND1 and DN5 were considered to be more reliable molecular beacons. Phylogenetic analyses based on the 13 protein-coding genes revealed that C. chinensis and C. taiwanicus form a monophyletic group with high statistical support, consistent with previous studies based on morphological characteristics. Our results also indicated that the phylogenetic position of the genus Cistopus is closer to Octopus than to Amphioctopus and Callistoctopus. The complete mtDNA sequence of C. chinensis and C. taiwanicus represent the first whole mt genomes in the genus Cistopus. These novel mtDNA data will be important in refining the phylogenetic relationships within Octopodiformes and enriching the resource of markers for systematic, population genetic and evolutionary biological studies of Cephalopoda.
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Affiliation(s)
- Rubin Cheng
- Fisheries College, Ocean University of China, Qingdao, China
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaodong Zheng
- Fisheries College, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- * E-mail:
| | - Yuanyuan Ma
- Fisheries College, Ocean University of China, Qingdao, China
| | - Qi Li
- Fisheries College, Ocean University of China, Qingdao, China
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DNA barcoding of sigmodontine rodents: identifying wildlife reservoirs of zoonoses. PLoS One 2013; 8:e80282. [PMID: 24244670 PMCID: PMC3823626 DOI: 10.1371/journal.pone.0080282] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/11/2013] [Indexed: 11/19/2022] Open
Abstract
Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.
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38
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Jörger KM, Schrödl M. How to describe a cryptic species? Practical challenges of molecular taxonomy. Front Zool 2013; 10:59. [PMID: 24073641 PMCID: PMC4015967 DOI: 10.1186/1742-9994-10-59] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/03/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment' in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and -at least for cryptic species - could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. RESULTS The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type'). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated. CONCLUSIONS To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.
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Affiliation(s)
- Katharina M Jörger
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Michael Schrödl
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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Parmentier I, Duminil J, Kuzmina M, Philippe M, Thomas DW, Kenfack D, Chuyong GB, Cruaud C, Hardy OJ. How effective are DNA barcodes in the identification of African rainforest trees? PLoS One 2013; 8:e54921. [PMID: 23565134 PMCID: PMC3615068 DOI: 10.1371/journal.pone.0054921] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/20/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species. METHODOLOGY/PRINCIPAL FINDINGS We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95-100% success), but less for species identification (71-88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84-90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA. CONCLUSIONS/SIGNIFICANCE Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.
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Affiliation(s)
- Ingrid Parmentier
- Evolutionary Biology and Ecology – Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Jérôme Duminil
- Evolutionary Biology and Ecology – Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- Sub-regional Office for Central Africa, Bioversity International, Yaoundé, Cameroon
| | - Maria Kuzmina
- Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Morgane Philippe
- Evolutionary Biology and Ecology – Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Duncan W. Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - David Kenfack
- Department of Botany, Smithsonian Institution, Washington, D.C., United States of America
| | - George B. Chuyong
- Department of Plant and Animal Sciences, University of Buea, Buea, Cameroon
| | - Corinne Cruaud
- Institut de Génomique – Génoscope, Commissariat à l′énergie atomique et aux énergies alternatives (CEA), Evry, France
| | - Olivier J. Hardy
- Evolutionary Biology and Ecology – Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
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40
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Young MK, McKelvey KS, Pilgrim KL, Schwartz MK. DNA
barcoding at riverscape scales: assessing biodiversity among fishes of the genus
C
ottus
(
T
eleostei) in northern
R
ocky
M
ountain streams. Mol Ecol Resour 2013; 13:583-95. [DOI: 10.1111/1755-0998.12091] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/24/2013] [Accepted: 02/06/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Michael K. Young
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Kevin S. McKelvey
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Kristine L. Pilgrim
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Michael K. Schwartz
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
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Zou S, Li Q, Kong L. Monophyly, distance and character-based multigene barcoding reveal extraordinary cryptic diversity in Nassarius: a complex and dangerous community. PLoS One 2012; 7:e47276. [PMID: 23071774 PMCID: PMC3469534 DOI: 10.1371/journal.pone.0047276] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/10/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Correct identification and cryptic biodiversity revelation for marine organisms are pressing since the marine life is important in maintaining the balance of ecological system and is facing the problem of biodiversity crisis or food safety. DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Nassarius, the common mudsnail, plays an important role in marine environment and has problem in food safety, but the classification of it is quite confused because of the complex morphological diversity. METHODOLOGY/PRINCIPAL FINDINGS Here we report a comprehensive barcoding analysis of 22 Nassarius species. We integrated the mitochondrial and nuclear sequences and the morphological characters to determine 13 Nassarius species studied and reveal four cryptic species and one pair synonyms. Distance, monophyly, and character-based barcoding methods were employed. CONCLUSIONS/SIGNIFICANCE Such successful identification and unexpected cryptic discovery is significant for Nassarius in food safety and species conversation and remind us to pay more attention to the hidden cryptic biodiversity ignored in marine life. Distance, monophyly, and character-based barcoding methods are all very helpful in identification but the character-based method shows some advantages.
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Affiliation(s)
- Shanmei Zou
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
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42
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van Velzen R, Weitschek E, Felici G, Bakker FT. DNA barcoding of recently diverged species: relative performance of matching methods. PLoS One 2012; 7:e30490. [PMID: 22272356 PMCID: PMC3260286 DOI: 10.1371/journal.pone.0030490] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 12/22/2011] [Indexed: 12/23/2022] Open
Abstract
Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.
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Affiliation(s)
- Robin van Velzen
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands.
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