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Tuliebieke T, Abdullah, Zhang H, Yan R, Li H, Zhang Y, Zhang T, Ahmed I, Li T, Tian X. Exploring the biological diversity and source species of medicinal horseflies through metabarcoding. Gene 2024; 913:148356. [PMID: 38462022 DOI: 10.1016/j.gene.2024.148356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/22/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Horseflies from the Tabanidae family play a significant role in traditional Chinese medicine to treat various health conditions, including coronary heart disease, stroke, headaches, liver cirrhosis, psoriasis, and hepatic carcinoma. There are 27 species of Tabaninae (Tabanidae) used as medicine, and they showed high morphological similarities with those for which medicinal properties have not been reported. Nonetheless, there have been reports suggesting that medicinal crude drugs sometimes contain irrelevant or false species, impacting the drug's efficacy. In this current study, we collected 14 batches, totaling 13,528 individuals, from various provinces in China. Instead of "classic" DNA barcoding strategy, we employed a high-throughput metabarcoding approach to assess the biological composition of crude drug mixtures derived from horseflies. Our analysis identified 40 Amplicon Sequence Variants (ASVs) with similarity percentages ranging from 92% to 100% with 12 previously reported species. Species delimitation methods revealed the presence of 11 Molecular Operational Taxonomic Units (MOTUs), with ten belonging to the Tabanus genus and one to Hybomitra. Tabanus sp6 displayed the highest relative abundance, and its ASVs showed close resemblance to Tabanus pleski. Our investigations revealed that the medicinal batches were biologically composed of 6 to 12 species. Some batches contained ASVs that closely resembled species previously associated with false Tabanus species. In conclusion, our findings offer valuable insights into the biological composition of crude drugs derived from horseflies and have the potential to enhance the quality of these traditional medicines.
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Affiliation(s)
- Tenukeguli Tuliebieke
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Abdullah
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
| | - Rushan Yan
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Hui Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Yue Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Tingting Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad 45710, Pakistan; Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards Band Science (KRISS), Daejeon 34113, Republic of Korea.
| | - Tianxiang Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
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2
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Wang HL, Lei T, Wang XW, Cameron S, Navas-Castillo J, Liu YQ, Maruthi MN, Omongo CA, Delatte H, Lee KY, Krause-Sakate R, Ng J, Seal S, Fiallo-Olivé E, Bushley K, Colvin J, Liu SS. A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex, a global pest-species group. INSECT SCIENCE 2024. [PMID: 38562016 DOI: 10.1111/1744-7917.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities. Bemisia tabaci is a cryptic species complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting and delimiting the evolution of this species complex has proved problematic. To develop a comprehensive framework for species delimitation and identification, we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B. tabaci species complex acquired worldwide. Distinct datasets include full mitogenomes, single-copy nuclear genes, restriction site-associated DNA sequencing, geographic range, host speciation, and reproductive compatibility datasets. Phylogenetically, our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B. tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B. tabaci species diversity. Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples. Native geographic range information provides a complementary assessment of species recognition, while the host range datasets provide low rate of delimiting resolution. We further summarized different data performances in species classification when compared with reproductive compatibility, indicating that combination of mtCOI divergence, nuclear markers, geographic range provide a complementary assessment of species recognition. Finally, we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.
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Affiliation(s)
- Hua-Ling Wang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Teng Lei
- College of Life Sciences, Taizhou University, Taizhou, Zhejiang Province, China
| | - Xiao-Wei Wang
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Stephen Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Malaga, Spain
| | - Yin-Quan Liu
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Kent, UK
| | | | - Hélène Delatte
- CIRAD, UMR PVBMT CIRAD, Pôle de Protection des Plantes, Saint-Pierre, France
| | - Kyeong-Yeoll Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | | | - James Ng
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Malaga, Spain
| | - Kathryn Bushley
- USDA Agricultural Research Service, 17123, Emerging Pests and Pathogens Research Unit, Ithaca, NY, USA
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Shu-Sheng Liu
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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3
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Dähn O, Werner D, Mathieu B, Kampen H. Large-Scale Cytochrome C Oxidase Subunit I Gene Data Analysis for the Development of a Multiplex Polymerase Chain Reaction Test Capable of Identifying Biting Midge Vector Species and Haplotypes (Diptera: Ceratopogonidae) of the Culicoides Subgenus Avaritia Fox, 1955. Genes (Basel) 2024; 15:323. [PMID: 38540382 PMCID: PMC10969821 DOI: 10.3390/genes15030323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
The emergence of culicoid-transmitted bluetongue and Schmallenberg viruses in several European countries demonstrated the ability of indigenous biting midge species to transmit pathogens. Entomologic research programs identified members of the Obsoletus Group (Culicoides subgenus Avaritia) as keyplayers in disease epidemiology in Europe. However, morphological identification of potential vectors is challenging due to the recent discovery of new genetic variants (haplotypes) of C. obsoletus sensu stricto (s.s.), forming distinct clades. In this study, 4422 GenBank entries of the mitochondrial cytochrome c oxidase subunit I (COI) gene of subgenus Avaritia members of the genus Culicoides were analyzed to develop a conventional multiplex PCR, capable of detecting all vector species and clades of the Western Palearctic in this subgenus. Numerous GenBank entries incorrectly assigned to a species were identified, analyzed and reassigned. The results suggest that the three C. obsoletus clades represent independent species, whereas C. montanus should rather be regarded as a genetic variant of C. obsoletus s.s. Based on these findings, specific primers were designed and validated with DNA material from field-caught biting midges which achieved very high diagnostic sensitivity (100%) when compared to an established reference PCR (82.6%).
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Affiliation(s)
- Oliver Dähn
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany
| | - Bruno Mathieu
- Institutes of Bacteriology and Parasitology, Medical Faculty, University of Strasbourg, UR 3073 PHAVI, 67000 Strasbourg, France
| | - Helge Kampen
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
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Shin CP, Allmon WD. How we study cryptic species and their biological implications: A case study from marine shelled gastropods. Ecol Evol 2023; 13:e10360. [PMID: 37680961 PMCID: PMC10480071 DOI: 10.1002/ece3.10360] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/10/2023] [Accepted: 07/13/2023] [Indexed: 09/09/2023] Open
Abstract
Methodological and biological considerations are intertwined when studying cryptic species. A potentially large component of modern biodiversity, the frequency of cryptic species among taxonomic groups is not well documented. The term "cryptic species" is imprecisely used in scientific literature, causing ambiguity when interpreting their evolutionary and ecological significance. This study reviews how cryptic species have been defined, discussing implications for taxonomy and biology, and explores these implications with a case study based on recently published literature on extant shelled marine gastropods. Reviewed gastropods were recorded by species. Records of cryptic gastropods were presented by authors with variable levels of confidence but were difficult to disentangle from inherent biases in the study effort. These complexities notwithstanding, most gastropod species discussed were not cryptic. To the degree that this review's sample represents extinct taxa, the results suggest that a high proportion of shelled marine gastropod species are identifiable for study in the fossil record. Much additional work is needed to provide a more adequate understanding of the relative frequency of cryptic species in shelled marine gastropods, which should start with more explicit definitions and targeted case studies.
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Affiliation(s)
- Caren P. Shin
- Department of Earth and Atmospheric SciencesCornell UniversityIthacaNew YorkUSA
- Paleontological Research InstitutionIthacaNew YorkUSA
| | - Warren D. Allmon
- Department of Earth and Atmospheric SciencesCornell UniversityIthacaNew YorkUSA
- Paleontological Research InstitutionIthacaNew YorkUSA
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5
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Adyrbekova K, Isbekov KB, Barakbayev TT, Iskhakhov GZ. Current State of Rare and Endangered Barbels of the Genus Luciobarbus Heckel, 1843 in the Aral-Syrdarya Basin (Kazakhstan) and Prospects for Their Conservation (A Review). BIOLOGY 2023; 12:biology12040489. [PMID: 37106690 PMCID: PMC10136032 DOI: 10.3390/biology12040489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/29/2023]
Abstract
The current status of the barbels inhabiting the Kazakhstan section of the Syrdarya River needs special study, as has been noted since the second half of the 20th century. Stocks of commercial fish valuable in the past as barbels in the Aral-Syrdarya basin are now catastrophically reduced as a result of anthropogenic impact on the ichthyofauna and natural environment of the Aral Sea region. The study of the condition; abundance and distribution range is necessary to determine measures for their restoration in natural habitats and their breeding in fish farms. Research on the biotechnology of barbel breeding with subsequent acclimatization and reacclimatization of these fish species will not only improve the composition of the ichthyofauna of the Aral-Syrdarya basin, but also preserve the genetic potential of natural populations. At present, the only way to restore the population of the Aral barbel is stocking hatchery reared juveniles in natural environments. Under the current situation, a way forward is seen in the creation of domesticated replacement-broodstocks of barbels. As a result of the influence of anthropogenic factors, the populations of this species have come to almost complete degradation and depletion and require the development and adoption of urgent measures for their conservation and restoration through reintroduction, which is a priority and urgent task for the fisheries of the republic.
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Affiliation(s)
- Kamila Adyrbekova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Fisheries Research and Production Center LLP, Almaty 100141, Kazakhstan
| | - Kuanysh B Isbekov
- Fisheries Research and Production Center LLP, Almaty 100141, Kazakhstan
| | - Tynysbek T Barakbayev
- Aral Branch of Fisheries Research and Production Center LLP, Kyzylorda 000090, Kazakhstan
| | - Galymzhan Zh Iskhakhov
- Aral Branch of Fisheries Research and Production Center LLP, Kyzylorda 000090, Kazakhstan
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6
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Species-specific molecular signatures for the commercially important scombrids using mitochondrial gene analysis; a tool for fisheries management. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2022. [DOI: 10.1016/j.japb.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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7
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Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years. J Fungi (Basel) 2022; 8:jof8080803. [PMID: 36012792 PMCID: PMC9410331 DOI: 10.3390/jof8080803] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique (RAPD, AFLP, ISSR, VNTR, SNP, InDels, and DNA barcoding); (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification.
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8
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Yu XQ, Jiang YZ, Folk RA, Zhao JL, Fu CN, Fang L, Peng H, Yang JB, Yang SX. Species discrimination in Schima (Theaceae): Next-generation super-barcodes meet evolutionary complexity. Mol Ecol Resour 2022; 22:3161-3175. [PMID: 35789203 DOI: 10.1111/1755-0998.13683] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022]
Abstract
Plastid genome and nrDNA arrays, proposed recently as "super barcodes", might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super barcodes. In this study, we generated multiple datasets comprising standard DNA barcodes (matK, rbcL, trnH-psbA, nrITS) and super-barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned datasets-the lowest estimated rate of super barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization, or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multi-locus nuclear markers for species discrimination in plant groups.
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Affiliation(s)
- Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | - Yin-Zi Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences.,College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, 39762, MS, United States
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | - Liang Fang
- College of Life Sciences, Jiujiang University, 332000, Jiujiang, Jiangxi, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Shi-Xiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
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9
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Fernandez Goya L, Lanteri AA, Confalonieri VA, Rodriguero MS. New host-parasitoid interactions in Naupactus cervinus (Coleoptera, Curculionidae) raise the question of Wolbachia horizontal transmission. Symbiosis 2022. [DOI: 10.1007/s13199-022-00838-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Agnihotri R, Sharma MP, Bucking H, Dames JF, Bagyaraj DJ. Methods for assessing the quality of AM fungal bio-fertilizer: Retrospect and future directions. World J Microbiol Biotechnol 2022; 38:97. [PMID: 35478267 DOI: 10.1007/s11274-022-03288-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/12/2022] [Indexed: 11/28/2022]
Abstract
In the recent past, the mass production of arbuscular mycorrhizal (AM) fungi has bloomed into a large biofertilizer industry. Due to their obligate symbiotic nature, these fungi are propagated on living roots in substrate-based pot cultures and RiTDNA in in vitro or root organ culture systems. The quality assessment of AM inocula remains critical for the production and efficacy evaluation of AM fungi. The vigour of AM inocula are assessed through microscopic methods such as inoculum potential, infectivity potential/infection units, most probable number (MPN) and spore density. These methods marginally depend on the researcher's skill. The signature lipids specific to AM fungi, e.g. 16:1ω5cis ester-linked, phospholipid, and neutral lipid fatty acids provide more robustness and reproducibility. The quantitative real-time PCR of AM fungal taxa specific primers and probes analyzing gene copy number is also increasingly used. This article intends to sensitize AM fungal researchers and inoculum manufacturers to various methods of assessing the quality of AM inocula addressing their merits and demerits. This will help AM producers to fulfil the regulatory requirements ensuring the supply of high-quality AM inocula to end-users, and tap a new dimension of AM research in the commercial production of AM fungi and its application in sustainable plant production systems.
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Affiliation(s)
- R Agnihotri
- ICAR-Indian Institute of Soybean Research, 452001, Indore, India.,M S Swaminathan Research Foundation (MSSRF), Thondamanatham post, Vazhuthavoor road, 605502, Pillaiyarkuppam, Puducherry, India
| | - M P Sharma
- ICAR-Indian Institute of Soybean Research, 452001, Indore, India.
| | - H Bucking
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, 65211, Columbia, Missouri, USA
| | - J F Dames
- Department of Biochemistry and Microbiology, Rhodes University, 6140, Makhanda, Grahamstown, South Africa
| | - D J Bagyaraj
- Centre for Natural Biological Resources and Community Development, 41 RBI Colony, Anand Nagar, 560024, Bengaluru, India.
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11
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Yang X, Yu X, Zhang X, Guo H, Xing Z, Xu L, Wang J, Shen Y, Yu J, Lv P, Wang Y, Liu M, Tian X. Development of Mini-Barcode Based on Chloroplast Genome and Its Application in Metabarcoding Molecular Identification of Chinese Medicinal Material Radix Paeoniae Rubra (Chishao). FRONTIERS IN PLANT SCIENCE 2022; 13:819822. [PMID: 35432422 PMCID: PMC9009180 DOI: 10.3389/fpls.2022.819822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Radix Paeoniae Rubra (Chishao), a typical multi-origin Chinese medicinal material, originates from the dried roots of Paeonia lactiflora or P. veitchii. The previous study suggested that these two commonly used Chishao showed variation in their chemical compositions and clinical efficacies. Therefore, accurate identification of different Chishao species was of great significance for the guide of clinical medication, and timely treatment of patients. In this study, the chloroplast genome sequences of P. lactiflora and P. veitchii were obtained by next-generation sequencing (NGS) technology, and then the hypervariable regions were selected to design two mini-barcode candidates for species identification. Combined with DNA metabarcoding technology, we performed qualitative and quantitative analysis on the artificially mixed samples of P. lactiflora and P. veitchii and evaluated the identification ability of these mini-barcode candidates. Furtherly, the mini-barcode with good performance was applied to distinguish the Chinese patent medicine "cerebral thrombosis tablets" containing Chishao. The results indicated that the chloroplast genomes of P. lactiflora and P. veitchii were 152,750 and 152,527 bp, respectively. As published previously, they exhibited a typical quadripartite structure including a large single-copy region (LSC), a small single-copy region (SSC) and a pair of inverted repeat regions (IRs). The nucleotide polymorphism analysis revealed seven variable protein-coding regions as petL, psaI, psbJ, rpl16, ycf1b, psaC, and ndhF, and two mini-barcodes were developed from ycf1b and ndhF respectively. The result suggested that both two mini-barcodes performed well distinguishing P. lactiflora from P. veitchii. Besides, P. lactiflora was the only raw material of Chishao in all collected "cerebral thrombosis tablets" samples. In general, this study has established a method to realize the qualitative and quantitative identification of Chishao as multi-origin Chinese medicinal materials, which can be applied to Chinese patent medicines containing Chishao.
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Affiliation(s)
- Xia Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaolei Yu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoying Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hua Guo
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhimei Xing
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Liuwei Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jia Wang
- Tianjin Tongrentang Group Co., Ltd., Tianjin, China
| | - Yuyan Shen
- Tianjin Tongrentang Group Co., Ltd., Tianjin, China
| | - Jie Yu
- Tianjin Tongrentang Group Co., Ltd., Tianjin, China
| | - Pengfei Lv
- Tianjin Tongrentang Group Co., Ltd., Tianjin, China
| | - Yuefei Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Mengyang Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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12
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Tsoupas A, Papavasileiou S, Minoudi S, Gkagkavouzis K, Petriki O, Bobori D, Sapounidis A, Koutrakis E, Leonardos I, Karaiskou N, Triantafyllidis A. DNA barcoding identification of Greek freshwater fishes. PLoS One 2022; 17:e0263118. [PMID: 35081163 PMCID: PMC8791500 DOI: 10.1371/journal.pone.0263118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.
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Affiliation(s)
- Alexandros Tsoupas
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Papavasileiou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Styliani Minoudi
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Olga Petriki
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Bobori
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail: (DB); (AT)
| | - Argyrios Sapounidis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Emmanouil Koutrakis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, Laboratory of Zoology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Nikoleta Karaiskou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
- * E-mail: (DB); (AT)
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13
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Gao J, Ke H, Wang Y, Tan W, Lin C. Characterization of the complete mitochondrial genome of Congrogadus subducens (Richardson, 1843). Mitochondrial DNA B Resour 2022; 7:255-256. [PMID: 35087947 PMCID: PMC8788349 DOI: 10.1080/23802359.2022.2026830] [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] [Indexed: 11/13/2022] Open
Abstract
The complete mitochondrial genome of Congrogadus subducens is first presented in this study. The whole mitogenome is a closed circular molecule of 16,881 bp in size, including 13 protein-coding, 22 transfer RNA, 2 ribosomal RNA genes and a non-coding control region. The overall base composition of the mitochondrial DNA is 30.2% for A, 28.6% for T, 26.4% for C and 14.8% for G. The phylogenetic analysis conducted using 18 protein-coding genes showed that C. subducens was most closely related to the Pseudochromidae. This work will be useful for further research on species identification and evolutionary relationships within related species.
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Affiliation(s)
- Jin Gao
- Ministry of Education, Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Sanya, China
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Hongji Ke
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Yongbo Wang
- Ministry of Education, Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Sanya, China
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Wei Tan
- Ministry of Education, Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Sanya, China
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Chuan Lin
- Department of Animal Cultivation, Hainan Agriculture School, Haikou, China
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14
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DNA barcoding of yellow croakers (Larimichthys spp.) and morphologically similar fish species for authentication. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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15
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Muñoz-Tebar N, González-Navarro EJ, López-Díaz TM, Santos JA, de Elguea-Culebras GO, García-Martínez MM, Molina A, Carmona M, Berruga MI. Biological Activity of Extracts from Aromatic Plants as Control Agents against Spoilage Molds Isolated from Sheep Cheese. Foods 2021; 10:1576. [PMID: 34359446 PMCID: PMC8303263 DOI: 10.3390/foods10071576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of this work was to assess the antifungal and antioxidant activity of essential oils and ethanolic extracts from distilled solid by-products from aromatic plants (Artemisia dracunculus, Hyssopus officinalis, Lavandula stoechas, Origanum vulgare and Satureja montana) against 14 fungi strains isolated from sheep cheese and identified at species level using DNA barcoding based on β-tubulin sequence analysis. In addition, capacity of fungi to produce ochratoxin A, patulin, cyclopiazonic acid and sterigmatocystin was analyzed. Of the isolates, 85.7% belonged to Penicillium (P. commune/biforme, P. crustosum) and 14.3% to Aspergillus (A. puulaauensis and A. jensenii), the first time that these Aspergillus species have been found in sheep's cheese. All P. commune isolates were producers of cyclopiazonic acid, and the two Aspergillus strains produced sterigmatocystin, but the others did not produce any tested mycotoxin. Among the essential oils tested, oregano, savory and tarragon had a significant antifungal activity against all the isolated strains, but no ethanolic extract showed antifungal activity. By contrast, ethanolic extracts showed great potential as antioxidants. The identification of new molds in cheese will help the dairy industry to know more about those molds affecting the sector, and the use of aromatic plants in the control of fungal spoilage could be a suitable alternative to chemical preservatives used in the agri-food industry.
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Affiliation(s)
- Nuria Muñoz-Tebar
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
| | - Emilio J. González-Navarro
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
| | - Teresa María López-Díaz
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (T.M.L.-D.); (J.A.S.)
| | - Jesús A. Santos
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (T.M.L.-D.); (J.A.S.)
| | | | - M. Mercedes García-Martínez
- Catedra de Química Agrícola, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain;
| | - Ana Molina
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
| | - Manuel Carmona
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
| | - María Isabel Berruga
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
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16
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Ge Y, Xia C, Wang J, Zhang X, Ma X, Zhou Q. The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates. Ecol Evol 2021; 11:5669-5681. [PMID: 34026038 PMCID: PMC8131818 DOI: 10.1002/ece3.7470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.
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Affiliation(s)
- Yihao Ge
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Chengxing Xia
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Jun Wang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Xiujie Zhang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Xufa Ma
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
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17
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Pereira LHG, Castro JRC, Vargas PMH, Gomez JAM, Oliveira C. The use of an integrative approach to improve accuracy of species identification and detection of new species in studies of stream fish diversity. Genetica 2021; 149:103-116. [PMID: 33877495 DOI: 10.1007/s10709-021-00118-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/05/2021] [Indexed: 11/26/2022]
Abstract
In this study, we made an inventory of the stream and headwater ichthyofauna of the left bank of the Itaipu Dam Reservoir, located in the lower part of the Upper Paraná River basin, using an integrative approach of molecular and morphological data. The area is located in the western portion of the Paraná state in Brazil, in an area of about 8,000 km2 highly impacted by deforestation and intensive agriculture. For taxonomic identification of species, we used an identification key combined with the DNA barcoding approach. We found 48 species belonging to six orders, 13 families, and 37 genera. The Siluriformes and Characiformes were the most representative orders (75%) and the Characidae was the most representative family (20.8%). Nine species prevailed in this region, making up to 86% of all specimens collected. The integrative approach proved to be useful by allowing the unambiguous identification of all species, including those cases in which morphological characters were not conclusive for species identification, cases of cryptic species, and species with high morphological plasticity. In addition, the integrative approach highlighted six to 13 new putative species depending on the approach considered. Our study provides a relevant contribution to the knowledge of fish diversity in a poorly studied area of the Paraná River basin. We showed that the use of an integrative approach in inventory studies improves species identification and the discovery of new, cryptic, and overlooked species, being a powerful and necessary tool to quantify biodiversity.
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Affiliation(s)
- Luiz Henrique Garcia Pereira
- Laboratório de Biodiversidade e Ecologia Molecular, Instituto Latino-Americano de Ciências da Vida e da Natureza - ILACVN, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brasil.
| | - Jerson Rogelio Chanchay Castro
- Laboratório de Biodiversidade e Ecologia Molecular, Instituto Latino-Americano de Ciências da Vida e da Natureza - ILACVN, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brasil
| | - Pilar Mireya Huatatoca Vargas
- Laboratório de Biodiversidade e Ecologia Molecular, Instituto Latino-Americano de Ciências da Vida e da Natureza - ILACVN, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brasil
| | - Jose Alejandro Morales Gomez
- Laboratório de Biodiversidade e Ecologia Molecular, Instituto Latino-Americano de Ciências da Vida e da Natureza - ILACVN, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brasil
| | - Claudio Oliveira
- Departamento de Biologia estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho - UNESP, Botucatu, SP, Brasil
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18
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Gonçalves LT, Bianchi FM, Deprá M, Calegaro-Marques C. Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda. Genome 2021; 64:705-717. [PMID: 33460338 DOI: 10.1139/gen-2020-0140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.
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Affiliation(s)
- Leonardo Tresoldi Gonçalves
- Laboratório de Helmintologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Filipe Michels Bianchi
- Laboratório de Entomologia Sistemática, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Laboratório de Drosophila, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cláudia Calegaro-Marques
- Laboratório de Helmintologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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19
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Yang X, Lian Y, Chen M, Li X, Yu D. Characterization and phylogenetic analysis of the complete mitochondrial genome of sun loach ( Yasuhikotakia eos). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:13-14. [PMID: 33490587 PMCID: PMC7801111 DOI: 10.1080/23802359.2020.1842263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complete mitochondrial genome of the sun loach (Yasuhikotakia eos) was determined based on Illumina data in this study. The result showed that the closed double-stranded circular mitogenome was 16,738 bp in total length (GenBank accession number: MT800510) with 58.41% AT. The mitochondrial DNA consisted of 13 protein-coding genes (PGCs), 22 transfer RNA (tRNA) genes, 2 ribosomal (rRNA) genes, and 1 non-coding control region. Phylogenetic analysis suggested that Y. eos was most closely related to its congener Y. modesta. This work provides molecular information for further research on species identification and evolutionary relationships.
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Affiliation(s)
- Xiaoge Yang
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Science, Anqing Normal University, Anqing, PR China
| | - Yuxi Lian
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Science, Anqing Normal University, Anqing, PR China
| | - Minmin Chen
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Science, Anqing Normal University, Anqing, PR China
| | - Xuequn Li
- Cambodian First Unite Construction Group, Phnom Penh, Cambodia
| | - Daoping Yu
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Science, Anqing Normal University, Anqing, PR China
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20
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Ortiz D, Pekár S, Bilat J, Alvarez N. Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider. Mol Phylogenet Evol 2020; 154:106997. [PMID: 33164854 DOI: 10.1016/j.ympev.2020.106997] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Julia Bilat
- Geneva Natural History Museum, Geneva, Switzerland
| | - Nadir Alvarez
- Geneva Natural History Museum, Geneva, Switzerland; Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
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21
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Molecular and morphometric divergence of four species of butterflies (Nymphalidae and Pieridae) from the Western Himalaya, India. Mol Biol Rep 2020; 47:8687-8699. [PMID: 33070284 DOI: 10.1007/s11033-020-05913-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/10/2020] [Indexed: 10/23/2022]
Abstract
Morphometric and molecular divergence among four butterfly species of the families Nymphalidae and Pieridae from the western Himalaya region were investigated using molecular tools, traditional morphometric measures and a truss network system. The considered species were Danaus chrysippus, Vanessa cardui, Pieris brassicae and Pieris canidia. Traditional taxonomy is sometimes unable to discriminate cryptic species or species that have close morphological features. Although taxonomists carefully examine external body features to differentiate the species; however, there is a risk for misidentification during a visual assessment of cryptic species. Therefore, we aimed to use the truss network system of 14 morphological landmarks interconnected to yield 90 variables about molecular taxonomy. Principal component analysis (PCA), discriminant function analysis (DFA) and cluster analysis (CA) were employed to determine morphometric variations. In the traditional analysis, 79, 68, 16 and 5 characters out of 90 were found significant (p < 0.05) for D. chrysippus, V. cardui, P. brassicae and P. canidia, respectively. One to seven principal components were extracted through PCA; they explained 87.5-100% of the total variance in samples. Notably, DFA correctly classified 100% of the original grouped cases and 100% of the cross-validated grouped cases. However, the variations were not the same for the two different methods (truss and traditional) employed for the analysis. We correctly identified all the species; the interspecies sequence divergence was between 0.1034 and 0.1398, and the intra-species sequence divergence range was 0.0001 to 0.0128 using the Cytochrome c oxidase subunit-I (COI) gene. The present study provides useful information about the application and complementary role of traditional with truss morphometric analysis for the precise identification and classification of the selected species.
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22
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Mori C, Matsumura S. Current issues for mammalian species identification in forensic science: a review. Int J Legal Med 2020; 135:3-12. [PMID: 32562039 DOI: 10.1007/s00414-020-02341-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022]
Abstract
Mammalian species identification is one of the important issues in forensic science. Determining the origins of non-human biological material found at crime scenes can increase the possibility of identifying the true culprit by narrowing down the range of suspects. Although many techniques based on mitochondrial DNA (mtDNA) have been developed, challenges remain to cost-effectively identify species from degraded samples containing a mixture of DNA from multiple species and to standardize procedures for mammalian species identification. This review evaluates the reliability and versatility of mtDNA-based techniques to reveal obstacles to the establishment of standard analytical methods, with a particular focus on DNA mixtures. When samples contain a mixture of DNA from multiple species, the interpretation of sequencing analysis results is difficult. Although DNA metabarcoding using next-generation sequencing (NGS) technologies can overcome the DNA mixture problem, DNA metabarcoding is not suitable for the type of small-scale analysis routinely performed by local forensic laboratories, primarily because it is costly and time-consuming. By contrast, fluorescent multiplex PCR analysis enables cost-effective and simultaneous species identification from suboptimal samples, although the number of identifiable species is currently limited in comparison with sequencing techniques. The advantages and limitations of current techniques presented in this review indicate that multiplex PCR analysis will continue to be important for mammalian species identification in forensic casework analysis. Further developments in multiplex PCR analysis that enable the identification of an increased number of species will play a key step for standardization efforts among forensic laboratories.
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Affiliation(s)
- Chikahiro Mori
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Forensic Science Laboratory, Gifu Prefectural Police Headquarters, 2-1-1 Yabutaminami, Gifu, 500-8501, Japan.
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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Genetic diversity of Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni in Shamva district, Zimbabwe: role on intestinal schistosomiasis transmission. Mol Biol Rep 2020; 47:4975-4987. [PMID: 32533403 DOI: 10.1007/s11033-020-05541-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 05/23/2020] [Indexed: 10/24/2022]
Abstract
The fresh water snail Biomphalaria pfeifferi is the intermediate host for Schistosoma mansoni, which causes human intestinal schistosomiasis in Zimbabwe. Despite the medical importance of this intermediate host, there are no current data on its molecular characterization in Zimbabwe. In 2016, human water contact sites were identified in four communities in Madziwa area, Shamva district, Zimbabwe. The survey sites were recorded and mapped using a global positioning system. A 655 bp region of the mitochondrial cytochrome oxidase subunit I gene was amplified in 70 B. pfeifferi snails. The sequence data were analysed to determine the relationships between the individual snails, their inter, intra population diversity and structure. Overall, four unique cox1 haplotypes, with a haplotype diversity of 0.608, were identified in the snails. One haplotype spanned across most of the sites. There was no clear geographical clustering of haplotypes. The mean diversity among the haplotypes was very low (0.009), while the net divergence among the collection sites ranged from 0.000 to 0.026. The diversity within and between the sites was 0.017 and 0.012 respectively. This data advances our knowledge of the understanding of the population structure of B. pfeifferi in Madziwa area, Zimbabwe, with the high occurrence of one haplotype indicating the possibility of a recent bottleneck followed by population expansion. The population genetic structure of B. pfeifferi snails described here has provided an opportunity to investigate the contribution of snail genetics to variation in disease burden; and development of control strategies that exploit genetic differences in susceptibility to parasites.
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Ran K, Li Q, Qi L, Li W, Kong L. Molecular identification of Cerithiidae (Mollusca: Gastropod) in Hainan island, China. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:57-63. [PMID: 32054368 DOI: 10.1080/24701394.2020.1726898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A number of same species of Cerithiidae are morphologically unlike, whereas most of species in the same genus are morphologically similar and just exhibit subtle differences. It is difficult to identify them by morphological methods alone. DNA barcoding is a modern molecular technique that can be used to identify species accurately, and is particularly helpful when distinguishing morphologically similar species. In order to identify species of Cerithiidae using DNA barcoding technology based on mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) genes, this study calculated intraspecific and interspecific genetic distance and constructed the phylogenetic trees. A total of 80 COI and 16S rRNA barcode sequences were obtained from 10 species and 3 genera. Some unknown specimens were further identified and a cryptic species may exist in Cerithium traillii, showing that DNA barcoding technology has the potential to discover new species and cryptic species. The phylogenetic trees revealed that all of the cerithiids could converge upon a monophyly with high support values and two genera (Cerithium and Clypeomorus) maybe support the reclassification. It is necessary for traditional morphological methods to combine with the DNA barcoding for classification and identification of Cerithiidae.
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Affiliation(s)
- Ke Ran
- 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.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lu Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Weidong Li
- College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
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A multigene and morphological analysis expands the diversity of the seabod shrimp Xiphopenaeus Smith, 1869 (Decapoda: Penaeidae), with descriptions of two new species. Sci Rep 2019; 9:15281. [PMID: 31653885 PMCID: PMC6814751 DOI: 10.1038/s41598-019-51484-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/05/2019] [Indexed: 11/09/2022] Open
Abstract
After being stable for nearly a century, the taxonomic history of the genus Xiphopenaeus has been marked by many changes in the last three decades. The taxonomic status of the Atlantic species has a low resolution, and many species are still undefined and grouped as cryptic species. Here we employed an integrative approach to define the species of Xiphopenaeus and the morphological characters needed to differentiate them. We combined the analyses of two molecular markers (COI and 16 S rDNA), scanning electron microscopy and light microscopy. Based on specimens from 17 localities from the Atlantic and Pacific oceans, we detected five divergent genetic groups, three in the Atlantic (A1, A2, A3) and two in the Pacific (P1, P2). Male secondary sexual characters were able to differentiate four out of the five genetic groups. Group A1 corresponds to X. kroyeri, and A2 and A3 correspond to new species. We redescribed the genus and two new species are described and illustrated: Xiphopenaeus dincao nov. sp. (A2) and Xiphopenaeus baueri nov. sp. (A3). Since the holotype of X. riveti was missing and the specimen analysed from group P2 was a female, the status of the species of Xiphopenaeus from the Pacific remains unresolved.
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Thu PT, Huang WC, Chou TK, Van Quan N, Van Chien P, Li F, Shao KT, Liao TY. DNA barcoding of coastal ray-finned fishes in Vietnam. PLoS One 2019; 14:e0222631. [PMID: 31536551 PMCID: PMC6752846 DOI: 10.1371/journal.pone.0222631] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/04/2019] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.
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Affiliation(s)
- Pham The Thu
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Hai Phong, Vietnam
| | - Wen-Chien Huang
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tak-Kei Chou
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Nguyen Van Quan
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Hai Phong, Vietnam
| | - Pham Van Chien
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Hai Phong, Vietnam
| | - Fan Li
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Kwang-Tsao Shao
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Te-Yu Liao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
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Zhang H, Zhang Y, Duan Y. DNA barcoding of Deltocephalus Burmeister leafhoppers (Cicadellidae, Deltocephalinae, Deltocephalini) in China. Zookeys 2019; 867:55-71. [PMID: 31404371 PMCID: PMC6684520 DOI: 10.3897/zookeys.867.35058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/10/2019] [Indexed: 11/25/2022] Open
Abstract
We investigated the feasibility of using the DNA barcode region in identifying Deltocephalus from China. Sequences of the barcode region of the mitochondrial COI gene were obtained for 98 specimens (Deltocephalusvulgaris – 88, Deltocephaluspulicaris – 5, Deltocephalusuncinatus – 5). The average genetic distances among morphological and geographical groups of D.vulgaris ranged from 0.9% to 6.3% and among the three species of Deltocephalus ranged from 16.4% to 21.9% without overlap, which effectively reveals the existence of a “DNA barcoding gap”. It is important to assess the status of these morphological variants and explore the genetic variation among Chinese populations of D.vulgaris because the status of this species has led to taxonomic confusion because specimens representing two distinct morphological variants based on the form of the aedeagus are often encountered at a single locality. Forty-five haplotypes (D.vulgaris – 36, D.pulicaris – 5, D.uncinatus – 4) were defined to perform the phylogenetic analyses; they revealed no distinct lineages corresponding either to the two morphotypes of D.vulgaris or to geographical populations. Thus, there is no evidence that these variants represent genetically distinct species.
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Affiliation(s)
- Hong Zhang
- School of Plant Protection, Anhui Agricultural University, Hefei, Anhui Province 230036, China Anhui Agricultural University Hefei China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi Province 712100, China Northwest A&F University Yangling China
| | - Yani Duan
- School of Plant Protection, Anhui Agricultural University, Hefei, Anhui Province 230036, China Anhui Agricultural University Hefei China
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Wang T, Qi D, Sun S, Liu Z, Du Y, Guo S, Ma J. DNA barcodes and their characteristic diagnostic sites analysis of Schizothoracinae fishes in Qinghai province. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:592-601. [PMID: 30952197 DOI: 10.1080/24701394.2019.1580273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Qinghai-Tibetan Plateau (QTP), the source and upper reaches of many Asian rivers, are crisscrossed by rivers and dotted with lakes. Schizothoracinae fishes, species native to the QTP, are distributed widely through these rivers and lakes. Over the past decades, ecological protection has become increasingly intense. The rapid acquisition of the genetic information and accurate gene sequence database are assumed to play an important role in the conservation of species diversity and biodiversity. In this study, 153 COI sequences (648bp in length) covering 13 species in 8 genera of Schizothoracinae fishes in Qinghai Province were used to determine whether barcode could identify Schizothoracinae species accurately. The average Kimura two parameter (K2P) genetic distances within and among species were 0.35% and 8.83%, respectively. The maximum K2P distance within species was observed in Gymnocypris eckloni (1.36%) while minimum K2P distance among species was observed between Chuanchia labiosa and Schizopygopsis pylzovi (0.23%). Overlaps existed in K2P distance intra- and inter- species based on both the genes. Eleven groups with 9 single-species groups and 2 multi-species groups were identified through Automatic Barcode Gap Discovery System, which were consistent with the overlaps of K2P distance. 96.7% as the accurate ratio for COI barcode was calculated and high solution was observed in the phylogenetic trees based on COI gene and Cyt b gene. Except for the similar results based on two genes above, COI barcode was more economical than Cyt b gene. The SOM model successfully predicted characteristic-diagnostic sites at species level: 36 characteristic-diagnostic sites from eight species, in which 12 from Gmnodiptychus pachycgeilus, 2 from Platypharodon extremus, 7 from Ptychobarbus kaznakovi, 2 from Schizopygopsis anteroventris, 2 from Schizopygopsis malacanthus, 3 from Schizopygopsis malacanthus chengi, 3 from Schizothorax dolichonema and 5 from Schizothorax lantsangensis. Our results show that Schizothoracinae fishes can be identified validly by using COI DNA barcode. Thirty-six characteristic-diagnostic sites were proposed to be applied into works of species identification for the Schizothoracinae fishes in Qinghai Province.
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Affiliation(s)
- Ting Wang
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Desheng Qi
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Shihao Sun
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Zhonghao Liu
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Yurong Du
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Songchang Guo
- c College of Animal Science and Technology , Hunan Agricultural University , Changsha , China
| | - Jianbin Ma
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
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29
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Pârvulescu L. Introducing a new Austropotamobius crayfish species (Crustacea, Decapoda, Astacidae): A Miocene endemism of the Apuseni Mountains, Romania. ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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30
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Ren F, Wang Y, Xu Z, Li Y, Xin T, Zhou J, Qi Y, Wei X, Yao H, Song J. DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae. Ecol Evol 2019; 9:1934-1945. [PMID: 30847083 PMCID: PMC6392370 DOI: 10.1002/ece3.4886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/02/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya-Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA-trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P-distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia-recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well-supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.
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Affiliation(s)
- Feng‐Ming Ren
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Chongqing Institute of Medicinal Plant Cultivation, Research and Utilization on Characteristic Biological Resources of Sichuan and Chongqing Co‐construction LabChinese Medicine Breeding and Evaluation Engineering Technology Research Center of ChongqingChongqingChina
| | - Ying‐Wei Wang
- Beijing Botanical Garden, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Zhi‐Chao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Tian‐Yi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jian‐Guo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yao‐Dong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Xue‐Ping Wei
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jing‐Yuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
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31
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Fotedar S, Lukehurst S, Jackson G, Snow M. Molecular tools for identification of shark species involved in depredation incidents in Western Australian fisheries. PLoS One 2019; 14:e0210500. [PMID: 30633772 PMCID: PMC6329513 DOI: 10.1371/journal.pone.0210500] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/23/2018] [Indexed: 11/19/2022] Open
Abstract
Shark depredation is an issue of concern in some Western Australian recreational and commercial fisheries where it can have economic, social and ecological consequences. Knowledge of the shark species involved is fundamental to developing effective management strategies to mitigate the impacts of depredation. Identification of the species responsible is difficult as direct observation of depredation events is uncommon and evaluating bite marks on fish has a high degree of uncertainty. The use of trace DNA techniques has provided an alternative method for species identification. We demonstrate proof of concept for a targeted DNA barcoding approach to identify shark species using trace DNA found at bite marks on recovered remains of hooked fish. Following laboratory validation, forensic analysis of swabs collected from samples of bitten demersal fish, led to the definitive identification of shark species involved in 100% of the incidences of depredation (n = 16).
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Affiliation(s)
- Seema Fotedar
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
- * E-mail:
| | - Sherralee Lukehurst
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
- Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Gary Jackson
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
| | - Michael Snow
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
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32
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Genotyping confirms significant cannibalism in northern Gulf of Mexico invasive red lionfish, Pterois volitans. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1791-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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33
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Wang L, Wu Z, Liu M, Liu W, Zhao W, Liu H, You F. DNA barcoding of marine fish species from Rongcheng Bay, China. PeerJ 2018; 6:e5013. [PMID: 29967722 PMCID: PMC6022726 DOI: 10.7717/peerj.5013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.
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Affiliation(s)
- Lijuan Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Zhihao Wu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Mengxia Liu
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Wei Liu
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Wenxi Zhao
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Hongjun Liu
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Feng You
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
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Raupach MJ, Hannig K, Moriniére J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae). Zookeys 2018; 759:57-80. [PMID: 29853775 PMCID: PMC5968077 DOI: 10.3897/zookeys.759.24129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.
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Affiliation(s)
- Michael J. Raupach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26111 Oldenburg, Germany
| | | | - Jérôme Moriniére
- Taxonomic coordinator – German Barcode of Life (GBOL), Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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35
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Havemann N, Gossner MM, Hendrich L, Morinière J, Niedringhaus R, Schäfer P, Raupach MJ. From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes. PeerJ 2018; 6:e4577. [PMID: 29736329 PMCID: PMC5936072 DOI: 10.7717/peerj.4577] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/14/2018] [Indexed: 11/20/2022] Open
Abstract
With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.
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Affiliation(s)
- Nadine Havemann
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Lars Hendrich
- Sektion Insecta varia, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Jèrôme Morinière
- Taxonomic coordinator-German Barcode of Life (GBOL), SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Rolf Niedringhaus
- Department of Biology, Earth and Environmental Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany
| | - Peter Schäfer
- B.U.G.S. (Biologische Umwelt-Gutachten Schäfer), Telgte, North-Rhine Westphalia, Germany
| | - Michael J Raupach
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
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Almerón-Souza F, Sperb C, Castilho CL, Figueiredo PICC, Gonçalves LT, Machado R, Oliveira LR, Valiati VH, Fagundes NJR. Molecular Identification of Shark Meat From Local Markets in Southern Brazil Based on DNA Barcoding: Evidence for Mislabeling and Trade of Endangered Species. Front Genet 2018; 9:138. [PMID: 29755504 PMCID: PMC5934587 DOI: 10.3389/fgene.2018.00138] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/03/2018] [Indexed: 11/13/2022] Open
Abstract
Elasmobranchs, the group of cartilaginous fishes that include sharks and rays, are especially vulnerable to overfishing due to low fecundity and late sexual maturation. A significant number of elasmobranch species are currently overexploited or threatened by fisheries activities. Additionally, several recent reports have indicated that there has been a reduction in regional elasmobranch population sizes. Brazil is an important player in elasmobranch fisheries and one of the largest importers of shark meat. However, carcasses entering the shark meat market have usually had their fins and head removed, which poses a challenge to reliable species identification based on the morphology of captured individuals. This is further complicated by the fact that the internal Brazilian market trades several different elasmobranch species under a common popular name: "cação." The use of such imprecise nomenclature, even among governmental agencies, is problematic for both controlling the negative effects of shark consumption and informing the consumer about the origins of the product. In this study, we used DNA barcoding (mtDNA, COI gene) to identify, at the species level, "cação" samples available in local markets from Southern Brazil. We collected 63 samples traded as "cação," which we found to correspond to 20 different species. These included two teleost species: Xiphias gladius (n = 1) and Genidens barbus (n = 6), and 18 species from seven elasmobranch orders (Carcharhiniformes, n = 42; Squaliformes, n = 3; Squatiniformes, n = 2; Rhinopristiformes, n = 4; Myliobatiformes, n = 3; Rajiformes, n = 1; and Torpediniformes, n = 1). The most common species in our sample were Prionace glauca (n = 15) and Sphyrna lewini (n = 14), while all other species were represented by four samples or less. Considering IUCN criteria, 47% of the elasmobranch species found are threatened at the global level, while 53% are threatened and 47% are critically endangered in Brazil. These results underline that labeling the meat of any shark species as "cação" is problematic for monitoring catch allocations from the fishing industry and discourages consumer engagement in conservationist practices through informed decision-making.
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Affiliation(s)
- Fernanda Almerón-Souza
- Laboratório de Genética Médica e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Christian Sperb
- Laboratório de Biologia Molecular, Centro de Ciências da Saúde, Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
| | - Carolina L Castilho
- Laboratório de Biologia Molecular, Centro de Ciências da Saúde, Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
| | - Pedro I C C Figueiredo
- Laboratório de Genética Médica e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Leonardo T Gonçalves
- Laboratório de Genética Médica e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rodrigo Machado
- Laboratório de Biologia Molecular, Centro de Ciências da Saúde, Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
| | - Larissa R Oliveira
- Laboratório de Ecologia de Mamíferos, Centro de Ciências da Saúde, Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
| | - Victor H Valiati
- Laboratório de Biologia Molecular, Centro de Ciências da Saúde, Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
| | - Nelson J R Fagundes
- Laboratório de Genética Médica e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Merten V, Christiansen B, Javidpour J, Piatkowski U, Puebla O, Gasca R, Hoving HJT. Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855) (Mollusca, Ommastrephidae) in the eastern tropical Atlantic. PLoS One 2017; 12:e0189691. [PMID: 29244845 PMCID: PMC5731754 DOI: 10.1371/journal.pone.0189691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 11/30/2017] [Indexed: 11/18/2022] Open
Abstract
In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855) (Cephalopoda, Ommastrephidae) is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding) were combined with stable isotope data (∂15N and ∂13C) of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp.), but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae), crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and nutrients from lower to higher trophic levels may be underestimated and important for understanding how a changing ocean impacts food webs in the eastern Atlantic.
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Affiliation(s)
- Véronique Merten
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- * E-mail:
| | - Bernd Christiansen
- Universität Hamburg, Institute for Hydrobiology and Fishery Sciences, Hamburg, Germany
| | | | - Uwe Piatkowski
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Oscar Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Yu M, Jiao L, Guo J, Wiedenhoeft AC, He T, Jiang X, Yin Y. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. PLANTA 2017; 246:1165-1176. [PMID: 28825134 DOI: 10.1007/s00425-017-2758-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.
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Affiliation(s)
- Min Yu
- 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
| | - 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
| | - Juan Guo
- 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
- Center for Wood Anatomy Research, USDA Forest Service, Forest Products Laboratory, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - 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
| | - Xiaomei Jiang
- 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
| | - 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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Niare S, Almeras L, Tandina F, Yssouf A, Bacar A, Toilibou A, Doumbo O, Raoult D, Parola P. MALDI-TOF MS identification of Anopheles gambiae Giles blood meal crushed on Whatman filter papers. PLoS One 2017; 12:e0183238. [PMID: 28817629 PMCID: PMC5560667 DOI: 10.1371/journal.pone.0183238] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/01/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Identification of the source of mosquito blood meals is an important component for disease control and surveillance. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as an effective tool for mosquito blood meal identification, using the abdomens of freshly engorged mosquitoes. In the field, mosquito abdomens are crushed on Whatman filter papers to determine the host feeding patterns by identifying the origin of their blood meals. The aim of this study was to test whether crushing engorged mosquito abdomens on Whatman filter papers was compatible with MALDI-TOF MS for mosquito blood meal identification. Both laboratory reared and field collected mosquitoes were tested. MATERIAL AND METHODS Sixty Anopheles gambiae Giles were experimentally engorged on the blood of six distinct vertebrate hosts (human, sheep, rabbit, dog, chicken and rat). The engorged mosquito abdomens were crushed on Whatman filter papers for MALDI-TOF MS analysis. 150 Whatman filter papers, with mosquitoes engorged on cow and goat blood, were preserved. A total of 77 engorged mosquito abdomens collected in the Comoros Islands and crushed on Whatman filter papers were tested with MALDI-TOF MS. RESULTS The MS profiles generated from mosquito engorged abdomens crushed on Whatman filter papers exhibited high reproducibility according to the original host blood. The blood meal host was correctly identified from mosquito abdomens crushed on Whatman filter papers by MALDI-TOF MS. The MS spectra obtained after storage were stable regardless of the room temperature and whether or not they were frozen. The MS profiles were reproducible for up to three months. For the Comoros samples, 70/77 quality MS spectra were obtained and matched with human blood spectra. This was confirmed by molecular tools. CONCLUSION The results demonstrated that MALDI-TOF MS could identify mosquito blood meals from Whatman filter papers collected in the field during entomological surveys. The application of MALDI-TOF MS has proved to be rapid and successful, making it a new and efficient tool for mosquito-borne disease surveillance.
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Affiliation(s)
- Sirama Niare
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, AP-HM, IHU Méditerranée Infection, Marseille, France
- Malaria Research and Training Center, DEAP/FMOS, UMI 3189, University of Science, Techniques and Technology, Bamako, Mali
| | - Lionel Almeras
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, AP-HM, IHU Méditerranée Infection, Marseille, France
- Unité de Parasitologie et d’Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Fatalmoudou Tandina
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, AP-HM, IHU Méditerranée Infection, Marseille, France
- Malaria Research and Training Center, DEAP/FMOS, UMI 3189, University of Science, Techniques and Technology, Bamako, Mali
| | - Amina Yssouf
- Malaria Control Program, Moroni, Union of the Comoros
| | - Affane Bacar
- Malaria Control Program, Moroni, Union of the Comoros
| | - Ali Toilibou
- Malaria Control Program, Moroni, Union of the Comoros
| | - Ogobara Doumbo
- Malaria Research and Training Center, DEAP/FMOS, UMI 3189, University of Science, Techniques and Technology, Bamako, Mali
| | - Didier Raoult
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - Philippe Parola
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, AP-HM, IHU Méditerranée Infection, Marseille, France
- * E-mail:
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Ye Z, Vollhardt IMG, Tomanovic Z, Traugott M. Evaluation of three molecular markers for identification of European primary parasitoids of cereal aphids and their hyperparasitoids. PLoS One 2017; 12:e0177376. [PMID: 28562603 PMCID: PMC5451020 DOI: 10.1371/journal.pone.0177376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 04/26/2017] [Indexed: 12/02/2022] Open
Abstract
Aphids are major pests of cereal crops and a suite of hymenopteran primary parasitoids play an important role in regulating their populations. However, hyperparasitoids may disrupt the biocontrol services provided by primary parasitoids. As such, understanding cereal aphid-primary parasitoid-hyperparasitoid interactions is vital for a reliable parasitoid-based control of cereal aphids. For this, the ability to identify the different primary and hyperparasitoid species is necessary. Unfortunately, this is often difficult due to a lack of morphologically diagnostic features. DNA sequence-based species identification of parasitoids can overcome these hurdles. However, comprehensive DNA sequence information is lacking for many of these groups, particularly for hyperparasitoids. Here we evaluate three genes [cytochrome c oxidase subunit I (COI), 16S ribosomal RNA (16S) and 18S ribosomal RNA (18S)] for their suitability to identify 24 species of primary parasitoids and 16 species of hyperparasitoids associated with European cereal aphids. To identify aphelinid primary parasitoid species and hyperparasitoids, we found 16S to be more suitable compared to COI sequences. In contrast, the Aphidiinae are best identified using COI due to better species-level resolution and a more comprehensive DNA sequence database compared to 16S. The 18S gene was better suited for group-specific identification of parasitoids, but did not provide resolution at the species level. Our results provide a DNA sequence database for cereal aphid primary parasitoids and their associated hyperparasitoids in Central Europe, which will allow further improvement of our understanding of cereal aphid-primary parasitoid-hyperparasitoid interactions in relation to aphid biological control.
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Affiliation(s)
- Zhengpei Ye
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
- * E-mail: ,
| | - Ines M. G. Vollhardt
- Agroecology, Department of Crop Sciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Zeljko Tomanovic
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Michael Traugott
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
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Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals. Parasitology 2017; 145:608-621. [PMID: 28534454 DOI: 10.1017/s0031182017000610] [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] [Indexed: 12/16/2022]
Abstract
Despite metabarcoding being widely used to analyse bacterial community composition, its application in parasitological research remains limited. What interest there has been has focused on previously intractable research settings where traditional methods are inappropriate, for example, in longitudinal studies and studies involving endangered species. In settings such as these, non-invasive sampling combined with metabarcoding can provide a fast and accurate assessment of component communities. In this paper we review the use of metabarcoding in the study of helminth communities in wild mammals, outlining the necessary procedures from sample collection to statistical analysis. We highlight the limitations of the metabarcoding approach and speculate on what type of parasitological study would benefit from such methods in the future.
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Ortiz D, Francke OF. Reconciling morphological and molecular systematics in tarantulas (Araneae: Theraphosidae): revision of the Mexican endemic genus Bonnetina. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ernieenor FCL, Ernna G, Mariana A. Phenotypic and genotypic identification of hard ticks of the genus Haemaphysalis (Acari: Ixodidae) in Peninsular Malaysia. EXPERIMENTAL & APPLIED ACAROLOGY 2017; 71:387-400. [PMID: 28409404 PMCID: PMC5437174 DOI: 10.1007/s10493-017-0120-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Morphotaxonomy based on phenotypic traits of immature hard ticks (Acari: Ixodidae) is a skill challenge and has prompted many inexperienced acarologists to adopt DNA-based methods for identifying and discriminating the species. The aim of this study is therefore to utilize COI gene for verifying the morphological status of Haemaphysalis ticks in Peninsular Malaysia. A total of 19 on-host ticks collected from four localities were first identified using specific illustrated taxonomic keys that lead to the genus of Haemaphysalis. Genotypic traits of tick species were then verified molecularly based on cytochrome oxidase subunit I (COI) gene using polymerase chain reaction and direct sequencing. Clustering analysis was carried out by constructing a phylogenetic tree to determine the genetic variation and diversity of local Haemaphysalis ticks. Based on external morphological characterizations, all immature ticks were successfully identified down to the genus level only. Molecular analysis of the genotypic using COI gene revealed 16 individuals (84%) as Haemaphysalis hystricis, and three individuals as H. humerosa with sequence homology of 97-99 and 86-87%, respectively. Haemaphysalis hystricis were clustered in their respective monophyletic group in the phylogeny trees with a bootstrap of 100%. Furthermore, a low intraspecific variation (<0.3%) was observed among Malaysian H. hystricis but high interspecific value (>15%) recorded. This study morphologically and molecularly confirms the presence of H. hystricis in Malaysia and the findings will add value to the existing knowledge in identification of ticks in this country.
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Affiliation(s)
- F C L Ernieenor
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research, Jalan Pahang, 50588, Kuala Lumpur, Malaysia.
| | - G Ernna
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research, Jalan Pahang, 50588, Kuala Lumpur, Malaysia
| | - A Mariana
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research, Jalan Pahang, 50588, Kuala Lumpur, Malaysia
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Wang X, Tu WC, Huang EJ, Chen YH, Chen JH, Yeh WB. Identification of Disease-Transmitting Mosquitoes: Development of Species-Specific Probes for DNA Chip Assay Using Mitochondrial COI and ND2 Genes and Ribosomal Internal Transcribed Spacer 2. JOURNAL OF MEDICAL ENTOMOLOGY 2017; 54:396-402. [PMID: 28028142 DOI: 10.1093/jme/tjw195] [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: 01/23/2016] [Accepted: 10/24/2016] [Indexed: 06/06/2023]
Abstract
Mosquitoes, which transmit infectious diseases, such as malaria and dengue fever, are harmful to human health. Thus, accurate and rapid identification of vectors is a critical step for the control of mosquito-borne diseases. However, phenotypic variations in adults, lack of recognizable features of the immature, and fragility of mosquitoes make identification difficult. Molecular approaches have been widely applied to identify mosquitoes, yet these methods have been focused only on the identification of a few species. This study used sequences of two mitochondrial genes, COI and ND2, and a ribosomal gene, ITS2, to design species-specific probes. Biochips thus developed were able to provide simultaneous identification of nine important medical and veterinary species, including the immature, from genera of Aedes, Anopheles, Armigeres, and Culex. This chip was also applied to samples collected from the field. Despite its inability to resolve the close affinity species of Culex quinquefasciatus and Culex pipiens molestus, pertinent biochips are expected to be applied to a mass screening method.
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Affiliation(s)
- Xi Wang
- International Travel Healthcare Center, 131 Dongjie Rd., Gulou District, Fuzhou, Fujian 350001, China (; )
- Beneficial Insects Institute, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Rd., Cangshan District, Fuzhou, Fujian 350002, China
- Department of Entomology, National Chung Hsing University, 250 Kuo-Kuan Rd., South District, Taichung 40227, Taiwan ( ; ; )
| | - Wu-Chun Tu
- Department of Entomology, National Chung Hsing University, 250 Kuo-Kuan Rd., South District, Taichung 40227, Taiwan (; ; )
| | - En-Jiong Huang
- International Travel Healthcare Center, 131 Dongjie Rd., Gulou District, Fuzhou, Fujian 350001, China (; )
| | - Yen-Hou Chen
- Department of Entomology, National Chung Hsing University, 250 Kuo-Kuan Rd., South District, Taichung 40227, Taiwan (; ; )
| | - Jia-Hua Chen
- Beneficial Insects Institute, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Rd., Cangshan District, Fuzhou, Fujian 350002, China
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, 250 Kuo-Kuan Rd., South District, Taichung 40227, Taiwan (; ; )
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45
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Wang DY, Wang Q, Wang YL, Xiang XG, Huang LQ, Jin XH. Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera. PLoS One 2017; 12:e0170286. [PMID: 28182623 PMCID: PMC5300163 DOI: 10.1371/journal.pone.0170286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/03/2017] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera.
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Affiliation(s)
- De-Yi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Wang
- Baotou Medical College, Donghe District, Baotou City, Inner Mongolia, China
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lu-Qi Huang
- National Resource Centre for Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Menglun, Mengla, Yunnan, China
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Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform. J Clin Microbiol 2017; 55:1011-1024. [PMID: 28179406 DOI: 10.1128/jcm.02084-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based dynamic data network platform.
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Cruaud P, Rasplus JY, Rodriguez LJ, Cruaud A. High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy. Sci Rep 2017; 7:41948. [PMID: 28165046 PMCID: PMC5292727 DOI: 10.1038/srep41948] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 01/03/2017] [Indexed: 11/09/2022] Open
Abstract
Until now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment.
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Affiliation(s)
| | | | - Lillian Jennifer Rodriguez
- INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France
- Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines
| | - Astrid Cruaud
- INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France
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Manawatthana S, Laosinchai P, Onparn N, Brockelman WY, Round PD. Phylogeography of bulbuls in the genus Iole (Aves: Pycnonotidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Abbadi M, Marciano S, Tosi F, De Battisti C, Panzarin V, Arcangeli G, Cattoli G. Species identification of bivalve molluscs by pyrosequencing. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:512-519. [PMID: 27068666 DOI: 10.1002/jsfa.7754] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/23/2016] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The increase in seafood consumption and the presence of different species of bivalves on the global markets has given rise to several commercial frauds based on species substitution. To prevent and detect wilful or unintentional frauds, reliable and rapid techniques are required to identify seafood species in different products. In the present work, a pyrosequencing-based technology has been used for the molecular identification of bivalve species. RESULTS Processed and unprocessed samples of 15 species belonging to the bivalve families Pectinidae, Mytilidae, Donacidae, Ostreidae, Pharide and Veneridae were analysed and correctly identified by the developed pyrosequencing-based method according to the homology between query sequences of the 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase I (COI) genes and their correspondent reference libraries. This technique exhibits great potential in automated and high-throughput processing systems, allowing the simultaneous analysis of 96 samples in shorter execution and turnaround times. CONCLUSIONS The correct identification of all the species shows how useful this technique may prove to differentiate species from different products, providing an alternative, simple, rapid and economical tool to detect seafood substitution frauds. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Miriam Abbadi
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Sabrina Marciano
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Federica Tosi
- National Reference Laboratory for Fish, Molluscs and Crustacean Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, 45011 Adria, Rovigo, Italy
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Cristian De Battisti
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Valentina Panzarin
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Giuseppe Arcangeli
- National Reference Laboratory for Fish, Molluscs and Crustacean Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, 45011 Adria, Rovigo, Italy
| | - Giovanni Cattoli
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
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Rossini BC, Oliveira CAM, de Melo FAG, Bertaco VDA, de Astarloa JMD, Rosso JJ, Foresti F, Oliveira C. Highlighting Astyanax Species Diversity through DNA Barcoding. PLoS One 2016; 11:e0167203. [PMID: 27992537 PMCID: PMC5167228 DOI: 10.1371/journal.pone.0167203] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/10/2016] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions.
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Affiliation(s)
- Bruno César Rossini
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- Instituto de Biotecnologia da UNESP, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- * E-mail:
| | - Carlos Alexandre Miranda Oliveira
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Paraná, Brazil
| | | | - Vinicius de Araújo Bertaco
- Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Juan M. Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan J. Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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