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Trieu LN, Bich TT, Van Ket N, Van Long N. Genetic diversity, variation, and structure of two populations of bigfin reef squid (Sepioteuthis lessoniana d'Orbigny) in Con Dao and Phu Quoc islands, Vietnam. J Genet Eng Biotechnol 2023; 21:116. [PMID: 37955754 PMCID: PMC10643773 DOI: 10.1186/s43141-023-00573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Bigfin squid is one of the economically important seafood resources in Vietnam's fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box-derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. RESULTS Con Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. CONCLUSIONS For the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species.
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Affiliation(s)
- Le Ngoc Trieu
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam.
| | - Thai Thach Bich
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam
| | - Nguyen Van Ket
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam
| | - Nguyen Van Long
- Institute of Oceanography, Vietnam Academy of Science and Technology (VAST), Khanh Hoa, Vietnam
- Graduated University of Science and Technology (GUST), VAST, Ha Noi, Vietnam
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2
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Zhao Y, Fan M, Li H, Cai W. Review of Kissing Bugs (Hemiptera: Reduviidae: Triatominae) from China with Descriptions of Two New Species. INSECTS 2023; 14:insects14050450. [PMID: 37233078 DOI: 10.3390/insects14050450] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/27/2023]
Abstract
Triatominae, the only blood-sucking subfamily in Reduviidae, are the vectors of Chagas disease. The majority of them are distributed in the Americas, while the diversity in China has been underestimated, as only two species have been recorded. Here, we describe two new species from China, Triatoma picta Zhao & Cai sp. nov. and T. atrata Zhao & Cai sp. nov., and provide a redescription of T. sinica Hsiao, 1965, along with remarks on T. rubrofasciata (De Geer, 1773). To facilitate the identification, we include photos, especially of genitalia, as well as a distribution map and a key to Chinese triatomines. We calculated the pairwise genetic distances between 23 Triatoma species, which further supported the validity of these new species. We anticipate that our taxonomic review will be useful for identifying Chinese Triatominae.
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Affiliation(s)
- Yisheng Zhao
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Mingyuan Fan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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KANTOR YURI, ZVONAREVA SOFIA, KRYLOVA ELENA. New species of the genus Astyris (Gastropoda: Neogastropoda: Buccinoidea: Columbellidae) from the vicinity of hydrothermal vents of the Piip Volcano, southwestern Bering Sea. Zootaxa 2023; 5263:441-450. [PMID: 37044976 DOI: 10.11646/zootaxa.5263.3.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Indexed: 04/08/2023]
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4
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An Authentication Survey on Retail Seafood Products Sold on the Bulgarian Market Underlines the Need for Upgrading the Traceability System. Foods 2023; 12:foods12051070. [PMID: 36900583 PMCID: PMC10000581 DOI: 10.3390/foods12051070] [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: 01/26/2023] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Economically motivated or accidental species substitutions lead to economic and potential health damage to consumers with a loss of confidence in the fishery supply chain. In the present study, a three-year survey on 199 retail seafood products sold on the Bulgarian market was addressed to assess: (1) product authenticity by molecular identification; (2) trade name compliance to the list of official trade names accepted in the territory; (3) adherence of the list in force to the market supply. DNA barcoding on mitochondrial and nuclear genes was applied for the identification of whitefish (WF), crustaceans (C) and mollusks (cephalopods-MC; gastropods-MG; bivalves-MB) except for Mytilus sp. products for which the analysis was conducted with a previously validated RFLP PCR protocol. Identification at the species level was obtained for 94.5% of the products. Failures in species allocation were reconducted due to low resolution and reliability or the absence of reference sequences. The study highlighted an overall mislabeling rate of 11%. WF showed the highest mislabeling rate (14%), followed by MB (12.5%), MC (10%) and C (7.9%). This evidence emphasized the use of DNA-based methods as tools for seafood authentication. The presence of non-compliant trade names and the ineffectiveness of the list to describe the market species varieties attested to the need to improve seafood labeling and traceability at the national level.
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Zhang L, Huang YW, Huang JL, Ya JD, Zhe MQ, Zeng CX, Zhang ZR, Zhang SB, Li DZ, Li HT, Yang JB. DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes. Mol Ecol Resour 2023; 23:424-439. [PMID: 36219539 DOI: 10.1111/1755-0998.13719] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 01/04/2023]
Abstract
Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.4% of members of the genus Cymbidium. Sequence-based analyses (barcoding gaps and automatic barcode gap discovery) and tree-based analyses (maximum likelihood, Bayesian inference and multirate Poisson tree processes model) were conducted for species identification of Cymbidium. Our work provides a comprehensive DNA barcode reference library for Cymbidium species identification. The results show that compared with standard DNA barcodes (rbcL + matK) as well as the plastid trnH-psbA, the species identification rate of the plastome increased moderately from 58% to 68%. At the same time, we propose an optimized identification strategy for Cymbidium species. The plastome cannot completely resolve the species identification of Cymbidium, the main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture. To further explore the potential use of nuclear data in identifying species, the Skmer method was adopted and the identification rate increased to 72%. It appears that nuclear genome data have a vital role in species identification and are expected to be used as next-generation nuclear barcodes.
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Affiliation(s)
- Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yi-Wei Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meng-Qing Zhe
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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6
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Liu CK, Lei JQ, Jiang QP, Zhou SD, He XJ. The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus. BMC PLANT BIOLOGY 2022; 22:101. [PMID: 35255817 PMCID: PMC8900453 DOI: 10.1186/s12870-022-03488-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/02/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants. RESULTS In the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum. CONCLUSION The plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.
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Affiliation(s)
- Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jia-Qing Lei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Qiu-Ping Jiang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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7
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Chen Q, Hu H, Zhang D. DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:764255. [PMID: 35283910 PMCID: PMC8914171 DOI: 10.3389/fpls.2022.764255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/21/2022] [Indexed: 05/10/2023]
Abstract
The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.
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Affiliation(s)
- Qi Chen
- College of Pharmacy, Dali University, Dali, China
| | - Haisu Hu
- College of Pharmacy, Dali University, Dali, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, China
- Institute of Materia Medica, Dali University, Dali, China
- *Correspondence: Dequan Zhang,
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8
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Ngwakum BB, Payne RP, Teske PR, Janson L, Kerwath SE, Samaai T. Hundreds of new DNA barcodes for South African sponges. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1915896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Benedicta B. Ngwakum
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Robyn P. Payne
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Liesl Janson
- Department of Forestry, Fisheries and the Environment, Oceans & Coasts Branch, Oceans & Coasts Research, Private Bag X4390, Cape Town, 8001, Western Cape, South Africa
| | - Sven E. Kerwath
- Department of Biological Sciences, University of Cape Town, Private Bag X 3, Rondebosch, Cape Town, 7701, South Africa
- Department of Forestry, Fisheries and the Environment, Fisheries Branch, Fisheries Research, Private Bag X2, Roggebaai, Cape Town, 8012, Western Cape, South Africa
| | - Toufiek Samaai
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, Cape Town, South Africa
- Department of Forestry, Fisheries and the Environment, Oceans & Coasts Branch, Oceans & Coasts Research, Private Bag X4390, Cape Town, 8001, Western Cape, South Africa
- Department of Biological Sciences, University of Cape Town, Private Bag X 3, Rondebosch, Cape Town, 7701, South Africa
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Wang Y, Wang C, Shi J, Yan L, Ge H, Wu L, Yan X, Liu Y, Tang J. The complete mitochondrial genome of Chelidonichthys spinosus (Scorpaeniformes: Triglidae) from Jiangsu Province, China. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:853-854. [PMID: 33796655 PMCID: PMC7971344 DOI: 10.1080/23802359.2021.1885317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In this study, we present the complete mitogenome and a phylogenetic analysis of Chelidonichthys spinosus characterized using Illumina next-generation and Pacific Biosciences (PacBio, Menlo Park, CA) sequencing technologies. The complete mitochondrial genome is a circular molecule 16,511 bp in length and contains the same set of 37 mitochondrial genes (13 protein-coding genes, two ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. The base composition of the entire mitogenome showed a slight AT bias. Phylogenetic analysis of the mitogenome of C. spinosus fully resolved it in a clade with other species classified to the Triglidae. The mitogenome data produced in this study provide the genomic resources available for future evolutionary studies.
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Affiliation(s)
- Yanping Wang
- Jiangsu Marine Fisheries Research Institute, Nantong, People's Republic of China
| | - Chuqing Wang
- Jiangsu Marine Fisheries Research Institute, Nantong, People's Republic of China
| | - Jinjin Shi
- Jiangsu Marine Fisheries Research Institute, Nantong, People's Republic of China
| | - Long Yan
- Modern Agricultural Production Development Service Center of Dalian, Dalian, People's Republic of China
| | - Hui Ge
- Jiangsu Marine Fisheries Research Institute, Nantong, People's Republic of China
| | - Lei Wu
- Jiangsu Marine Fisheries Research Institute, Nantong, People's Republic of China
| | - Xin Yan
- Jiangsu Marine Fisheries Research Institute, Nantong, People's Republic of China
| | - Yanshan Liu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, People's Republic of China
| | - Jianhua Tang
- Jiangsu Marine Fisheries Research Institute, Nantong, People's Republic of China
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Jia H, Xu H, Xian W, Li Y, Zhang H. The complete mitochondrial genome of the spiny red gurnard Chelidonichthys spinosus McClelland, 1844 (Scorpaeniformes: Triglidae). Mitochondrial DNA B Resour 2021; 6:980-982. [PMID: 33796707 PMCID: PMC7995838 DOI: 10.1080/23802359.2021.1889412] [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: 11/04/2022] Open
Abstract
The spiny red gurnard, Chelidonichthys spinosus is a common marine economic fish species along the coast of China. In the present study, the complete mitochondrial genome of spiny red gurnard collected from the Yangtze Estuary was determined by next-generation sequencing (NGS). The mitogenome is a circular nucleotide 16,466 bp in length and has the typical vertebrate genome structure of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and two control regions (Origin of Heavy chain and Origin of Light chain). The termination associated sequence (TAS), the central conserved sequence block (central CSB), and the conserved sequence block (CSB) were detected in the control region. Phylogenetic analysis of C. spinosus places in a fully supported clade with C. kumu in a sister position to Eutrigla gurnardus. The complete mitochondrial genome sequence of the spiny red gurnard provides baseline genetic information for future studies on the molecular systematics and phylogeny of bony fishes in the Triglidae.
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Affiliation(s)
- Hui Jia
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Hao Xu
- Qingdao Marine Hazard Mitigation Service, Qingdao, China
| | - Weiwei Xian
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yuquan Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Hui Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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Molecular approach for insect detection in feed and food: the case of Gryllodes sigillatus. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03573-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractThe production of insects on an industrial scale has attracted the attention of the research and agricultural industry as novel protein sources. To detect the presence of Gryllodes sigillatus (GS) in feed and food, a real-time PCR method based on the mitochondrial cytochrome b (CYB) gene is proposed by this study. Forty DNA samples of animal and plant origin were used to confirm the specificity of the qPCR system. The detection method’s performance was evaluated on different processed GS matrices including native GS (UnGS) and different commercial products: crunchy roasted samples (RoGS), insect meal mixtures (ACGS) and energetic snacks containing GS (GSS). Data on sequencing were aligned with the reference gene to confirm the PCR products. The regression curve (y = −3.394 x + 42.521; R2 = 0.994, d.f. 14) between Ct values and Log DNA concentrations of Gryllodes sigillatus resulted in an efficiency of 96.4%. The severity of the technological processing treatments and the matrix structure affected the intensity of the PCR signal with the same amount of insect DNA as observed by different y-intercepts of the three-regression lines for RoGS, ACGS, and GSS. The real-time PCR method resulted in robust and sensitive outcomes able to detect low amounts of GS DNA (5 g/100 g) in a complex matrix, making it suitable for detecting the presence or absence of labeled Gryllodes sigillatus material both in feed and food.
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Ji Y, Liu C, Yang Z, Yang L, He Z, Wang H, Yang J, Yi T. Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in
Panax
(Araliaceae). Mol Ecol Resour 2019; 19:1333-1345. [DOI: 10.1111/1755-0998.13050] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Changkun Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Zhenyan Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Lifang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- School of Life Science Yunnan University Kunming China
| | - Zhengshan He
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Sciences Wuhan China
| | - Junbo Yang
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
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Do TD, Choi TJ, Kim JI, An HE, Park YJ, Karagozlu MZ, Kim CB. Assessment of marine fish mislabeling in South Korea's markets by DNA barcoding. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Najafi A, Moradinasab M, Seyedabadi M, Haghighi MA, Nabipour I. First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran. Open Microbiol J 2018; 12:323-332. [PMID: 30450139 PMCID: PMC6198412 DOI: 10.2174/1874285801812010323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/21/2018] [Accepted: 09/23/2018] [Indexed: 11/22/2022] Open
Abstract
Background Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran. Methods Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning. Results In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group. Conclusion The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad Seyedabadi
- Department of Pharmacology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad A Haghighi
- Department of Microbiology and Parasitology, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
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Oruç AÇ, Engin S. The taxonomic status of the Black Sea and Marmara Sea populations of the Broadnosed Pipefish Syngnathus cf. argentatus Pallas (Teleostei: Syngnathidae) based on morphological and molecular characters. ZOOLOGY IN THE MIDDLE EAST 2018. [DOI: 10.1080/09397140.2018.1444569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Semih Engin
- Faculty of Fisheries, İzmir Katip Çelebi University, İzmir, Turkey
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16
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Pollack SJ, Kawalek MD, Williams-Hill DM, Hellberg RS. Evaluation of DNA barcoding methodologies for the identification of fish species in cooked products. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.08.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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A phylogeny of Southern Hemisphere whelks (Gastropoda: Buccinulidae) and concordance with the fossil record. Mol Phylogenet Evol 2017; 114:367-381. [PMID: 28669812 DOI: 10.1016/j.ympev.2017.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/31/2017] [Accepted: 06/26/2017] [Indexed: 11/24/2022]
Abstract
Under current marine snail taxonomy, the majority of whelks from the Southern Hemisphere (Buccinulidae) are hypothesised to represent a monophyletic clade that has evolved independently from Northern Hemisphere taxa (Buccinidae). Phylogenetic analysis of mitochondrial genomic and nuclear ribosomal DNA sequence data indicates that Southern Hemisphere taxa are not monophyletic, and results suggest that dispersal across the equator has occurred in both directions. New Zealand buccinulid whelks, noted for their high endemic diversity, are also found to not be monophyletic. Using independent fossil calibrations, estimated genetic divergence dates show remarkable concordance with the fossil record of the Penion and Kelletia. The divergence dates and the geographic distribution of the genera through time implies that some benthic marine snails are capable of dispersal over long distances, despite varied developmental strategies. Phylogenetic results also indicate that one species, P. benthicolus belongs in Antarctoneptunea.
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18
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Turanov SV, Kartavtsev YP, Lipinsky VV, Zemnukhov VV, Balanov AA, Lee YH, Jeong D. DNA-barcoding of perch-like fishes (Actinopterygii: Perciformes) from far-eastern seas of Russia with taxonomic remarks for some groups. ACTA ACUST UNITED AC 2014; 27:1188-209. [DOI: 10.3109/19401736.2014.945525] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Tan MH, Gan HM, Lee YP, Austin CM. The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1313-4. [PMID: 25090387 DOI: 10.3109/19401736.2014.945572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the moon crab Ashtoret lunaris was obtained from a partial genome scan using the MiSeq sequencing system. The Ashtoret lunaris mitogenome is 15,807 base pairs in length (70% A + T content) and made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 956 bp non-coding AT-rich region. This A. lunaris mitogenome sequence is the first for the genus, as well as the family Matutidae and superfamily Calappoidea.
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Affiliation(s)
- Mun Hua Tan
- a School of Science, Monash University Malaysia , Jalan Lagoon Selatan, Bandar Sunway , Petaling Jaya , Selangor , Malaysia and.,b Monash University Malaysia Genomics Facility , Jalan Lagoon Selatan, Bandar Sunway , Petaling Jaya , Selangor , Malaysia
| | - Han Ming Gan
- a School of Science, Monash University Malaysia , Jalan Lagoon Selatan, Bandar Sunway , Petaling Jaya , Selangor , Malaysia and.,b Monash University Malaysia Genomics Facility , Jalan Lagoon Selatan, Bandar Sunway , Petaling Jaya , Selangor , Malaysia
| | - Yin Peng Lee
- a School of Science, Monash University Malaysia , Jalan Lagoon Selatan, Bandar Sunway , Petaling Jaya , Selangor , Malaysia and.,b Monash University Malaysia Genomics Facility , Jalan Lagoon Selatan, Bandar Sunway , Petaling Jaya , Selangor , Malaysia
| | - Christopher M Austin
- a School of Science, Monash University Malaysia , Jalan Lagoon Selatan, Bandar Sunway , Petaling Jaya , Selangor , Malaysia and.,b Monash University Malaysia Genomics Facility , Jalan Lagoon Selatan, Bandar Sunway , Petaling Jaya , Selangor , Malaysia
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Markert A, Raupach MJ, Segelken-Voigt A, Wehrmann A. Molecular identification and morphological characteristics of native and invasive Asian brush-clawed crabs (Crustacea: Brachyura) from Japanese and German coasts: Hemigrapsus penicillatus (De Haan, 1835) versus Hemigrapsus takanoi Asakura & Watanabe 2005. ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0176-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Chakraborty M, Ghosh SK. An assessment of the DNA barcodes of Indian freshwater fishes. Gene 2014; 537:20-8. [DOI: 10.1016/j.gene.2013.12.047] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 11/17/2022]
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Pereira LHG, Hanner R, Foresti F, Oliveira C. Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genet 2013; 14:20. [PMID: 23497346 PMCID: PMC3608943 DOI: 10.1186/1471-2156-14-20] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. RESULTS Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species. CONCLUSIONS Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.
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Affiliation(s)
- Luiz H G Pereira
- Laboratory of Biology and Genetic of Fish, Department of Morphology, Biosciences Institute, State University of São Paulo, São Paulo, Brazil.
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