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Morales-Pulido JM, Galindo-Sánchez CE, Jiménez-Rosenberg SPA, Batta-Lona PG, Herzka SZ, Arteaga MC. A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39375852 DOI: 10.1111/jfb.15921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 07/28/2024] [Accepted: 08/13/2024] [Indexed: 10/09/2024]
Abstract
Sparisoma species (parrotfish) comprise an important functional group contributing to coral-reef resilience. The morphological diagnostic characteristics for species identification are clearly described for adult forms but not for the early stages. Consequently, many taxonomical listings of Sparisoma larvae are restricted to the genus level. The aims of this study are to determine whether the morphological and molecular identification techniques are useful to assign the species taxonomic level to Sparisoma larvae occurring in the Gulf of Mexico and whether there is a set of diagnostic features that could be used to discriminate between species in larvae of different developmental stages. Morphological assignment of Sparisoma was performed based on morphological and meristic features for 30 larvae collected in the Gulf of Mexico from late August to mid-September 2015. To corroborate and complement the morphological assignments, molecular identification was carried out using DNA sequences from regions of two mitochondrial genes, mitochondrial cytochrome oxidase I (mtDNA COI) and mitochondrial 16S rRNA (mtDNA 16S rRNA). COI and 16S gene trees for Sparisoma and related fish taxa were constructed using sequences available in the NCBI (National Center for Biotechnology Information) GenBank and BOLD (Barcode of Life Data) databases. Two morphotypes were identified based on morphology, but no diagnostic characteristics for species discrimination were found. Molecular identification, in contrast, successfully discriminated four early development stages of Sparisoma atomarium, three stages of Sparisoma radians, and two stages of Sparisoma chrysopterum and Sparisoma aurofrenatum, therefore demonstrating the successful and necessary application of molecular taxonomic approaches for species-level identifications of Sparisoma larvae.
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Affiliation(s)
- José Manuel Morales-Pulido
- Laboratorio de Genómica Funcional, Departamento de Biotecnología Marina, Centro de Investigación y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Clara Elizabeth Galindo-Sánchez
- Laboratorio de Genómica Funcional, Departamento de Biotecnología Marina, Centro de Investigación y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | | | | | - Sharon Zinah Herzka
- Marine Science Department, The University of Texas at Austin, Marine Science Institute, Austin, Texas, USA
| | - María Clara Arteaga
- Laboratorio de Genética de la Conservación, Departamento de Biología de la Conservación, Centro de Investigación y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
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Nascimento MHS, Birindelli JLO, Fraga E, Barros MC. Exploring hidden diversity: Molecular insights into the Leporinus species of the rivers of the Brazilian states of Maranhão and Piauí. JOURNAL OF FISH BIOLOGY 2024; 104:2056-2067. [PMID: 38590289 DOI: 10.1111/jfb.15753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 03/10/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
The present study delved into the world of hidden diversity by examining specimens identified as Leporinus piau from the river basins of the northern Brazilian states of Maranhão and Piauí. Using genetic analyses that combined data from three mitochondrial markers and one nuclear marker, the study identified two well-supported groups, reinforcing the findings of previous publications. The first group, found in samples from the Itapecuru, Mearim, Turiaçu, and Pericumã basins, in Maranhão, appears to represent a relatively ancient diversification and the possibility of concealed cryptic diversity. The second group, comprising specimens from the Parnaíba (Piauí) and Mearim (Maranhão) basins, appears to have resulted from a more recent process of diversification and has a close relationship with Leporinus friderici from the type locality. Our findings not only confirm the existence of a complex scenario of cryptic diversity in the genus Leporinus from the study basins but also underscore the taxonomic inconsistencies within this group of fish. This study offers a comprehensive analysis of the species diversity of the Maranhão and Piauí basins, which are critical regions for the conservation of Amazonian fish, providing valuable insights for the sustainable management and conservation of these fish.
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Affiliation(s)
- Maria Histelle Sousa Nascimento
- Departamento de Desenvolvimento e Ensino, Instituto Federal de Educação, Ciência e Tecnologia do Maranhão, Caxias, Brazil
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Universidade Federal do Maranhão, São Luis, Brazil
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
| | | | - Elmary Fraga
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
| | - Maria Claudene Barros
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Universidade Federal do Maranhão, São Luis, Brazil
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
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Li H, Miao X, Wang R, Liao Y, Wen Y, Zhang R, Lin L. Biodiversity of Demersal Fish Communities in the Cosmonaut Sea Revealed by DNA Barcoding Analyses. Genes (Basel) 2024; 15:691. [PMID: 38927627 PMCID: PMC11202926 DOI: 10.3390/genes15060691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I (COI) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses.
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Affiliation(s)
- Hai Li
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (H.L.); (X.M.); (R.W.); (Y.L.); (Y.W.); (R.Z.)
| | - Xing Miao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (H.L.); (X.M.); (R.W.); (Y.L.); (Y.W.); (R.Z.)
| | - Rui Wang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (H.L.); (X.M.); (R.W.); (Y.L.); (Y.W.); (R.Z.)
| | - Yuzhuo Liao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (H.L.); (X.M.); (R.W.); (Y.L.); (Y.W.); (R.Z.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yilin Wen
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (H.L.); (X.M.); (R.W.); (Y.L.); (Y.W.); (R.Z.)
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Ran Zhang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (H.L.); (X.M.); (R.W.); (Y.L.); (Y.W.); (R.Z.)
| | - Longshan Lin
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (H.L.); (X.M.); (R.W.); (Y.L.); (Y.W.); (R.Z.)
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
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Salam MR, Ezaouine A, Zekhnini H, El Messal M, El Mellouli F, Chegdani F, Bennis F. Morphological, molecular identification and evaluation of antioxidant activity of seahorses from the Moroccan coasts. Saudi J Biol Sci 2024; 31:103898. [PMID: 38188538 PMCID: PMC10770750 DOI: 10.1016/j.sjbs.2023.103898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/09/2024] Open
Abstract
Seahorses, part of the small marine teleost fish family Syngnathidae, are increasingly under threat due to habitat degradation and overfishing. Notably used in traditional Chinese medicine, these fish have demonstrated significant pharmacological and cosmetic properties. In Morocco, however, seahorses are minimally exploited. This study aims to explore the biodiversity of Moroccan seahorses, focusing on identifying species from the Atlantic and Mediterranean coasts both morphologically and molecularly, and evaluating their antioxidant activity. The research involved collecting 62 dried seahorses from local fishermen. These specimens were subjected to detailed morphological and molecular identification through the DNA barcoding method, concentrating on the mitochondrial marker Cytochrome Oxidase I (COI) gene. Following DNA extraction and amplification, the sequences were analyzed for species identification and phylogenetic relationships. Additionally, the antioxidant activities of the seahorses were quantified using assays such as ABTS, reducing power, phosphomolybdenum, and β-carotene-linoleic acid. The combined morphological and molecular analyses consistently identified all specimens as Hippocampus hippocampus, and phylogenetic trees suggested a close relation with European and Turkish counterparts. Furthermore, the antioxidant assays revealed significant activity, with the ABTS assay showing an IC50 of 14.571 mg/mL ± 0.334, and the β-carotene-linoleic acid assay showing an IC50 of 1.273 mg/mL ± 0.166. The reducing power and phosphomolybdenum assays recorded EC50 values of 1.868 mg/mL ± 0.033 and 1.156 mg/mL ± 0.112, respectively. These results confirm the high antioxidant potential of Moroccan seahorses, suggesting their therapeutic value and necessitating measures for their biodiversity preservation at a national level.
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Affiliation(s)
- Mohamed Rida Salam
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
| | - Abdelkarim Ezaouine
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
| | - Hasnae Zekhnini
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
- National Office for Food Safety (ONSSA), Regional Laboratory for Analysis and Research of Casablanca, Casablanca, Morocco
| | - Mariame El Messal
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
| | - Fatiha El Mellouli
- National Office for Food Safety (ONSSA), Regional Laboratory for Analysis and Research of Casablanca, Casablanca, Morocco
| | - Fatima Chegdani
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
| | - Faiza Bennis
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
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Zhang H, Dong J, Yan Y, Liu S, Ye X, Gao F, Sun C. Development of a Highly Permissive Mandarin Fish ( Siniperca chuatsi) Kidney Cell Line for Mandarin Fish Ranavirus Using a Single-Cell Cloning Method. Cells 2023; 13:18. [PMID: 38201223 PMCID: PMC10778425 DOI: 10.3390/cells13010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Mandarin fish ranavirus (MRV) infection poses a substantial challenge to the mandarin fish culture industry as no effective preventive or therapeutic measures currently exist. The creation of a highly permissive cell line from a natural host is crucial for developing a vaccine for MRV and understanding its pathogenic mechanisms. In this research, the mandarin fish (Siniperca chuatsi) kidney cell line (SCK) was isolated from mandarin fish kidneys. Subsequently, SCK-a to SCK-g monoclonal cell lines were derived from the SCK cell population, distinguished by morphological variations. Notably, MRV infection induced an advanced cytopathic effect (CPE) in almost all cells of the SCK-f clone. Further tests showed that MRV achieved a peak viral titer of 1010.7 50% tissue culture infectious dose (TCID50)/mL and consistently exceeded 1010 TCID50/mL across nine passages in SCK-f cells. Electron microscopy verified the MRV virion integrity within SCK-f. In vivo experiments revealed that MRV infections led to cumulative mortality rates of 86.9% in mandarin fish and 88.9% in largemouth bass (Micropterus salmoides). Such results suggest that SCK-f is highly permissive to MRV. This study underscores the importance of cellular diversity in developing viral permissive cell lines. The SCK monoclonal cell line pool may offer potential for generating highly permissive cell lines for other mandarin fish viruses.
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Affiliation(s)
- Hetong Zhang
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China; (H.Z.); (J.D.); (Y.Y.); (X.Y.)
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China
| | - Junjian Dong
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China; (H.Z.); (J.D.); (Y.Y.); (X.Y.)
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China
| | - Yunyun Yan
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China; (H.Z.); (J.D.); (Y.Y.); (X.Y.)
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China
- College of Oceanography, Agriculture University of Hebei, Qinhuangdao 066000, China
| | - Shanshan Liu
- School of Ecology, Sun Yat-sen University, Guangzhou 510275, China;
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China; (H.Z.); (J.D.); (Y.Y.); (X.Y.)
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China
- School of Ecology, Sun Yat-sen University, Guangzhou 510275, China;
| | - Fengying Gao
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China; (H.Z.); (J.D.); (Y.Y.); (X.Y.)
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China
- School of Ecology, Sun Yat-sen University, Guangzhou 510275, China;
| | - Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China; (H.Z.); (J.D.); (Y.Y.); (X.Y.)
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510310, China
- School of Ecology, Sun Yat-sen University, Guangzhou 510275, China;
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Jiang C, Yi M, Luo Z, He X, Lin H, Hubert N, Yan Y. DNA barcoding the ichthyofauna of the Beibu Gulf: Implications for fisheries management in a seafood market hub. Ecol Evol 2023; 13:e10822. [PMID: 38089891 PMCID: PMC10711522 DOI: 10.1002/ece3.10822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/10/2023] [Accepted: 11/28/2023] [Indexed: 10/16/2024] Open
Abstract
The Beibu Gulf in China is situated in the tropics, in the western Pacific Ocean. It is an emblematic region combining proximity to a marine biodiversity hotspot and a major seafood hub. Intensification of marine fishing and ocean warming led to a drastic decline in fish populations in the Beibu Gulf during the last decades. This situation urges the development of molecular resources of the Beibu Gulf fish fauna in order to enable automated molecular identifications at the species level for next-generation monitoring. With this objective, we present the results of a large-scale campaign to DNA barcode fishes of the Beibu Gulf. We successfully generated 789 new DNA barcodes corresponding to 263 species which, together with 291 sequences mined from Genbank and BOLD, resulted in a reference library of 1080 sequences from 285 species. Based on the use of four DNA-based species delimitation methods (BIN, ASAP, mPTP, mGMYC), a total of 285 Molecular Operational Taxonomical Units (MOTUs). A single case of cryptic diversity was detected in Scomberomorus guttatus and a single species pair was not captured by delimitation methods. Intraspecific K2P genetic distances averaged 0.36% among sequences within species, whereas K2P genetic distances among species within genera averaged 6.96%. The most speciose families in open water trawling differ from those at fish market, and discrepancies with historical data are discussed in the light of recently documented stock collapses.
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Affiliation(s)
- Changping Jiang
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
| | - Murong Yi
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang)ZhanjiangChina
| | - Zhisen Luo
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
| | - Xiongbo He
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
- Guangdong Provincial Engineering and Technology Research Center of Far Sea Fisheries Management and Fishing of South China SeaGuangdong Ocean UniversityZhanjiangChina
| | - Hung‐Du Lin
- The Affiliated School of National Tainan First Senior High SchoolTainanTaiwan
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 226 ISEM (IRD, UM, CNRS)Université de MontpellierMontpellierFrance
| | - Yunrong Yan
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang)ZhanjiangChina
- Guangdong Provincial Engineering and Technology Research Center of Far Sea Fisheries Management and Fishing of South China SeaGuangdong Ocean UniversityZhanjiangChina
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Habib KA, Islam MJ, Sakib MN, Brishti PS, Neogi AK. DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh. Ecol Evol 2023; 13:e10641. [PMID: 37877103 PMCID: PMC10590961 DOI: 10.1002/ece3.10641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023] Open
Abstract
This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.
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Affiliation(s)
- Kazi Ahsan Habib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Jayedul Islam
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Nazmus Sakib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Parsha Shanjana Brishti
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Amit Kumer Neogi
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
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Huang WC, Evacitas FC, Balisco RA, Nañola CL, Chou TK, Jhuang WC, Chang CW, Shen KN, Shao KT, Liao TY. DNA barcoding of marine teleost fishes (Teleostei) in Cebu, the Philippines, a biodiversity hotspot of the coral triangle. Sci Rep 2023; 13:14867. [PMID: 37684303 PMCID: PMC10491795 DOI: 10.1038/s41598-023-41832-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.
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Affiliation(s)
- 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
| | - Florence Chan Evacitas
- Department of Biology and Environmental Science, University of the Philippines Cebu, Cebu City, Philippines
| | - Rodulf Anthony Balisco
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
- College of Fisheries and Aquatic Sciences, Western Philippines University, Puerto Princesa, Philippines
| | - Cleto L Nañola
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Davao City, Philippines
| | - Tak-Kei Chou
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wei-Cheng Jhuang
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Chih-Wei Chang
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
- Marine Ecology and Conservation Research Center, National Academy of Marine Research, Kaohsiung, Taiwan
- Institute of Marine Ecology and Conservation, National Sun Yat-sen University, Kaohsiung, Taiwan
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Kang-Ning Shen
- Marine Ecology and Conservation Research Center, National Academy of Marine Research, Kaohsiung, Taiwan
| | - Kwang-Tsao Shao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Te-Yu Liao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan.
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Goswami M, Pinto N, Yashwanth BS, Sathiyanarayanan A, Ovissipour R. Development of a cell line from skeletal trunk muscle of the fish Labeo rohita. Cytotechnology 2023; 75:349-361. [PMID: 37389130 PMCID: PMC10299978 DOI: 10.1007/s10616-023-00581-3] [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: 04/09/2023] [Accepted: 05/08/2023] [Indexed: 07/01/2023] Open
Abstract
Labeo rohita is a widely cultivated tropical freshwater carp and found in rivers of South Asian region. A new cell line, designated LRM, has been developed from the muscle tissue of L. rohita. Muscle cells were subcultured up to 38 passages in a Leibovitz's-15 (L-15) supplemented with 10% FBS (Fetal Bovine Serum) and 10 ng/ml bFGF. The LRM cells exhibited fibroblastic morphology with a doubling time of 28 h, and a plating efficiency of 17%. A maximum growth rate was observed for LRM cells at 28 °C, 10% FBS and 10 ng/ml bFGF. A cytochrome C oxidase subunit I (COI) gene sequence was used to authenticate the developed cell line. Chromosome analysis revealed 50 diploid chromosomes. The fibroblastic characteristics of the of the LRM cells was confirmed by immunocytochemistry. The expression of MyoD gene in LRM cells was analyzed by quantitative PCR in comparison with passages 3, 18 and 32. The expression of MyoD was higher at passage 18 compared to the passages 3 and 32. The LRM cells attached properly onto the 2D scaffold and the expression of the F-actin filament protein was confirmed by phalloidin staining followed by counter staining with DAPI to observe the distribution of the muscle cell nuclei and the cytoskeleton protein. A revival rate of 70-80% was achieved when the LRM cells were cryopreserved at - 196 °C using liquid nitrogen. This study would further contribute to understanding the in vitro myogenesis and progress toward cultivated fish meat production.
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Affiliation(s)
- Mukunda Goswami
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, 400061 Mumbai, India
| | - Nevil Pinto
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, 400061 Mumbai, India
| | - B. S. Yashwanth
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, 400061 Mumbai, India
| | - A. Sathiyanarayanan
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, 400061 Mumbai, India
| | - Reza Ovissipour
- Future Foods Lab and Cellular Agriculture Initiative, Department of Food Science and Technology, Seafood Agricultural Research and Extension Centre, Virginia Polytechnic Institute and State University (VT), Blacksburg, VA USA
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10
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Filonzi L, Ardenghi A, Rontani PM, Voccia A, Ferrari C, Papa R, Bellin N, Nonnis Marzano F. Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species. Foods 2023; 12:2420. [PMID: 37372635 DOI: 10.3390/foods12122420] [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: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.
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Affiliation(s)
- Laura Filonzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Alessia Ardenghi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Pietro Maria Rontani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Andrea Voccia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Claudio Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Riccardo Papa
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Nicolò Bellin
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Francesco Nonnis Marzano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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11
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Yashwanth BS, Pinto N, Sathiyanarayanan A, Chaudhari A, Rasal KD, Goswami M. Functional characterization of Labeo rohita muscle cell line for in vitro research. Mol Biol Rep 2023:10.1007/s11033-023-08427-z. [PMID: 37179501 DOI: 10.1007/s11033-023-08427-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/04/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Labeo rohita represents the most dominant fish species in Indian aquaculture and the fish cell lines have been used as an excellent in vitro platform for performing various biological research. METHODS AND RESULTS The LRM cell culture developed from the muscle tissue of L. rohita was used to study the in vitro applications. The developed muscle cells were maintained in a Leibovitz's-15 (L-15) supplemented with 10% FBS (Fetal Bovine Serum) and 10 ng/ml bFGF at 28 oC temperature. The LRM cells showed fibroblastic-like morphology and was authenticated by sequencing mitochondrial gene 16S rRNA. The expression of myogenic regulatory factors (MRFs) was studied in different stages of LRM cells; however, the expression patterns varied at different passages. The MEF2A, Mrf-4, and Myogenin expressions were higher in passage 25, while the expression of MyoD was maximum in passage 15, and the expression of Myf-5 was highest in passage 1. The transfection efficiency of LRM cells revealed 14 % of the GFP expression with a pmaxGFP vector DNA. The LRM cells were susceptible to the extracellular products prepared from Aeromonas hydrophilla and Edwardsiella tarda. The acute cytotoxicity of six heavy metals (Hg, Cd, Zn, Cu, Pb, Ni) was assessed in LRM cells by a dose-dependent manner in comparison to IC50 values obtained from MTT and NR assays. A revival rate of 70-75% was achieved when the LRM cells were cryopreserved at - 196 °C using liquid nitrogen. CONCLUSION The developed muscle cells serve as an functional in vitro tool for toxicological and biotechnological studies.
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Affiliation(s)
- B S Yashwanth
- Fish Genetics and Biotechnology Division, ICAR- Central Institute of Fisheries Education, Panch Marg, Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - Nevil Pinto
- Fish Genetics and Biotechnology Division, ICAR- Central Institute of Fisheries Education, Panch Marg, Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - A Sathiyanarayanan
- Fish Genetics and Biotechnology Division, ICAR- Central Institute of Fisheries Education, Panch Marg, Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - Aparna Chaudhari
- Fish Genetics and Biotechnology Division, ICAR- Central Institute of Fisheries Education, Panch Marg, Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology Division, ICAR- Central Institute of Fisheries Education, Panch Marg, Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - Mukunda Goswami
- Fish Genetics and Biotechnology Division, ICAR- Central Institute of Fisheries Education, Panch Marg, Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India.
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12
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Pragmatic applications of DNA barcoding markers in identification of fish species – a review. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.
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13
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DNA Barcoding of Fish Species Diversity in Guizhou, China. DIVERSITY 2023. [DOI: 10.3390/d15020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Guizhou is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River basins with abundant fish species. However, fish from these regions are threatened by anthropogenic activities, including overfishing and habitat destruction. Here, we assessed the fish diversity including more than half of the species from the region using DNA barcoding (partial sequence of cytochrome c oxidase subunit I (COI) gene). We obtained 800 mitochondrial COI barcode sequences from 82 genera, 18 families and 8 orders of fishes. The average Kimura two-parameter (K2P) distances within species and genera were 0.35% and 5.44%, respectively. The average interspecific distance was 15.54 times higher than the mean intraspecific distance. Moreover, DNA barcodes revealed 175 operational taxonomic units (OTUs) based on consensus demarcation schemes. Barcoding gaps were detected in 94.81% of morphospecies. Three fish species (Schistura fasciolata, Vanmanenia pingchowensis, and Misgurnus dabryanus) have considerable intraspecific variability, and each was divided into multiple molecular operational taxonomic units (MOTUs) using molecular definition methods (Automatic Barcode Gap Discovery, Refined Single Linkage, General Mixed Yule Coalescent, and Poisson Tree Processes), possibly indicating the occurrence of cryptic species. Altogether, our study reveals the complex diversity of fish species in Guizhou Province, serving as a reference for the conservation and monitoring of fish species in this region.
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14
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Master-Key Regulators of Sex Determination in Fish and Other Vertebrates-A Review. Int J Mol Sci 2023; 24:ijms24032468. [PMID: 36768795 PMCID: PMC9917144 DOI: 10.3390/ijms24032468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/12/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
In vertebrates, mainly single genes with an allele ratio of 1:1 trigger sex-determination (SD), leading to initial equal sex-ratios. Such genes are designated master-key regulators (MKRs) and are frequently associated with DNA structural variations, such as copy-number variation and null-alleles. Most MKR knowledge comes from fish, especially cichlids, which serve as a genetic model for SD. We list 14 MKRs, of which dmrt1 has been identified in taxonomically distant species such as birds and fish. The identification of MKRs with known involvement in SD, such as amh and fshr, indicates that a common network drives SD. We illustrate a network that affects estrogen/androgen equilibrium, suggesting that structural variation may exert over-expression of the gene and thus form an MKR. However, the reason why certain factors constitute MKRs, whereas others do not is unclear. The limited number of conserved MKRs suggests that their heterologous sequences could be used as targets in future searches for MKRs of additional species. Sex-specific mortality, sex reversal, the role of temperature in SD, and multigenic SD are examined, claiming that these phenomena are often consequences of artificial hybridization. We discuss the essentiality of taxonomic authentication of species to validate purebred origin before MKR searches.
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Sathiyanarayanan A, Yashwanth BS, Pinto N, Thakuria D, Chaudhari A, Gireesh Babu P, Goswami M. Establishment and characterization of a new fibroblast-like cell line from the skin of a vertebrate model, zebrafish (Danio rerio). Mol Biol Rep 2023; 50:19-29. [PMID: 36289143 DOI: 10.1007/s11033-022-08009-5] [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: 07/23/2022] [Accepted: 10/05/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND The available fully sequenced genome and genetic similarities compared to humans make zebrafish a prominent in vitro vertebrate model for drug discovery & screening, toxicology, and radiation biology. Zebrafish also possess well developed immune systems which is ideal for studying infectious diseases. Fish skin confers immunity by serving as a physical barrier against the invading pathogens in the aquatic habitat. Therefore in vitro models from the skin tissue of zebrafish help to study the physiology, functional genes in vitro, wound healing, and pathogenicity of microbes. Hence the study aimed to develop and characterize a skin cell line from the wild-type zebrafish Danio rerio. METHODS AND RESULTS A novel cell line designated as DRS (D. rerio skin) was established and characterized from the skin tissue of wild-type zebrafish, D. rerio, by the explant technique. The cells thrived well in the Leibovitz's -15 medium supplemented with 15% FBS and routinely passaged at regular intervals. The DRS cells mainly feature fibroblast-like morphology. The culture conditions of the cells were determined by incubating the cells at varying concentrations of FBS and temperature; the optimum was 15% FBS and 28 °C, respectively. Cells were cryopreserved and revived with 70-75% viability at different passage levels. Two extracellular products from bacterial species Aeromonas hydrophila and Edwardsiella tarda were tested and found toxic to the DRS cells. Mitochondrial genes, namely COI and 16S rRNA PCR amplification and partial sequencing authenticated the species of origin of cells. The modal diploid (2n) chromosome number of the cells was 50. The cell line DRS was found to be free from mycoplasma. The cells were transfected with pMaxGFP plasmid and tested positive for green fluorescence at 24-48 h post-transfection. CONCLUSION The findings from this study thus confirm the usefulness of the developed cell line in bacterial susceptibility and transgene expression studies.
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Affiliation(s)
- Arjunan Sathiyanarayanan
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - B S Yashwanth
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - Nevil Pinto
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - Dimpal Thakuria
- ICAR-Directorate of Coldwater Fisheries Research, Anusandhan Bhawan, Industrial Area, Bhimtal, 263136, India
| | - Aparna Chaudhari
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India
| | - P Gireesh Babu
- ICAR-National Research Centre on Meat, Chengicherla, Boduppal Post, Hyderabad, 500092, India
| | - Mukunda Goswami
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Panch Marg, Off Yari Road, Versova, Andheri West, Mumbai, Maharashtra, 400061, India.
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DNA barcoding provides insights into Fish Diversity and Molecular Taxonomy of the Amundsen Sea. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01273-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Curzon AY, Shirak A, Benet-Perlberg A, Naor A, Low-Tanne SI, Sharkawi H, Ron M, Seroussi E. Absence of Figla-like Gene Is Concordant with Femaleness in Cichlids Harboring the LG1 Sex-Determination System. Int J Mol Sci 2022; 23:ijms23147636. [PMID: 35886982 PMCID: PMC9316214 DOI: 10.3390/ijms23147636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Oreochromis niloticus has been used as a reference genome for studies of tilapia sex determination (SD) revealing segregating genetic loci on linkage groups (LGs) 1, 3, and 23. The master key regulator genes (MKR) underlying the SD regions on LGs 3 and 23 have been already found. To identify the MKR in fish that segregate for the LG1 XX/XY SD-system, we applied short variant discovery within the sequence reads of the genomic libraries of the Amherst hybrid stock, Coptodon zillii and Sarotherodon galilaeus, which were aligned to a 3-Mbp-region of the O. aureus genome. We obtained 66,372 variants of which six were concordant with the XX/XY model of SD and were conserved across these species, disclosing the male specific figla-like gene. We further validated this observation in O. mossambicus and in the Chitralada hybrid stock. Genome alignment of the 1252-bp transcript showed that the figla-like gene’s size was 2664 bp, and that its three exons were capable of encoding 99 amino acids including a 45-amino-acid basic helix–loop–helix domain that is typical of the ovary development regulator—factor-in-the-germline-alpha (FIGLA). In Amherst gonads, the figla-like gene was exclusively expressed in testes. Thus, the figla-like genomic presence determines male fate by interrupting the female developmental program. This indicates that the figla-like gene is the long-sought SD MKR on LG1.
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Affiliation(s)
- Arie Yehuda Curzon
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Ayana Benet-Perlberg
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Alon Naor
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Shay Israel Low-Tanne
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Haled Sharkawi
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
- Correspondence:
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18
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Abstract
With the development of computer science technology, theory and method of image segmentation are widely used in fish discrimination, which plays an important role in improving the efficiency of fisheries sorting and biodiversity studying. However, the existing methods of fish images segmentation are less accurate and inefficient, which is worthy of in-depth exploration. Therefore, this paper proposes an atrous pyramid GAN segmentation network aimed at increasing accuracy and efficiency. This paper introduces an atrous pyramid structure, and the GAN module is added before the CNN backbone in order to augment the dataset. The Atrous pyramid structure first fuses the input and output of the dilated convolutional layer with a small sampling rate and then feeds the fused features into the subsequent dilated convolutional layer with a large sampling rate to obtain dense multiscale contextual information. Thus, by capturing richer contextual information, this structure improves the accuracy of segmentation results. In addition to the aforementioned innovation, various data enhancement methods, such as MixUp, Mosaic, CutMix, and CutOut, are used in this paper to enhance the model’s robustness. This paper also improves the loss function and uses the label smoothing method to prevent model overfitting. The improvement is also tested by extensive ablation experiments. As a result, our model’s F1-score, GA, and MIoU were tested on the validation dataset, reaching 0.961, 0.981, and 0.973, respectively. This experimental result demonstrates that the proposed model outperforms all the other contrast models. Moreover, in order to accelerate the deployment of the encapsulated model on hardware, this paper optimizes the execution time of the matrix multiplication method on Hbird E203 based on Strassen’s algorithm to ensure the efficient operation of the model on this hardware platform.
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Girard MG, Davis MP, Baldwin CC, Dettaï A, Martin RP, Smith WL. Molecular phylogeny of the threadfin fishes (Polynemidae) using ultraconserved elements. JOURNAL OF FISH BIOLOGY 2022; 100:793-810. [PMID: 35137410 DOI: 10.1111/jfb.14997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/24/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Threadfins (Teleostei: Polynemidae) are a group of fishes named for their elongated and threadlike pectoral-fin rays. These fishes are commonly found in the world's tropical and subtropical waters, and are an economically important group for people living in these regions, with more than 100,000 t harvested in recent years. However, we do not have a detailed understanding of polynemid evolutionary history such that these fishes can be monitored, managed and conserved as an important tropical food source. Recent studies hypothesize at least one genus of threadfins is polyphyletic, and no studies have focused on generating a hypothesis of relationship for the Polynemidae using DNA sequences. In this study, we analyse a genomic dataset of ultraconserved-element and mitochondrial loci to construct a phylogeny of the Polynemidae. We recover the threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad-scale phylogenies of fishes have incorporated mislabelled, misidentified or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.
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Affiliation(s)
- Matthew G Girard
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Matthew P Davis
- Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota, USA
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Agnès Dettaï
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, FRA
| | - Rene P Martin
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - W Leo Smith
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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Parvez I, Rumi RA, Ray PR, Hassan MM, Sultana S, Pervin R, Suwanno S, Pradit S. Invasion of African Clarias gariepinus Drives Genetic Erosion of the Indigenous C. batrachus in Bangladesh. BIOLOGY 2022; 11:biology11020252. [PMID: 35205117 PMCID: PMC8869340 DOI: 10.3390/biology11020252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/15/2022] [Accepted: 02/01/2022] [Indexed: 12/05/2022]
Abstract
Simple Summary Bangladesh has substantially increased aquaculture production over the last few decades, and the exotic species share a significant portion of the total fish production. Although exotic species are contributing to aquaculture production, a few of them are causing biodiversity loss and genetic erosion of native species. The African catfish Clarias gariepinus is a highly carnivorous species and predates small indigenous freshwater fishes when escaping into natural water bodies. In addition, the hybridization of C. batrachus and C. gariepinus is considered a threat to the indigenous population. Although the government of Bangladesh has banned the farming of C. gariepinus, this species has been identified in local markets, and evidence of hybridization between C. gariepinus and C. batrachus has been found. This study revealed genetic erosion of native C. batrachus by the gene sequences of cytochrome c oxidase subunit I and cytochrome b. The phylogenetic tree confirmed the occurrences of hybridization between C. gariepinus and C. batrachus. Genetic erosion in the native catfish population is alarming for aquaculture sustainability and biodiversity conservation in Bangladesh. Abstract The African catfish Clarias gariepinus has been introduced for aquaculture in Bangladesh due to the scarcity of indigenous C. batrachus fingerlings. However, the government of Bangladesh has banned the farming of C. gariepinus due to the carnivorous nature of this species. Recently C. gariepinus has been reported by fish farmers and consumers in Bangladesh, and unplanned hybridization between native and exotic species has been suspected. This study attempts to know the purity of C. batrachus by analyzing mitochondrial genes. Both directly sequenced and retrieved Cytochrome C Oxidase subunit I (COI) and cytochrome b (Cytb) genes from C. gareipinus and C. batrachus were analyzed by MEGA software. The morphologically dissimilar C. batrachus showed the least genetic distance (0.295) from C. gariepinus, which provided evidence of hybridization between the two species. Maximum likelihood (ML) phylogenetic trees showed that C. batrachus from Bangladesh did not cluster with C. batrachus of other countries, instead C. batrachus clustered with the exotic C. gariepinus. The suspected hybrid formed sister taxa with the exotic C. gariepinus. The study corroborates the genetic deterioration of C. batrachus by unplanned hybridization with the invasive C. gariepinus. Unplanned hybridization has deleterious consequences; therefore, immediate action is necessary for aquaculture sustainability and biodiversity conservation in Bangladesh.
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Affiliation(s)
- Imran Parvez
- Faculty of Environmental Management, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand; (I.P.); (S.S.)
- Department of Fisheries Biology and Genetics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh; (R.A.R.); (P.R.R.); (M.M.H.)
| | - Rukaya Akter Rumi
- Department of Fisheries Biology and Genetics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh; (R.A.R.); (P.R.R.); (M.M.H.)
| | - Purnima Rani Ray
- Department of Fisheries Biology and Genetics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh; (R.A.R.); (P.R.R.); (M.M.H.)
| | - Mohammad Mahbubul Hassan
- Department of Fisheries Biology and Genetics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh; (R.A.R.); (P.R.R.); (M.M.H.)
- School of Forest, Fisheries, and Geomatic Sciences, University of Florida/IFAS, 7922 NW 71st Street, Gainesville, FL 32653, USA
| | - Shirin Sultana
- Fisheries Biotechnology Division, National Institute of Biotechnology, Ministry of Science and Technology, Dhaka 1000, Bangladesh;
| | - Rubaiya Pervin
- Department of Fisheries Management, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh;
| | - Suvit Suwanno
- Faculty of Environmental Management, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand; (I.P.); (S.S.)
| | - Siriporn Pradit
- Faculty of Environmental Management, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand; (I.P.); (S.S.)
- Coastal and Climate Change Research Center, Faculty of Environmental Management, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
- Correspondence:
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21
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Vulnerability Assessment of Target Shrimps and Bycatch Species from Industrial Shrimp Trawl Fishery in the Bay of Bengal, Bangladesh. SUSTAINABILITY 2022. [DOI: 10.3390/su14031691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Productivity susceptibility analysis (PSA) is a semi-quantitative ecological risk assessment tool, widely used to determine the relative vulnerability of target and non-target species to fishing impacts. Considering the available information on species-specific life-history and fishery-specific attributes, we used PSA to assess the relative risk of the 60 species interacting with the shrimp trawl fishery in the Bay of Bengal, Bangladesh. Penaeus monodon, the most important target, and Metapenaeus monoceros, the highest catch contributor, along with other 15 species were in the moderate-risk category, while seven non-target bycatch species were in the high-risk category. PSA-derived vulnerability results were validated with IUCN extinction risk, exploitation rate and stocks’ catch trend. The majority of the identified species showed high productivity (37%) and high susceptibility (46%), and all the moderately and highly vulnerable species were subjected to overfishing conditions by shrimp trawl fishery, which coincided with the vulnerability scores (V ≥ 1.8). Species with V ≥ 1.8 mostly showed a decreasing catch trend, while the species with a stable or increasing catch trend had a V ≤ 1.72. Data quality analysis of productivity and susceptibility attributes indicated that the majority of species were considered data-limited, which emphasizes the acquisition of data on spatio-temporal abundance, catch and effort, and biological information specifically relating to species age, growth, and reproduction. However, our findings can assist fishery administrators in implementing an ecosystem approach to ensure the sustainability and conservation of marine biodiversity in the Bay of Bengal.
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Ahmed MS, Datta SK, Saha T, Hossain Z. Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes. Ecol Evol 2021; 11:3696-3709. [PMID: 33976769 PMCID: PMC8093680 DOI: 10.1002/ece3.7355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022] Open
Abstract
This study describes the molecular characterization of marine and coastal fishes of Bangladesh based on the mitochondrial cytochrome c oxidase subunit I (COI) gene as a marker. A total of 376 mitochondrial COI barcode sequences were obtained from 185 species belonging to 146 genera, 74 families, 21 orders, and two classes of fishes. The mean length of the sequences was 652 base pairs. In Elasmobranchii (Sharks and rays), the average Kimura two parameter (K2P) distances within species, genera, families, and orders were 1.20%, 6.07%, 11.08%, and 14.68%, respectively, and for Actinopterygii, the average K2P distances within species, genera, families, and orders were 0.40%, 6.36%, 14.10%, and 24.07%, respectively. The mean interspecies distance was 16-fold higher than the mean intraspecies distance. The K2P neighbor-joining (NJ) trees based on the sequences generally clustered species in accordance with their taxonomic position. A total of 21 species were newly recorded in Bangladesh. High efficiency and fidelity in species identification and discrimination were demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used as an authentic identification marker for Bangladesh marine fish species.
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Affiliation(s)
| | | | - Tonmoy Saha
- Department of ZoologyJagannath UniversityDhakaBangladesh
| | - Zarif Hossain
- Department of OceanographyUniversity of DhakaDhakaBangladesh
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Characterization of a new cell line from ornamental fish Amphiprion ocellaris (Cuvier, 1830) and its susceptibility to nervous necrosis virus. Sci Rep 2020; 10:20051. [PMID: 33208823 PMCID: PMC7676255 DOI: 10.1038/s41598-020-76807-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Amphiprion ocellaris (ocellaris clownfish) is one of the most commercially important marine ornamental fish. A cell line designated as OCF was developed for the first time from the caudal fin of this fish species. The cell line was maintained in Leibovitz’s—15 medium supplemented with 15% FBS (Fetal Bovine Serum) and was successfully subcultured up to 34 passages. The cell line was authenticated by sequencing mitochondrial cytochrome C oxidase subunit I (COI) and 16S rRNA genes. The growth rate of the OCF cell line was maximum in medium containing 20% FBS and 1% of 0.2 M NaCl at 28 °C. Chromosome analysis revealed 48 diploid chromosomes. The OCF cell line was transfected with the pMaxGFP plasmid vector with 7% efficiency and GFP expression was observed. The OCF cell line was used for testing nervous necrosis virus (NNV) susceptibility. Cytopathic effect (CPE) was observed in terms of plaque formation after virus inoculation. Nested PCR confirmed the susceptibility of the OCF cell line to NNV. The cell line was successfully cryopreserved by a slow freezing procedure at − 80 °C with a revival efficiency of 70–75%. The study revealed that the OCF cell line would be useful for virological studies. In addition, the cell line would play an important role as an in vitro tool for carrying out toxicological and biotechnological studies.
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DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau. BMC Evol Biol 2020; 20:151. [PMID: 33183225 PMCID: PMC7663858 DOI: 10.1186/s12862-020-01718-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/04/2020] [Indexed: 01/12/2023] Open
Abstract
Background The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs). Results After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions. Conclusions The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.
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Santamaria CA, Locascio J, Greenan TM. First report of lionfish prey from Western Florida waters as identified by DNA barcoding. PeerJ 2020; 8:e9922. [PMID: 32974106 PMCID: PMC7489240 DOI: 10.7717/peerj.9922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/21/2020] [Indexed: 11/23/2022] Open
Abstract
DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets.
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Affiliation(s)
- Carlos A. Santamaria
- Biology Program, Thomas University, Thomasville, GA, USA
- Biology Program, College of Science and Mathematics, University of South Florida Sarasota-Manatee, Sarasota, FL, USA
| | - James Locascio
- Fisheries Habitat Ecology and Acoustics Program, Mote Marine Laboratory, Sarasota, FL, USA
| | - Taylor M. Greenan
- Biology Program, College of Science and Mathematics, University of South Florida Sarasota-Manatee, Sarasota, FL, USA
- Fisheries Habitat Ecology and Acoustics Program, Mote Marine Laboratory, Sarasota, FL, USA
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Fadli N, Mohd Nor SA, Othman AS, Sofyan H, Muchlisin ZA. DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia. PeerJ 2020; 8:e9641. [PMID: 32844060 PMCID: PMC7414767 DOI: 10.7717/peerj.9641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.
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Affiliation(s)
- Nur Fadli
- Faculty of Marine and Fisheries, Syiah Kuala University, Banda Aceh, Aceh, Indonesia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hizir Sofyan
- Faculty of Mathematics and Natural Science, Syiah Kuala University, Banda Aceh, Aceh, Indonesia
| | - Zainal A Muchlisin
- Faculty of Marine and Fisheries, Syiah Kuala University, Banda Aceh, Aceh, Indonesia
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Wang C, Bi H, Xie J. Visualization of the Distance among Fishes by MALDI MS for Rapid Determination of the Taxonomic Status of Fish Fillets. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8438-8446. [PMID: 32648743 DOI: 10.1021/acs.jafc.0c01291] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Taxonomic research plays an important role in the classification of organisms. Molecular techniques provide useful tools for the determination of the taxonomic status of species, although often time-consuming and not cost-efficient. Herein, we developed a strategy to analyze fish samples in a rapid mode. Experimentally, fish fillet samples were pretreated with trifluoroacetic acid aqueous solution, and the obtained protein fraction was analyzed by matrix-assisted laser desorption/ionization mass spectrometry. Principal component analysis of mass spectrometric datasets was used to visualize the taxonomical distance among the analyzed 13 seafood species. The results were illustrated using treemaps where the fish relationship distance can be visualized. The obtained mass spectral results can be taken as reference and successfully used for the identification of unknown fish fillet samples. It is promising to utilize the present strategy to provide clues for the taxonomy study among ambiguous species and identify fish species.
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Affiliation(s)
- Chengyu Wang
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China
| | - Hongyan Bi
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China
| | - Jing Xie
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China
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DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01155-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractWithin Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.
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Stern N, Gouws G, Golani D, Goren M, Gon O. Champsodontidae (Pisces: Trachinoidei) in the Eastern Mediterranean: how many species are there? J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1758820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nir Stern
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Gavin Gouws
- National Research Foundation – South African Institute for Aquatic Biodiversity, Makhanda, South Africa
| | - Daniel Golani
- Department of Ecology, Evolution and Behaviour & National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Menachem Goren
- The Steinhardt Museum of Natural History and School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Gon
- National Research Foundation – South African Institute for Aquatic Biodiversity, Makhanda, South Africa
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Ma Q, He K, Wang X, Jiang J, Zhang X, Song Z. Better Resolution for Cytochrome b than Cytochrome c Oxidase Subunit I to Identify Schizothorax Species (Teleostei: Cyprinidae) from the Tibetan Plateau and Its Adjacent Area. DNA Cell Biol 2020; 39:579-598. [PMID: 32069124 DOI: 10.1089/dna.2019.5031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Schizothorax is one of the most diverse groups of schizothoracine fish. Many species within this genus possess highly similar morphological characters and are very difficult to be identified accurately only based on morphology. The present study aims to test the effectiveness of mitochondrial cytochrome c oxidase subunit I (COI) gene and cytochrome b (Cytb) gene for discriminating the Schizothorax fish. A total of 185 individuals of 11 species for COI gene and 264 individuals of 23 species for Cytb gene were used for analyzing, respectively. According to the genetic distances, only one species based on COI gene and five species based on Cytb gene had "barcoding gaps," respectively. The tree-based analysis displayed that four species based on COI gene and six species based on Cytb gene clustered monophyletic group with strong support, respectively. The optimal threshold value of Schizothorax is 0.005 based on COI gene and 0.008 based on Cytb gene. The results of genetic similarity tests performed through online BLAST showed that 108 of 185 similarity searches succeeded in identifying conspecific sequences based on COI gene and 199 of 264 succeeded in identifying conspecific sequences based on Cytb gene. Considering greater interspecific genetic distance in Kimura 2-parameter (K2P) analysis and many clades with higher supporting values in tree-based analysis, we suggest that Cytb gene has better resolution in discrimination of Schizothorax species than COI gene. However, there are still many confused clustering relationships based on molecular data currently available. Incomplete lineage sorting, the existence of possible cryptic species and problematic morphological identification, etc. might have greatly weakened the resolution of Cytb gene in discrimination of Schizothorax species.
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Affiliation(s)
- Qingzhan Ma
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun He
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaodong Wang
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiuyue Zhang
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhaobin Song
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China.,College of Life Sciences, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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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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Fish diversity of the largest deltaic formation in the Americas - a description of the fish fauna of the Parnaíba Delta using DNA Barcoding. Sci Rep 2019; 9:7530. [PMID: 31101898 PMCID: PMC6525184 DOI: 10.1038/s41598-019-43930-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/03/2019] [Indexed: 01/29/2023] Open
Abstract
Deltas are dynamic and productive systems of enormous ecological significance, encompassing unique and biologically diverse wetland habitats. Here, we present the first data on the molecular diversity of the fish fauna of the Parnaíba Delta, the largest deltaic formation of the Americas. Partial sequences (626 bp) of the mitochondrial COI gene (Cytochrome c oxidase subunit I) were used to barcode 402 individuals, representing 128 species, belonging to 98 genera, 57 families, 17 orders and two classes. The most abundant orders were the Perciformes, Siluriformes, Gobiiformes, and Pleuronectiformes. The Neighbor-Joining (NJ), Bayesian Inference (BI), and BIN analyses produced 103 molecular clusters, while the Automatic Barcode Gap Discovery (ABGD) and Maximum Likelihood (ML) approaches revealed 102 clusters. The mean conspecific, congeneric and confamilial genetic distances were 0.33%, 14.37%, and 18.60%, respectively. Intraspecific divergence ranged from 0.0% to 1.4%, and all species presented barcode gaps, with the exception of two clusters of Cathorops spixii (OTU 96 and OTU 103), which were separated by a low interspecific distance (1.2%), which overlaps the maximum intraspecific genetic distance (1.4%). The barcode data provide new insights into the fish diversity of the Parnaíba Delta, which will be important for the development of further research on this fauna.
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Oyama H, Itoi S, Ueda H, Mochizuki Y, Tanaka M, Ito T, Shishido H, Masuda Y, Takai N, Sugita H. Genetic difference between African and Japanese scombropid populations based on cytochrome c oxidase subunit I gene sequences. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1584056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Hikaru Oyama
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Shiro Itoi
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Hiroyuki Ueda
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Yukako Mochizuki
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Minori Tanaka
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Takeshi Ito
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Hirotoshi Shishido
- Kagoshima Prefectural Fisheries Technology and Development Center, Ibusuki, Japan
| | - Yasuji Masuda
- Faculty of Fisheries, Kagoshima University, Kagoshima, Japan
| | - Noriyuki Takai
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Haruo Sugita
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
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Verrez-Bagnis V, Sotelo CG, Mendes R, Silva H, Kappel K, Schröder U. Methods for Seafood Authenticity Testing in Europe. BIOACTIVE MOLECULES IN FOOD 2019. [DOI: 10.1007/978-3-319-78030-6_69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Underwood JN, Travers MJ, Snow M, Puotinen M, Gouws G. Cryptic lineages in the Wolf Cardinalfish living in sympatry on remote coral atolls. Mol Phylogenet Evol 2018; 132:183-193. [PMID: 30528081 DOI: 10.1016/j.ympev.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 10/11/2018] [Accepted: 12/04/2018] [Indexed: 10/27/2022]
Abstract
Coral reef health and biodiversity is under threat worldwide due to rapid climate change. However, much of the inter- and intra-specific diversity of coral reefs are undescribed even in well studied taxa such as fish. Delimiting previously unrecognised diversity is important for understanding the processes that generate and sustain biodiversity in coral reef ecosystems and informing strategies for their conservation and management. Many taxa that inhabit geographically isolated coral reefs rely on self-recruitment for population persistence, providing the opportunity for the evolution of unique genetic lineages through divergent selection and reproductive isolation. Many such lineages in corals and fish are morphologically similar or indistinguishable. Here, we report the discovery and characterisation of cryptic lineages of the Wolf Cardinalfish, Cheilodipterus artus, from the coral atolls of northwest Australia using multiple molecular markers from mitochondrial (CO1 and D-loop) and nuclear (microsatellites) DNA. Concordant results from all markers identified two highly divergent lineages that are morphologically cryptic and reproductively isolated. These lineages co-occurred at daytime resting sites, but the relative abundance of each lineage was strongly correlated with wave exposure. It appears, therefore, that fish from each lineage are better adapted to different microhabitats. Such cryptic and ecologically based diversity appears to be common in these atolls and may well aid resilience of these systems. Our results also highlight that underwater surveys based on visual identification clearly underestimate biodiversity, and that a taxonomic revision of the Cheilodipterus genus is necessary.
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Affiliation(s)
- Jim N Underwood
- Australian Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA 6009, Australia.
| | - Michael J Travers
- Australian Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA 6009, Australia; Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, PO Box 20, North Beach, Western Australia 6920, Australia
| | - Michael Snow
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, PO Box 20, North Beach, Western Australia 6920, Australia
| | - Marji Puotinen
- Australian Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA 6009, Australia
| | - Gavin Gouws
- National Research Foundation - South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown 6140, South Africa
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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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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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Rosas U, Menendez F, Cornejo R, Canales R, Velez-Zuazo X. Fish DNA barcoding around large marine infrastructure for improved biodiversity assessment and monitoring. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1174-1179. [PMID: 29373939 DOI: 10.1080/24701394.2018.1431225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Accurate species-level identification is pivotal for environmental assessments and monitoring. The PERU LNG terminal is composed of large marine infrastructure located on the central coast of Peru. Since construction, taxonomically challenging species such as drum fishes (Sciaenidae) have been attracted to the new hard-bottom habitat. We conducted a DNA barcoding study to investigate fish diversity and constructed a DNA barcode reference library. We examined 56 vouchered specimens and identified 24 unique species. Intra- and interspecific divergence estimates ranged between 0 and 0.64% and 11 and 35.5%, respectively. We assessed the efficiency of the reference library to identify 29 non-vouchered specimens. We had 82.5% efficiency by using both our reference library (n = 17) and GenBank (n = 24). We highlight the importance of implementing molecular barcoding for complementing biodiversity assessments in marine environments. This study represents a first step towards generating a comprehensive DNA barcode reference library for marine fishes in Peru.
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Affiliation(s)
- Ulises Rosas
- a Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park , Washington , DC , USA.,b Departamento de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos , Lima , Peru
| | - Francisco Menendez
- a Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park , Washington , DC , USA
| | - Rodolfo Cornejo
- c Instituto del Mar del Peru (IMARPE) , Callao , Peru.,d Facultad de Oceanografía, Pesquería, Alimentarias y Acuicultura , Universidad Nacional Federico Villarreal , Miraflores , Peru
| | - Remy Canales
- b Departamento de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos , Lima , Peru
| | - Ximena Velez-Zuazo
- a Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park , Washington , DC , USA
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Hou G, Chen WT, Lu HS, Cheng F, Xie SG. Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification, accuracy and cryptic diversity. Mol Ecol Resour 2017; 18:137-146. [DOI: 10.1111/1755-0998.12718] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/14/2017] [Accepted: 08/14/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Gang Hou
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
- Guangdong Ocean University; Zhanjiang China
| | - Wei-Tao Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | | | - Fei Cheng
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Song-Guang Xie
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- Huai'an Research Center; Institute of Hydrobiology; Chinese Academy of Sciences; Huai'an China
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Engin S, Seyhan D. A new species of Pomatoschistus (Teleostei, Gobiidae): the Mediterranean's smallest marine fish. JOURNAL OF FISH BIOLOGY 2017; 91:1208-1223. [PMID: 28905379 DOI: 10.1111/jfb.13455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
The new sand goby species Pomatoschistus nanus (Teleostei: Gobiidae) is described from the northern coast of the Levantine Sea (eastern Mediterranean Sea) based on both morphological and DNA barcoding data. The new species is the smallest fish in the Mediterranean Sea and may be distinguished from congeners by the following features: predorsal area, first dorsal-fin base and breast naked; δ-pore missing; anterior point of the suborbital row b not reaching level of posterior point of suborbital row d; slightly emarginated caudal fin and nape coloration pattern. DNA barcode data clearly discriminate Pomatoschistus spp. in the neighbour-joining tree with an average of 17·7% interspecific K2P distance. The most closely related taxon to P. nanus sp. nov. is Pomatoschistus bathi and the most distantly related is Pomatoschistus tortonesei with 11·9 and 21·9% K2P distances respectively. Morphometric and genetic data are also provided for Pomatoschistus bathi.
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Affiliation(s)
- S Engin
- Izmir Katip Celebi University, Faculty of Fisheries, 35620 Cigli/Izmir, Turkey
| | - D Seyhan
- Izmir Katip Celebi University, Faculty of Fisheries, 35620 Cigli/Izmir, Turkey
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Mascolo C, Ceruso M, Sordino P, Palma G, Anastasio A, Pepe T. Development of a Method to Extract and Amplify the Complete Mitogenome of Some Sparidae Species. Ital J Food Saf 2017; 6:6154. [PMID: 28713786 PMCID: PMC5505091 DOI: 10.4081/ijfs.2017.6154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/13/2017] [Indexed: 11/28/2022] Open
Abstract
Previous studies showed that fish mitochondrial DNA (mtDNA) is set up by a closed circular molecule of 16-17 kilobases (kb), comprising 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), 13 protein-coding genes and 2 non-coding regions. The analysis of single mtDNA genes, such as Cytb, COI, 16S and 12S, or short segment of them, has been widely used against species substitution in both fresh and processed fish products. The analysis of the complete mitochondrial genome of fishery products allows to better study and characterise fish species. The aim of this research was to extract and amplify the complete mtDNA of some fish species of commercial interest belonging to the Sparidae family. The studied species were Dentex dentex, Dentex gibbosus, Dentex nufar, Pagellus acarne and Pagellus erythrinus. The entire mitogenome was obtained by gene amplification using long polymerase chain reactions. The analysis of the complete mitochondrial sequences will allow to gain further insights on these species and to find polymorphic sites that assess the degree of genetic variability of the species belonging to the family Sparidae.
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Affiliation(s)
- Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy.,Biology and Evolution of Marine Organisms, Research Centre Anton Dohrn Zoological Station, Naples, Italy
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Paolo Sordino
- Biology and Evolution of Marine Organisms, Research Centre Anton Dohrn Zoological Station, Naples, Italy
| | | | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
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Clusa L, Ardura A, Fernández S, Roca AA, García-Vázquez E. An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples. PeerJ 2017; 5:e3045. [PMID: 28265514 PMCID: PMC5333537 DOI: 10.7717/peerj.3045] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/30/2017] [Indexed: 11/20/2022] Open
Abstract
Background Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings. Methods Here we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples. Results The method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain). Discussion This new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms.
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Affiliation(s)
- Laura Clusa
- Department of Functional Biology, University of Oviedo , Oviedo , Asturias , Spain
| | - Alba Ardura
- USR3278-CRIOBE-CNRS-EPHE-UPVD, Laboratoire d'Excellence "CORAIL", Université de Perpignan , Perpignan , France
| | - Sara Fernández
- Department of Functional Biology, University of Oviedo , Oviedo , Asturias , Spain
| | - Agustín A Roca
- Department of Functional Biology, University of Oviedo , Oviedo , Asturias , Spain
| | - Eva García-Vázquez
- Department of Functional Biology, University of Oviedo , Oviedo , Asturias , Spain
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Cariani A, Messinetti S, Ferrari A, Arculeo M, Bonello JJ, Bonnici L, Cannas R, Carbonara P, Cau A, Charilaou C, El Ouamari N, Fiorentino F, Follesa MC, Garofalo G, Golani D, Guarniero I, Hanner R, Hemida F, Kada O, Lo Brutto S, Mancusi C, Morey G, Schembri PJ, Serena F, Sion L, Stagioni M, Tursi A, Vrgoc N, Steinke D, Tinti F. Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library. PLoS One 2017; 12:e0170244. [PMID: 28107413 PMCID: PMC5249125 DOI: 10.1371/journal.pone.0170244] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/30/2016] [Indexed: 11/18/2022] Open
Abstract
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.
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Affiliation(s)
- Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Silvia Messinetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Marco Arculeo
- Department STEBICEF, University of Palermo, Palermo, Italy
| | | | | | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | | | - Alessandro Cau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Charis Charilaou
- Department of Fisheries and Marine Research, Ministry of Agriculture, Rural Development and Environment, Nicosia, Republic of Cyprus
| | - Najib El Ouamari
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | - Fabio Fiorentino
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | | | - Germana Garofalo
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | - Daniel Golani
- Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilaria Guarniero
- Department DIMEVET, University of Bologna, Ozzano dell'Emilia, Italy
| | - Robert Hanner
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Farid Hemida
- Ecole Nationale Superieure des Sciences de la Mer et d'Amenagement du Littoral, Campus Universitaire de Dely Ibrahim, Alger, Algeria
| | - Omar Kada
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | | | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | | | | | - Fabrizio Serena
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Letizia Sion
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Angelo Tursi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Nedo Vrgoc
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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DNA barcoding reveals substitution of Sablefish (Anoplopoma fimbria) with Patagonian and Antarctic Toothfish (Dissostichus eleginoides and Dissostichus mawsoni) in online market in China: How mislabeling opens door to IUU fishing. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.06.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chang CH, Shao KT, Lin HY, Chiu YC, Lee MY, Liu SH, Lin PL. DNA barcodes of the native ray-finned fishes in Taiwan. Mol Ecol Resour 2016; 17:796-805. [DOI: 10.1111/1755-0998.12601] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Chia-Hao Chang
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Kwang-Tsao Shao
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Han-Yang Lin
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Yung-Chieh Chiu
- Department of Aquaculture; National Taiwan Ocean University; Keelung Taiwan
| | - Mao-Ying Lee
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Shih-Hui Liu
- Department of Biology; Saint Louis University; 3507 Laclede Avenue, Macelwane Hall St. Louis MO 63103 USA
| | - Pai-Lei Lin
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
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Molecular Identification and Traceability of Illegal Trading in Lignobrycon myersi (Teleostei: Characiformes), a Threatened Brazilian Fish Species, Using DNA Barcode. ScientificWorldJournal 2016; 2016:9382613. [PMID: 27668281 PMCID: PMC5030449 DOI: 10.1155/2016/9382613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 11/18/2022] Open
Abstract
Lignobrycon myersi is a threatened freshwater fish species and endemic of a few coastal rivers in northeastern Brazil. Even though the Brazilian laws prohibit the fisheries of threatened species, L. myersi is occasionally found in street markets, being highly appreciated by local population. In order to provide a reliable DNA barcode dataset for L. myersi, we compared mitochondrial sequences of cytochrome c oxidase subunit I (COI) from fresh, frozen, and salt-preserved specimens. Phylogenetically related species (Triportheus spp.) and other fish species (Astyanax fasciatus) commonly mixed with L. myersi in street markets were also included to test the efficiency of molecular identification. In spite of the differences in conservation processes and advanced deterioration of some commercial samples, high-quality COI sequences were obtained and effective in discriminating L. myersi specimens. In addition, while populations from Contas and Almada River basins seem to comprise a single evolutionary lineage, the specimens from Cachoeira River were genetically differentiated, indicating population structuring. Therefore, DNA barcoding has proved to be useful to trace the illegal trading of L. myersi and to manage threatened populations, which should focus on conservation of distinct genetic stocks and mitigation on human impacts along their range.
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Chaveerach A, Tanee T, Sanubol A, Monkheang P, Sudmoon R. Efficient DNA barcode regions for classifying Piper species (Piperaceae). PHYTOKEYS 2016; 70:1-10. [PMID: 27829794 PMCID: PMC5088699 DOI: 10.3897/phytokeys.70.6766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 09/02/2016] [Indexed: 05/23/2023]
Abstract
Piper species are used for spices, in traditional and processed forms of medicines, in cosmetic compounds, in cultural activities and insecticides. Here barcode analysis was performed for identification of plant parts, young plants and modified forms of plants. Thirty-six Piper species were collected and the three barcode regions, matK, rbcL and psbA-trnH spacer, were amplified, sequenced and aligned to determine their genetic distances. For intraspecific genetic distances, the most effective values for the species identification ranged from no difference to very low distance values. However, Piper betle had the highest values at 0.386 for the matK region. This finding may be due to Piper betle being an economic and cultivated species, and thus is supported with growth factors, which may have affected its genetic distance. The interspecific genetic distances that were most effective for identification of different species were from the matK region and ranged from a low of 0.002 in 27 paired species to a high of 0.486. Eight species pairs, Piper kraense and Piper dominantinervium, Piper magnibaccum and Piper kraense, Piper phuwuaense and Piper dominantinervium, Piper phuwuaense and Piper kraense, Piper pilobracteatum and Piper dominantinervium, Piper pilobracteatum and Piper kraense, Piper pilobracteatum and Piper phuwuaense and Piper sylvestre and Piper polysyphonum, that presented a genetic distance of 0.000 and were identified by independently using each of the other two regions. Concisely, these three barcode regions are powerful for further efficient identification of the 36 Piper species.
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Affiliation(s)
- Arunrat Chaveerach
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
- Genetics and Environmental Toxicology (GET) Research Group, Khon Kaen University, Thailand
| | - Tawatchai Tanee
- Genetics and Environmental Toxicology (GET) Research Group, Khon Kaen University, Thailand
- Faculty of Environment and Resource Studies, Mahasarakham University, Mahasarakham 44150, Thailand
| | - Arisa Sanubol
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
- Genetics and Environmental Toxicology (GET) Research Group, Khon Kaen University, Thailand
| | - Pansa Monkheang
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
- Genetics and Environmental Toxicology (GET) Research Group, Khon Kaen University, Thailand
| | - Runglawan Sudmoon
- Genetics and Environmental Toxicology (GET) Research Group, Khon Kaen University, Thailand
- Faculty of Law, Khon Kaen University, Thailand
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Thiel R, Knebelsberger T. How reliably can northeast Atlantic sand lances of the genera Ammodytes and Hyperoplus be distinguished? A comparative application of morphological and molecular methods. Zookeys 2016:139-64. [PMID: 27667958 PMCID: PMC5027774 DOI: 10.3897/zookeys.617.8866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/06/2016] [Indexed: 11/21/2022] Open
Abstract
Accurate stock assessments for each of the dominant species of sand lances in the northeast Atlantic Ocean and adjacent areas are not available due to the lack of a reliable identification procedure; therefore, appropriate measures of fisheries management or conservation of sand lances cannot be implemented. In this study, detailed morphological and molecular features are assessed to discriminate between four species of sand lances belonging to the genera Ammodytes and Hyperoplus. Morphological characters described by earlier authors as useful for identification of the genera are confirmed, and two additional distinguishing characters are added. A combination of the following morphological characters is recommended to distinguish between the genera Hyperoplus and Ammodytes: the protrusibility of the premaxillae, the presence of hooked ends of the prevomer, the number of dermal plicae, and the pectoral-fin length as a percentage of the standard length. The discriminant function analysis revealed that morphometric data are not very useful to distinguish the species of each of the two genera. The following meristic characters improve the separation of Hyperopluslanceolatus from Hyperoplusimmaculatus: the number of lower arch gill rakers, total number of gill rakers, numbers of caudal vertebrae and total vertebrae, and numbers of dorsal-fin and anal-fin rays. It is confirmed that Ammodytestobianus differs from Ammodytesmarinus by its belly scales that are organised in tight chevrons, scales which are present over the musculature at the base of the caudal fin, as well as by the lower numbers of dermal plicae, dorsal-fin rays, and total vertebrae. In contrast to the morphological data, mitochondrial COI sequences (DNA barcodes) failed to separate unambiguously the four investigated species. Ammodytestobianus and Hyperopluslanceolatus showed an overlap between intraspecific and interspecific K2P genetic distances and cannot be reliably distinguished using the common DNA barcoding approach. Ammodytesmarinus and Hyperoplusimmaculatus exhibited gaps between intraspecific and interspecific K2P distances of 2.73 and 3.34% respectively, indicating that their DNA barcodes can be used for species identification. As an alternative, short nuclear Rhodopsin sequences were analysed and one diagnostic character was found for each of the species Ammodytesmarinus, Hyperopluslanceolatus, and Hyperoplusimmaculatus. Ammodytestobianus can be characterised by the lack of species-specific mutations when compared to the other three species. In contrast to COI, the short nuclear sequences represent a useful alternative for rapid species identification whenever an examination of morphological characters is not available.
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Affiliation(s)
- Ralf Thiel
- University of Hamburg, Center of Natural History, Zoological Museum, 20146 Hamburg, Germany
| | - Thomas Knebelsberger
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382 Wilhelmshaven, Germany
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Falade MO, Opene AJ, Benson O. DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria. F1000Res 2016; 5:1268. [PMID: 27990256 PMCID: PMC5133684 DOI: 10.12688/f1000research.7895.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/20/2022] Open
Abstract
DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5' region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodonmelanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.
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Affiliation(s)
- Mofolusho O. Falade
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Anthony J. Opene
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Otarigho Benson
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
- Department of Biological Science, Edo University, Iyamho, Edo State, Nigeria
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Pugedo ML, de Andrade Neto FR, Pessali TC, Birindelli JLO, Carvalho DC. Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin. Genetica 2016; 144:341-9. [PMID: 27170425 DOI: 10.1007/s10709-016-9903-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
Molecular identification through DNA barcoding has been proposed as a way to standardize a global biodiversity identification system using a partial sequence of the mitochondrial COI gene. We applied an integrative approach using DNA barcoding and traditional morphology-based bioassessment to identify fish from a neotropical region possessing low taxonomic knowledge: the Jequitinhonha River Basin (Southeastern Brazil). The Jequitinhonha River Basin (JRB) has a high rate of endemism and is considered an area of high priority for fish conservation, with estimates indicating the presence of around 110 native and non-indigenous species. DNA barcodes were obtained from 260 individuals belonging to 52 species distributed among 35 genera, 21 families and 6 orders, including threatened and rare species such as Rhamdia jequitinhonha and Steindachneridion amblyurum. The mean Kimura two-parameter genetic distances within species, genera and families were: 0.44, 12.16 and 20.58 %, respectively. Mean intraspecific genetic variation ranged from 0 to 11.43 %, and high values (>2 %) were recovered for five species. Species with a deep intraspecific distance, possibly flagging overlooked taxa, were detected within the genus Pimelodella. Fifteen species, only identified to the genus level, had unique BINs, with a nearest neighbor distance over 2 % and therefore, potential new candidate species supported by DNA barcoding. The integrative taxonomy approach using DNA barcoding and traditional taxonomy may be a remedy to taxonomy impediment, accelerating species identification by flagging potential new candidate species and to adequately conserve the megadiverse neotropical ichthyofauna.
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Affiliation(s)
- Marina Lages Pugedo
- Programa de Pós-graduação em Zoologia de Vertebrados, Laboratório de Genética da Conservação, PUC Minas, Rua Dom José Gaspar, 500, 30535-901, Belo Horizonte, Minas Gerais, Brazil
| | | | - Tiago Casarim Pessali
- Laboratório de Ictiologia, Museu de Ciências Naturais, PUC Minas, Belo Horizonte, Minas Gerais, Brazil
| | | | - Daniel Cardoso Carvalho
- Programa de Pós-graduação em Zoologia de Vertebrados, Laboratório de Genética da Conservação, PUC Minas, Rua Dom José Gaspar, 500, 30535-901, Belo Horizonte, Minas Gerais, Brazil.
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