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Bemis KE, Girard MG, Santos MD, Carpenter KE, Deeds JR, Pitassy DE, Flores NAL, Hunter ES, Driskell AC, Macdonald KS, Weigt LA, Williams JT. Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens. Sci Data 2023; 10:411. [PMID: 37355644 PMCID: PMC10290705 DOI: 10.1038/s41597-023-02306-9] [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: 02/08/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.
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Affiliation(s)
- Katherine E Bemis
- National Systematics Laboratory, Office of Science and Technology, NOAA Fisheries, Washington, D.C., 20560, USA.
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA.
| | - Matthew G Girard
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA.
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, USA.
| | - Mudjekeewis D Santos
- Genetic Fingerprinting Laboratory, National Fisheries Research and Development Institute, Quezon City, 1103, Philippines
| | - Kent E Carpenter
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Jonathan R Deeds
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, USA
| | - Diane E Pitassy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA
| | - Nicko Amor L Flores
- Genetic Fingerprinting Laboratory, National Fisheries Research and Development Institute, Quezon City, 1103, Philippines
| | - Elizabeth S Hunter
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, USA
| | - Amy C Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA
| | - Lee A Weigt
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA
| | - Jeffrey T Williams
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, USA.
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Zhao M, Plough LV, Behringer DC, Bojko J, Kough AS, Alper NW, Xu L, Schott EJ. Cross-Hemispheric Genetic Diversity and Spatial Genetic Structure of Callinectes sapidus Reovirus 1 (CsRV1). Viruses 2023; 15:v15020563. [PMID: 36851777 PMCID: PMC9962310 DOI: 10.3390/v15020563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The movement of viruses in aquatic systems is rarely studied over large geographic scales. Oceanic currents, host migration, latitude-based variation in climate, and resulting changes in host life history are all potential drivers of virus connectivity, adaptation, and genetic structure. To expand our understanding of the genetic diversity of Callinectes sapidus reovirus 1 (CsRV1) across a broad spatial and host life history range of its blue crab host (Callinectes sapidus), we obtained 22 complete and 96 partial genomic sequences for CsRV1 strains from the US Atlantic coast, Gulf of Mexico, Caribbean Sea, and the Atlantic coast of South America. Phylogenetic analyses of CsRV1 genomes revealed that virus genotypes were divided into four major genogroups consistent with their host geographic origins. However, some CsRV1 sequences from the US mid-Atlantic shared high genetic similarity with the Gulf of Mexico genotypes, suggesting potential human-mediated movement of CsRV1 between the US mid-Atlantic and Gulf coasts. This study advances our understanding of how climate, coastal geography, host life history, and human activity drive patterns of genetic structure and diversity of viruses in marine animals and contributes to the capacity to infer broadscale host population connectivity in marine ecosystems from virus population genetic data.
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Affiliation(s)
- Mingli Zhao
- Institute of Marine and Environmental Technology, University of Maryland Baltimore County, Baltimore, MD 21202, USA
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London AL9 7TA, UK
| | - Louis V. Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
| | - Donald C. Behringer
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL 32653, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, USA
| | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
| | - Andrew S. Kough
- John G. Shedd Aquarium, Haerther Center for Conservation Research, Chicago, IL 60605, USA
| | - Nathaniel W. Alper
- Baltimore Polytechnic Institute, Columbia University, New York, NY 20027, USA
| | - Lan Xu
- Department of Marine Biotechnology and Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD 21202, USA
| | - Eric J. Schott
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
- Correspondence:
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Phylogeography of the Atlantic Blue Crab Callinectes sapidus (Brachyura: Portunidae) in the Americas versus the Mediterranean Sea: Determining Origins and Genetic Connectivity of a Large-Scale Invasion. BIOLOGY 2022; 12:biology12010035. [PMID: 36671728 PMCID: PMC9854962 DOI: 10.3390/biology12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
The American blue crab Callinectes sapidus is a particularly successful invader in estuarine ecosystems worldwide. Despite increasing awareness of its potential harm, the invasion history and underlying genetic diversity of this species within the Mediterranean Sea remain unknown. This study constitutes the first large-scale approach to study phylogeographic patterns of C. sapidus in Europe, facilitated by the first comparison of all currently available COI sequence data. For this investigation, 71 individuals of C. sapidus were newly analyzed and the entire COI gene was sequenced and used for a comparative phylogeographic analyses. For the first time, two separately used adjacent regions of this gene were combined in a single dataset. This allowed emphasizing the prevalence of three geographically defined lineages within the native range: (1) eastern North America, including the Gulf of Mexico, (2) the Caribbean, and (3) Brazil. New data from the Mediterranean reveal that non-native populations of C. sapidus are characterized by a conspicuously low genetic diversity (except for Turkey, where stocking took place), and that there is surprisingly low connectivity among established populations. The occurrence of strong genetic bottlenecks suggests few founder individuals. This confirms that, even under a scenario of restricted large-scale gene flow, a very limited number of invasive individuals is sufficient for a massive impact.
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Munguia-Vega A, Terrazas-Tapia R, Dominguez-Contreras JF, Reyna-Fabian M, Zapata-Morales P. DNA barcoding reveals global and local influences on patterns of mislabeling and substitution in the trade of fish in Mexico. PLoS One 2022; 17:e0265960. [PMID: 35421106 PMCID: PMC9009668 DOI: 10.1371/journal.pone.0265960] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/10/2022] [Indexed: 11/18/2022] Open
Abstract
Mislabeling of seafood is a global phenomenon that can misrepresent the status and level of consumption of wild fish stocks while concealing the use of many other wild species or those originating from aquaculture and sold as substitutes. We conducted a DNA barcoding study in three cities within Mexico (Mazatlan, Mexico City and Cancun) and sequenced the COI gene in 376 fish samples sold as 48 distinct commercial names at fish markets, grocery stores, and restaurants. Our goal was to identify the main species sold, their mislabeling rates and the species most used as substitutes. Overall, the study-wide mislabeling rate was 30.8% (95% CI 26.4–35.6). Half of the samples collected belonged to five species traded globally (yellowfin tuna, Atlantic salmon, mahi, swai, and tilapia), most of them with important aquaculture or ranching production levels. These species were commonly used as substitutes for other species and showed low mislabeling rates themselves (≤ 11%, except mahi mahi with 39% mislabeling). The other half of the samples revealed nearly 100 species targeted by small-scale fishers in Mexico and sold under 42 distinct commercial names. Popular local commercial names (dorado, marlin, mero, robalo, mojarra, huachinango, pargo, sierra) showed the highest mislabeling rates (36.3% to 94.4%) and served to sell many of the 53 species identified as substitutes in our study. We discuss the observed patterns in relation to landing and import data showing differences in availability of commercial species and the links to explain observed mislabeling rates and the use of a species as a substitute for other species. We also outline some of the implications of establishing a labeling and traceability standard as an alternative to improve transparency in the trade of seafood products in Mexico.
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Affiliation(s)
- Adrian Munguia-Vega
- Conservation Genetics Laboratory & Desert Laboratory on Tumamoc Hill, The University of Arizona, Tucson, Arizona, United States of America
- Applied Genomics Lab, La Paz, Baja California Sur, México
- * E-mail:
| | | | - Jose F. Dominguez-Contreras
- Instituto Politécnico Nacional–Centro Interdisciplinario de Ciencias Marinas (IPN- CICIMAR), La Paz, Baja California Sur, México
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, La Paz, Baja California Sur, México
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DNA barcoding allows identification of undescribed crab megalopas from the open sea. Sci Rep 2021; 11:20573. [PMID: 34663862 PMCID: PMC8523566 DOI: 10.1038/s41598-021-99486-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Megalopas of 15 brachyuran crab species collected in the open sea plankton, and unknown until now, were identified using DNA barcodes (COI and 16S rRNA). Specimens belonging to the families Portunidae, Pseudorhombilidae and Xanthidae (Crustacea, Decapoda, Brachyura), and corresponding to the species Achelous floridanus, Arenaeus mexicanus, Callinectes amnicola, C. arcuatus, C. ornatus, C. toxones, Charybdis (Charybdis) hellerii, Portunus hastatus, Thalamita admete, Scopolius nuttingi, Etisus odhneri, Liomera cinctimanus, Neoliomera cerasinus, Pseudoliomera variolosa, and Williamstimpsonia stimpsoni, are described and illustrated, and compared with other congeneric species previously described. We also provide a new geographical record for N. cerasinus and the most remarkable features for each species.
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Bachvaroff TR, McDonald RC, Plough LV, Chung JS. Chromosome-level genome assembly of the blue crab, Callinectes sapidus. G3-GENES GENOMES GENETICS 2021; 11:6304867. [PMID: 34544121 PMCID: PMC8496215 DOI: 10.1093/g3journal/jkab212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/14/2022]
Abstract
The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200× coverage Illumina paired-end reads, a 60× 8 kb mate-paired library, and 50× PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The 50 largest scaffolds span 810 Mb are 1.5-37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10 kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but 9 scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.
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Affiliation(s)
- Tsvetan R Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Ryan C McDonald
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Louis V Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Horn Point, MD 21613, USA
| | - J Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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