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Vilas-Arrondo N, Gomes-dos-Santos A, Pérez M, Baldó F, Veríssimo A, Catarino D, Machado AM, Román-Marcote E, Bañón R, Froufe E, Castro LFC. A mitochondrial genome assembly of the opal chimaera, Chimaera opalescens Luchetti, Iglésias et Sellos 2011, using PacBio HiFi long reads. Mitochondrial DNA B Resour 2022; 7:434-437. [PMID: 35274036 PMCID: PMC8903783 DOI: 10.1080/23802359.2022.2044403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chondrichthyans (sharks, rays and chimeras) are a fascinating and highly vulnerable group of early branching gnathostomes. However, they remain comparatively poorly sampled from the point of view of molecular resources, with deep water taxa being particularly data deficient. The development of long-read sequencing technologies enables the analysis of phylogenetic relationships through a precise and reliable assembly of complete mtDNA genomes. The sequencing and characterization of the complete mitogenome of the opal chimera Chimera opalescens Luchetti, Iglésias et Sellos 2011, using the long-read technique PacBio HiFi is presented. The entire mitogenome was 23,411 bp long and shows the same overall content, i.e. 13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes, as all other examined Chondrichthyan mitogenomes. Phylogenetic reconstructions using all available Chondrichthyan mitogenomes, including 11 Holocephali (chimeras and ratfishes), places C. opalescens within the Chimaeridae family. Furthermore, the results reinforce previous findings, showing the genus Chimera as paraphyletic and thus highlighting the need to expand molecular approaches in this group of cartilaginous fishes.
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Affiliation(s)
- Nair Vilas-Arrondo
- AQUACOV, Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de Vigo, Vigo, Spain
- UVIGO, PhD Program “Marine Science, Technology and Management” (Do*MAR), Faculty of Biology, University of Vigo, Vigo, Spain
| | - André Gomes-dos-Santos
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Montse Pérez
- AQUACOV, Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de Vigo, Vigo, Spain
| | - Francisco Baldó
- Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de Cádiz, Cádiz, Spain
| | - Ana Veríssimo
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Diana Catarino
- Ocean Sciences Institute - Okeanos, Universidade dos Açores, Horta, Portugal
| | - André M. Machado
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Esther Román-Marcote
- Servizo de Planificación, Consellería do Mar, Xunta de Galicia, Santiago de Compostela, Spain; BIOPESLE, Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de Vigo, Vigo, Spain
| | - Rafael Bañón
- Ocean Sciences Institute - Okeanos, Universidade dos Açores, Horta, Portugal
- Grupo de Estudos do Medio Mariño (GEMM), Ribeira, Spain
| | - Elsa Froufe
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - L. Filipe C. Castro
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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Catarino D, Jakobsen K, Jakobsen J, Giacomello E, Menezes GM, Diogo H, Canha Â, Porteiro FM, Melo O, Stefanni S. First record of the opal chimaera, Chimaera opalescens (Holocephali: Chimaeridae) and revision of the occurrence of the rabbitfish Chimaera monstrosa in the Azores waters. JOURNAL OF FISH BIOLOGY 2020; 97:763-775. [PMID: 32520391 DOI: 10.1111/jfb.14432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
The presence of the opal chimaera, Chimaera opalescens, is reported for the first time in the deep waters of the Azores, with the capture of four specimens by fishermen and the video recording of an additional five individuals. Species identification was supported by the 646 bp sequenced fragment of the mitochondrial gene cytochrome oxidase subunit I. Because C. opalescens is a recently recognised species that had been recurrently misidentified as rabbitfish, Chimaera monstrosa, the historical data of C. monstrosa in the Azores were reviewed to assess the possible presence of both Chimaera species in the region. Although several authors have reported the occurrence of C. monstrosa in the Azorean waters since the 1800s, the majority of these are based on only three specimens caught during the late 1800s. The investigation performed using literature and examination of the museum specimens still available concluded that the most likely scenario is that C. monstrosa is absent from the Azores and past records of that species in the region are most likely misidentifications of C. opalescens.
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Affiliation(s)
- Diana Catarino
- MARE, Marine and Environmental Sciences Centre, Horta, Portugal
- OKEANOS Centre, University of the Azores, Horta, Portugal
- IMAR-Instituto do Mar, Horta, Portugal
- Department of Natural Sciences, Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | | | | | - Eva Giacomello
- MARE, Marine and Environmental Sciences Centre, Horta, Portugal
- OKEANOS Centre, University of the Azores, Horta, Portugal
- IMAR-Instituto do Mar, Horta, Portugal
| | - Gui M Menezes
- Regional Directorate of Fisheries, Secretariat of Sea, Science and Technology, Azores Regional Government, Horta, Portugal
- Department of Oceanography and Fisheries (DOP), University of the Azores, Horta, Portugal
| | - Hugo Diogo
- OKEANOS Centre, University of the Azores, Horta, Portugal
- Regional Directorate of Fisheries, Secretariat of Sea, Science and Technology, Azores Regional Government, Horta, Portugal
| | - Ângela Canha
- OKEANOS Centre, University of the Azores, Horta, Portugal
- Regional Directorate of Fisheries, Secretariat of Sea, Science and Technology, Azores Regional Government, Horta, Portugal
| | - Filipe M Porteiro
- Department of Oceanography and Fisheries (DOP), University of the Azores, Horta, Portugal
- Regional Directorate of Sea Affairs, Secretariat of Sea, Science and Technology, Azores Regional Government, Horta, Portugal
| | - Octávio Melo
- OKEANOS Centre, University of the Azores, Horta, Portugal
- IMAR-Instituto do Mar, Horta, Portugal
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A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses. PLoS One 2019; 14:e0218904. [PMID: 31891586 PMCID: PMC6938304 DOI: 10.1371/journal.pone.0218904] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/09/2019] [Indexed: 02/08/2023] Open
Abstract
Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.
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