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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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Barcelos LMD, Azevedo JMN, Barreiros JP. Updated checklist of Azores Chondrichthyes (Vertebrata: Gnathostomata). Biodivers Data J 2021; 9:e62813. [PMID: 36761997 PMCID: PMC9848621 DOI: 10.3897/bdj.9.e62813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/18/2021] [Indexed: 11/12/2022] Open
Abstract
Background Several lists of marine fish from Azores have been published in the past. Most of those publications are difficult to access on line and several were not published in peer-reviewed journals. New information This checklist updates all the chondrichthyan records for the Azores Exclusive Economic Zone (EEZ), according to the most recent taxonomic classification of cartilaginous fish, as well as providing information on the conservation status for all species. We also present recent literature data on rare species and recent records for Azores. This is the first comprehensive list of cartilaginous fishes from Azores to be published in the GBIF database.
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Affiliation(s)
- Luís M. D. Barcelos
- University of the Azores, Angra do Heroísmo, PortugalUniversity of the AzoresAngra do HeroísmoPortugal,Centre for Ecology, Evolution and Environmental Changes (cE3c), Angra do Heroísmo, PortugalCentre for Ecology, Evolution and Environmental Changes (cE3c)Angra do HeroísmoPortugal
| | - José M. N. Azevedo
- University of the Azores, Angra do Heroísmo, PortugalUniversity of the AzoresAngra do HeroísmoPortugal,Centre for Ecology, Evolution and Environmental Changes (cE3c), Ponta Delgada, PortugalCentre for Ecology, Evolution and Environmental Changes (cE3c)Ponta DelgadaPortugal
| | - João Pedro Barreiros
- University of the Azores, Angra do Heroísmo, PortugalUniversity of the AzoresAngra do HeroísmoPortugal,Centre for Ecology, Evolution and Environmental Changes (cE3c), Angra do Heroísmo, PortugalCentre for Ecology, Evolution and Environmental Changes (cE3c)Angra do HeroísmoPortugal
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Gomes-Dos-Santos A, Vilas-Arrondo N, Machado AM, Veríssimo A, Pérez M, Baldó F, Castro LFC, Froufe E. Shedding light on the Chimaeridae taxonomy: the complete mitochondrial genome of the cartilaginous fish Hydrolagus mirabilis (Collett, 1904) (Holocephali: Chimaeridae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:420-422. [PMID: 33659699 PMCID: PMC7872578 DOI: 10.1080/23802359.2020.1870887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Cartilaginous fish are fascinating taxa, present in the folklore and art of many different cultures. Moreover, they display several unique anatomical, physiological, molecular, and behavioral characteristics making them extremely interesting from a biological perspective. Nevertheless, some crucial knowledge gaps remain, including phylogenetic relationships among extant species. Here, we produced the complete mitogenome sequence of the large-eyed rabbitfish, Hydrolagus mirabilis (Chimaeriformes). The complete mitogenome is 19,435 bp long and shows the same overall content, i.e. 13 protein-coding genes, 22 transfer RNA, and two ribosomal RNA genes, as all other examined Chondrichthyan mitogenomes. Phylogenetic reconstructions including 12 Holocephalan and three outgroup Elasmobranch mitogenomes place the H. mirabilis within the family Chimaeridae but revealed paraphyletic Hydrolagus and Chimaera, in line with a previous study, highlighting the importance for collecting additional molecular data to improve phylogenetic reconstruction in this group of vertebrates.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros de Leixões, Av. General Norton De Matos s/n, University of Porto, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nair Vilas-Arrondo
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Vigo, Spain.,Faculty of Biology, UVIGO, PhD Program "Marine Science, Technology and Management" (Do MAR), University of Vigo, Vigo, Spain
| | - André M Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros de Leixões, Av. General Norton De Matos s/n, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO - Research Centre in Biodiversity and Genetic Resources, Vairão, Portugal
| | - Montse Pérez
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Vigo, Spain
| | - Francisco Baldó
- Instituto Español de Oceanografía, Centro Oceanográfico de Cádiz, Puerto Pesquero, Muelle de Levante s/n, Cádiz, Spain
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros de Leixões, Av. General Norton De Matos s/n, University of Porto, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros de Leixões, Av. General Norton De Matos s/n, University of Porto, Matosinhos, Portugal
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