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Kawai K, Fujita H, Umino T. The complete mitochondrial genome of Acanthopagrus pacificus (Perciformes, Sparidae) from Iriomotejima Island, Okinawa, Japan. Mitochondrial DNA B Resour 2022; 7:1027-1029. [PMID: 35756456 PMCID: PMC9225699 DOI: 10.1080/23802359.2022.2080606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Kentaro Kawai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hiroki Fujita
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Tetsuya Umino
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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Isolation and characterization of 112 SNP markers in Yellowfin seabream (Acanthopagrus latus) using RAD sequencing. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01265-4] [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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Pan C, Gao C, Chen T, Chen X, Yang C, Zeng D, Feng P, Jiang W, Peng M. The complete mitochondrial genome of yellowfin seabream, Acanthopagrus latus (Percoiformes, Sparidae) from Beibu Bay. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1313-1314. [PMID: 33855186 PMCID: PMC8018338 DOI: 10.1080/23802359.2021.1907804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The yellowfin seabream, Acanthopagrus latus Houttuyn 1782, is a commercially and ecologically important species and a good model for studies of sexual differentiation. In this study, the complete mitochondrial genome of A. latus has been determined, which is 16,635 base pairs (54.3% A + T content) in length and consists of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a 948 bp D-loop region. The phylogenetic analyses showed that A. latus has a close relationship with Acanthopagrus schlegelii Bleeker 1854.
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Affiliation(s)
- Chuanyan Pan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Chongmin Gao
- Guangxi Agricultural Vocational College, Nanning, China
| | - Tao Chen
- Guangxi Agricultural Vocational College, Nanning, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Pengfei Feng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Weiming Jiang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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Ceruso M, Mascolo C, De Luca P, Venuti I, Smaldone G, Biffali E, Anastasio A, Pepe T, Sordino P. A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds. Foods 2020; 9:E1397. [PMID: 33023115 PMCID: PMC7600753 DOI: 10.3390/foods9101397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.
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Affiliation(s)
- Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Giorgio Smaldone
- Department Agricultural Sciences, University of Naples Federico II, via Università, n.100, Portici, 80055 Naples, Italy;
| | - Elio Biffali
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
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Comparison of mitochondrial DNA enrichment and sequencing methods from fish tissue. Food Chem 2019; 294:333-338. [PMID: 31126471 DOI: 10.1016/j.foodchem.2019.05.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 01/06/2023]
Abstract
Sparid fish species have different commercial values related to their organoleptic features. Mitochondrial (mt) DNA provides a potential tool to distinguish species, but the enrichment of high-quality mtDNA from total genomic DNA is critical to obtain entire mtDNA sequences. Conventional mtDNA isolation is relatively low-cost and proficient. However, high numbers of PCR cycles can lead to artefacts (10-6 mutations/bp). We describe a rapid protocol for mtDNA extraction and enrichment from fish tissues, based on conventional miniprep columns and paramagnetic bead-based purification, without the need to employ PCR amplification. This newly described method generates a substrate for next-generation sequencing (NGS) analysis and is likely to have wider applications for mitochondrial studies in other fish families to help ensure traceability and differentiation of fish with high commercial values.
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Mascolo C, Ceruso M, Palma G, Anastasio A, Sordino P, Pepe T. The complete mitochondrial genome of the axillary seabream, Pagellus acarne (Perciformes: Sparidae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:434-435. [PMID: 33474194 PMCID: PMC7800612 DOI: 10.1080/23802359.2018.1450674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The axillary seabream (Pagellus acarne, Risso 1827) belongs to the Sparidae family, order Perciformes. This high-valued commercial fish species is distributed along the northern and eastern Atlantic coasts from Norway to Senegal, and throughout the Mediterranean Sea. Its complete mitochondrial genome is 16,486 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions (D-loop, 808 bp and L-origin, 29 bp). Its overall base composition is A: 26,8%, C: 29,0%, G: 17.6%, and T: 26.6%.
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Affiliation(s)
- Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University "Federico II", Naples, Italy.,Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University "Federico II", Naples, Italy
| | | | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University "Federico II", Naples, Italy
| | - Paolo Sordino
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University "Federico II", Naples, Italy
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Dray L, Neuhof M, Diamant A, Huchon D. The complete mitochondrial genome of the gilthead seabream Sparus aurata L. (Sparidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:781-2. [PMID: 24963773 DOI: 10.3109/19401736.2014.928861] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the gilthead seabream Sparus aurata Linnaeus 1758, one of the world's most important mariculture species, was sequenced using next generation sequencing technology. The genome sequence is comprised of 16,652 bp exhibiting the canonical vertebrate mitochondria gene order. Regions of gene overlap, tRNA length, as well as start and stop codon were similar to those observed in other Sparidae. Phylogenetic reconstructions based on mitochondrial protein coding genes corroborate the view that Sparidae is paraphyletic and includes Centracanthidae.
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Affiliation(s)
- Liran Dray
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| | - Moran Neuhof
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| | - Arik Diamant
- b National Center for Mariculture, Israel Oceanographic and Limnological Research , Eilat Israel
| | - Dorothée Huchon
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
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Shi X, Su Y, Wang J, Ding S, Mao Y. Complete mitochondrial genome of black porgy Acanthopagrus schlegelii (Perciformes, Sparidae). ACTA ACUST UNITED AC 2012; 23:310-2. [PMID: 22591205 DOI: 10.3109/19401736.2012.683182] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Black porgy, Acanthopagrus schlegelii, is a marine protandrous hermaphrodite and belongs to one of the most important species commercialized for food in various areas of Asia. In this study, the complete mitochondrial genome of A. schlegelii has been determined. The mitogenome was 16,649 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions. It shared 90.2%, 82.3%, and 82.1% mitogenome sequence with Acanthopagrus latus, Parargyrops edita, and Pagrus major, respectively.
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Affiliation(s)
- Xiaofeng Shi
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
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Oh DJ, Oh BS, Jung MM, Jung YH. Complete mitochondrial genome of three Branchiostegus (Perciformes, Malacanthidae) species: genome description and phylogenetic considerations. ACTA ACUST UNITED AC 2011; 21:151-9. [PMID: 20958223 DOI: 10.3109/19401736.2010.503241] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three tilefishes (Branchiostegus albus, Branchiostegus argentatus, and Branchiostegus japonicus) to characterize and compare their mitochondrial genomes (mitogenomes). The mitogenomes of B. albus, B. argentatus, and B. japonicus were 16,532, 16,550, and 16,541 bp long, respectively, and all consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA (tRNAs)), which are typical for vertebrate mtDNA. As in other bony fishes, most genes were encoded on the H-strand, except for the nad6 and eight tRNA genes that were encoded on the L-strand. Among the 13 protein-coding genes of all three tilefishes, 2 reading-frame overlaps were found on the same strand: atp8 and atp6 overlapped by 10 nucleotides, and nad4L and nad4 overlapped by 7 nucleotides. The identity of the nad4 gene between B. albus and B. argentatus was the lowest at 87%. Conversely, the identity of the nad6 gene between B. albus and B. japonicus was the highest at 99%. Most tRNA genes were similar in length among the three species, while the tRNA-Ser((AGY)) of B. japonicus was 9 bp longer than those of B. albus and B. argentatus. The control region of the mitogenome spanned 853, 862, and 856 bp in B. albus, B. argentatus, and B. japonicus, respectively. A maximum likelihood tree constructed using 11,035 sites contained five independent groups with bootstrap values of 100% in support of their divergence. All three tilefishes examined were clustered with the Pomacanthidae species in Group II.
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Affiliation(s)
- Dae-Ju Oh
- Jeju Biodiversity Research Institute, Jeju HiDI, Seogwipo, Jeju, Republic of Korea
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