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Tang T, Huang Y, Peng C, Liao Y, Lv Y, Shi Q, Gao B. A Chromosome-Level Genome Assembly of the Reef Stonefish (Synanceia verrucosa) Provides Novel Insights into Stonustoxin (sntx) Genes. Mol Biol Evol 2023; 40:msad215. [PMID: 37770059 PMCID: PMC10566576 DOI: 10.1093/molbev/msad215] [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: 02/19/2023] [Revised: 08/22/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023] Open
Abstract
Reef stonefish (Synanceia verrucosa) is one of the most venomous fishes, but its biomedical study has been restricted to molecular cloning and purification of its toxins, instead of high-throughput genetic research on related toxin genes. In this study, we constructed a chromosome-level haplotypic genome assembly for the reef stonefish. The genome was assembled into 24 pseudo-chromosomes, and the length totaled 689.74 Mb, reaching a contig N50 of 11.97 Mb and containing 97.8% of complete BUSCOs. A total of 24,050 protein-coding genes were annotated, of which metalloproteinases, C-type lectins, and stonustoxins (sntx) were the most abundant putative toxin genes. Multitissue transcriptomic and venom proteomic data showed that sntx genes, especially those clustered within a 50-kb region on the chromosome 2, had higher transcription levels than other types of toxins as well as those sntx genes scatteringly distributed on other chromosomes. Further comparative genomic analysis predicted an expansion of sntx-like genes in the Percomorpha lineage including nonvenomous fishes, but Scorpaenoidei species experienced extra independent sntx duplication events, marking the clear-cut origin of authentic toxic stonustoxins. In summary, this high-quality genome assembly and related comparative analysis of toxin genes highlight valuable genetic differences for potential involvement in the evolution of venoms among Scorpaeniformes fishes.
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Affiliation(s)
- Tianle Tang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
- BGI-Marine Research Institute for Biomedical Technology, Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, Guangdong, China
| | - Yanling Liao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Yunyun Lv
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
- BGI-Marine Research Institute for Biomedical Technology, Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, Guangdong, China
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan, China
| | - Bingmiao Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
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Pappalardo AM, Giuga M, Raffa A, Nania M, Rossitto L, Calogero GS, Ferrito V. COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products. Foods 2022; 11:foods11111569. [PMID: 35681319 PMCID: PMC9180250 DOI: 10.3390/foods11111569] [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] [Received: 04/01/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/03/2022] Open
Abstract
The DNA analysis is the best approach to authenticate species in seafood products and to unveil frauds based on species substitution. In this study, a molecular strategy coupling Cytochrome Oxidase I (COI) DNA barcoding with the consolidated methodology of Restriction Fragment Length Polymorphisms (RFLPs), named COIBar-RFLP, was applied for searching pattern of restriction enzyme digestion, useful to discriminate seven different fish species (juveniles of Engraulis encrasicolus and Sardina pilchardus sold in Italy as “bianchetto” and Aphia minuta sold as “rossetto”; icefish Neosalanx tangkahkeii; European perch, Perca fluviatilis and the Nile Perch, Lates niloticus; striped catfish, Pangasianodon hypophthalmus). A total of 30 fresh and frozen samples were processed for DNA barcoding, analyzed against a barcode library of COI sequences retrieved from GenBank, and validated for COIBar–RFLP analysis. Cases of misdescription were detected: 3 samples labeled as “bianchetto” were substituted by N. tangkahkeii (2 samples) and A. minuta (1 sample); 3 samples labeled as “persico reale” (P. fluviatilis) were substituted by L. niloticus and P. hypophthalmus. All species were simultaneously discriminated through the restriction pattern obtained with MspI enzyme. The results highlighted that the COIBar-RFLP could be an effective tool to authenticate fish in seafood products by responding to the emerging interest in molecular identification technologies.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology “M. La Greca”, University of Catania, Via Androne 81, 95124 Catania, Italy; (A.M.P.); (M.G.); (A.R.); (M.N.); (L.R.); (G.S.C.)
| | - Marta Giuga
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology “M. La Greca”, University of Catania, Via Androne 81, 95124 Catania, Italy; (A.M.P.); (M.G.); (A.R.); (M.N.); (L.R.); (G.S.C.)
- Institute for the Study of Antropic Impact and Sustainability in the Marine Environment, IAS-CNR, 91021 Trapani, Italy
| | - Alessandra Raffa
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology “M. La Greca”, University of Catania, Via Androne 81, 95124 Catania, Italy; (A.M.P.); (M.G.); (A.R.); (M.N.); (L.R.); (G.S.C.)
| | - Marco Nania
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology “M. La Greca”, University of Catania, Via Androne 81, 95124 Catania, Italy; (A.M.P.); (M.G.); (A.R.); (M.N.); (L.R.); (G.S.C.)
| | - Luana Rossitto
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology “M. La Greca”, University of Catania, Via Androne 81, 95124 Catania, Italy; (A.M.P.); (M.G.); (A.R.); (M.N.); (L.R.); (G.S.C.)
| | - Giada Santa Calogero
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology “M. La Greca”, University of Catania, Via Androne 81, 95124 Catania, Italy; (A.M.P.); (M.G.); (A.R.); (M.N.); (L.R.); (G.S.C.)
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology “M. La Greca”, University of Catania, Via Androne 81, 95124 Catania, Italy; (A.M.P.); (M.G.); (A.R.); (M.N.); (L.R.); (G.S.C.)
- Correspondence: ; Tel.: +39-095-730-6030
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