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Mwamburi SM, Kawato S, Furukawa M, Konishi K, Nozaki R, Hirono I, Kondo H. De Novo Assembly and Annotation of the Siganus fuscescens (Houttuyn, 1782) Genome: Marking a Pioneering Advance for the Siganidae Family. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10325-9. [PMID: 38850360 DOI: 10.1007/s10126-024-10325-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
This study presents the first draft genome of Siganus fuscescens, and thereby establishes the first whole-genome sequence for a species in the Siganidae family. Leveraging both long and short read sequencing technologies, i.e., Oxford Nanopore and Illumina sequencing, we successfully assembled a mitogenome spanning 16.494 Kb and a first haploid genome encompassing 498 Mb. The assembled genome accounted for a 99.6% of the estimated genome size and was organized into 164 contigs with an N50 of 7.2 Mb. This genome assembly showed a GC content of 42.9% and a high Benchmarking Universal Single-Copy Orthologue (BUSCO) completeness score of 99.5% using actinopterygii_odb10 lineage, thereby meeting stringent quality standards. In addition to its structural aspects, our study also examined the functional genomics of this species, including the intricate capacity to biosynthesize long-chain polyunsaturated fatty acids (LC-PUFAs) and secrete venom. Notably, our analyses revealed various repeats elements, which collectively constituted 17.43% of the genome. Moreover, annotation of 28,351 genes uncovered both shared genetic signatures and those that are unique to S. fuscescens. Our assembled genome also displayed a moderate prevalence of gene duplication compared to other fish species, which suggests that this species has a distinctive evolutionary trajectory and potentially unique functional constraints. Taken altogether, this genomic resource establishes a robust foundation for future research on the biology, evolution, and the aquaculture potential of S. fuscescens.
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Affiliation(s)
- Samuel Mwakisha Mwamburi
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
- Department of Fisheries, Kenya Marine and Fisheries Research Institute, P.O BOX 81651-80100, Mombasa, Kenya
| | - Satoshi Kawato
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Miho Furukawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Kayo Konishi
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Reiko Nozaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Ikuo Hirono
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Hidehiro Kondo
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan.
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Balchan NR, Smith CF, Mackessy SP. A plethora of rodents: Rattlesnake predators generate unanticipated patterns of venom resistance in a grassland ecosystem. Toxicon X 2024; 21:100179. [PMID: 38144228 PMCID: PMC10746501 DOI: 10.1016/j.toxcx.2023.100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Predation has the potential to impart strong selective pressures on organisms within their environments, resulting in adaptive changes in prey that minimize risk of predation. Pressures from venomous snakes present an exceptional challenge to prey, as venom represents a unique chemical arsenal evolutionarily tailored to incapacitate prey. In response, venom resistance has been detected in various snake prey species, and to varying degrees. This study analyzes venom resistance in an eastern Colorado grassland habitat, where the Prairie Rattlesnake (Crotalus viridis) and Desert Massasauga Rattlesnake (Sistrurus tergeminus edwardsii) co-occur with a suite of grassland rodents. We test for venom resistance across rodent and snake pairings using two geographically distant field sites to determine the role of 1) predation pressure and trophic ecology, and 2) sympatric and allopatric patterns of venom resistance. Resistance was measured using serum-based metalloproteinase inhibition assays to determine potential inhibition of proteolytic activity, augmented by median lethal dose (LD50) assays on rodent species to assess toxicity of crude venoms. Resistance is present in several rodent species, with strong resistance present in populations of Eastern Woodrat (Neotoma floridana), Ord's Kangaroo Rat (Dipodomys ordii), and Northern Grasshopper Mouse (Onychomys leucogaster). Resistance is less developed in other species, including the House Mouse (Mus musculus) and Plains Pocket Mouse (Perognathus flavescens). An unexpected differential is present, where Lincoln County Kangaroo Rats are highly resistant to venom of co-occurring Prairie Rattlesnakes yet are sensitive to an allopatric population of Prairie Rattlesnakes in Weld County. Lincoln Co. Northern Grasshopper Mice also demonstrate extremely elevated resistance to Weld Co. Prairie Rattlesnake venoms, and they may possess resistance mechanisms for myotoxin a, an abundant component of Weld Co. C. v viridis venoms. This study illustrates the complexity of venom resistance in biological communities that can exist when incorporating multiple species interactions. Future studies aimed at characterizing resistance mechanisms at the molecular level will provide a more detailed physiological context for understanding mechanisms by which resistance to venoms occurs.
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Affiliation(s)
- Neil R. Balchan
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, 80639, USA
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Cara F. Smith
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, 80639, USA
- Department of Biochemistry and Molecular Genetics, 12801 East 17th Avenue, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Stephen P. Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, 80639, USA
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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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Bédry R, de Haro L, Bentur Y, Senechal N, Galil BS. Toxicological risks on the human health of populations living around the Mediterranean Sea linked to the invasion of non-indigenous marine species from the Red Sea: A review. Toxicon 2021; 191:69-82. [PMID: 33359388 DOI: 10.1016/j.toxicon.2020.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/07/2020] [Accepted: 12/19/2020] [Indexed: 10/22/2022]
Abstract
The Mediterranean region is, by far, a prime travel destination, having hosted more than 330 million tourists in 2016, mostly for seaside holidays. A greatly increased influx of thermophilic Red Sea species, introduced through the Suez Canal in a process referred to as Lessepsian invasion (in honor of Ferdinand de Lesseps who instigated the building of the Suez Canal), have raised awareness among scientists, medical personnel, and the public, of health risks caused by some venomous and poisonous marine species. The main species of concern are the poisonous Lagocephalus sceleratus, and the venomous Plotosus lineatus, Siganus luridus, Siganus rivulatus, Pterois miles, Synancea verrucosa, Rhopilema nomadica, Macrorhynchia philippina and Diadema setosum. Recognizing that the main factors that drive the introduction and dispersal of Red Sea biota in the Mediterranean, i.e., Suez Canal enlargements and warming seawater, are set to increase, and international tourist arrivals are forecasted to increase as well, to 500 million in 2030, an increase in intoxications and envenomations by alien marine species is to be expected and prepared for.
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Affiliation(s)
- R Bédry
- UHSI, Pellegrin University Hospital, 33000, Bordeaux, France.
| | - L de Haro
- Centre Antipoison de Marseille, Hôpital Sainte Marguerite, 13009, Marseille, France
| | - Y Bentur
- Israel Poison Information Center, Rambam Health Care Campus, The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - N Senechal
- Bordeaux University, UMR EPOC, 5805, Pessac, France
| | - B S Galil
- Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
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Costa FLS, De Lima ME, Figueiredo SG, Ferreira RS, Prates NS, Sakamoto T, Salas CE. Sequence analysis of the cDNA encoding for SpCTx: a lethal factor from scorpionfish venom ( Scorpaena plumieri). J Venom Anim Toxins Incl Trop Dis 2018; 24:24. [PMID: 30181739 PMCID: PMC6114736 DOI: 10.1186/s40409-018-0158-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/03/2018] [Indexed: 12/03/2022] Open
Abstract
Background Lethal factors are multifunctional oligomeric proteins found in the venomous apparatus of Scorpaeniformes fish. These toxins elicit not only an array of biological responses in vitro but also cardiovascular disorders and strong hemolytic, nociceptive and edematogenic activities in vivo. This work describes the cloning and molecular identification of two toxin subunits, denominated Sp-CTx-α and Sp-CTx-β, from scorpionfish venom (Scorpaena plumieri). Methods The primary structures were deduced after cDNA amplification by PCR with primers from conserved sequences described in Scorpaeniformes toxins. Following DNA sequencing and bioinformatic analysis, the tridimensional structures of both subunits were modeled. Results The translated sequences (702 amino acids, each subunit) show homology with other lethal factors, while alignment between Sp-CTx-α and Sp-CTx-β shows 54% identity. The subunits lack N-terminal signal sequences and display masses of approximately 80 kDa each. Both Sp-CTx subunits display a B30.2/SPRY domain at the C-terminal region with typically conserved motifs as described in these toxins. Secondary structure prediction identified six α-helices 18 residues long in both α and β subunits, some of them amphiphilic with their N-terminal flanked by many basic residues, creating a cationic site associated with the cytolytic activity of these toxins. Antimicrobial potential sites were identified in Sp-CTx and share some features with other peptides presenting variable and broad-spectrum activity. A phylogenetic tree built to represent these toxins supports the proximity between scorpionfish, lionfish and stonefish. Conclusion The study identified a putative toxin protein whose primary structure is similar to other fish toxins and with potential for production of antivenom against scorpionfish envenomation in Brazil. As a prelude to structure-function studies, we propose that the toxin is structurally related to pore-forming marine toxins. Electronic supplementary material The online version of this article (10.1186/s40409-018-0158-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fábio L S Costa
- 1Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901 Brazil
| | - Maria Elena De Lima
- 1Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901 Brazil
| | - Suely G Figueiredo
- 2Departamento de Ciências Fisiológicas, Universidade Federal do Espírito Santo, Vitória, ES Brazil
| | - Rafaela S Ferreira
- 1Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901 Brazil
| | - Núbia S Prates
- 1Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901 Brazil
| | - Tetsu Sakamoto
- 1Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901 Brazil
| | - Carlos E Salas
- 1Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901 Brazil
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