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Jackson TK, Rhode C. Comparative genomics of dusky kob (Argyrosomus japonicus, Sciaenidae) conspecifics: Evidence for speciation and the genetic mechanisms underlying traits. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38885946 DOI: 10.1111/jfb.15844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/17/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
Dusky kob (Argyrosomus japonicus) is a commercially important finfish, indigenous to South Africa, Australia, and China. Previous studies highlighted differences in genetic composition, life history, and morphology of the species across geographic regions. A draft genome sequence of 0.742 Gb (N50 = 5.49 Mb; BUSCO completeness = 97.8%) and 22,438 predicted protein-coding genes was generated for the South African (SA) conspecific. A comparison with the Chinese (CN) conspecific revealed a core set of 32,068 orthologous protein clusters across both genomes. The SA genome exhibited 440 unique clusters compared to 1928 unique clusters in the CN genome. Transportation and immune response processes were overrepresented among the SA accessory genome, whereas the CN accessory genome was enriched for immune response, DNA transposition, and sensory detection (FDR-adjusted p < 0.01). These unique clusters may represent an adaptive component of the species' pangenome that could explain population divergence due to differential environmental specialisation. Furthermore, 700 single-copy orthologues (SCOs) displayed evidence of positive selection between the SA and CN genomes, and globally these genomes shared only 92% similarity, suggesting they might be distinct species. These genes primarily play roles in metabolism and digestion, illustrating the evolutionary pathways that differentiate the species. Understanding these genomic mechanisms underlying adaptation and evolution within and between species provides valuable insights into growth and maturation of kob, traits that are particularly relevant to commercial aquaculture.
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Affiliation(s)
- Tassin Kim Jackson
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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Luján-Amoraga L, Delgado-Martín B, Lourenço-Marques C, Gavaia PJ, Bravo J, Bandarra NM, Dominguez D, Izquierdo MS, Pousão-Ferreira P, Ribeiro L. Exploring Omega-3's Impact on the Expression of Bone-Related Genes in Meagre ( Argyrosomus regius). Biomolecules 2023; 14:56. [PMID: 38254657 PMCID: PMC10813611 DOI: 10.3390/biom14010056] [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: 10/31/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Dietary supplementation with Omega-3 fatty acids seems to promote skeletal health. Therefore, their consumption at imbalanced or excessive levels has offered less beneficial or even prejudicial effects. Fish produced in aquaculture regimes are prone to develop abnormal skeletons. Although larval cultures are usually fed with diets supplemented with Omega-3 Long Chain Polyunsaturated fatty acids (LC-PUFAs), the lack of knowledge about the optimal requirements for fatty acids or about their impact on mechanisms that regulate skeletal development has impeded the design of diets that could improve bone formation during larval stages when the majority of skeletal anomalies appear. In this study, Argyrosomus regius larvae were fed different levels of Omega-3s (2.6% and 3.6% DW on diet) compared to a commercial diet. At 28 days after hatching (DAH), their transcriptomes were analyzed to study the modulation exerted in gene expression dynamics during larval development and identify impacted genes that can contribute to skeletal formation. Mainly, both levels of supplementation modulated bone-cell proliferation, the synthesis of bone components such as the extracellular matrix, and molecules involved in the interaction and signaling between bone components or in important cellular processes. The 2.6% level impacted several genes related to cartilage development, denoting a special impact on endochondral ossification, delaying this process. However, the 3.6% level seemed to accelerate this process by enhancing skeletal development. These results offered important insights into the impact of dietary Omega-3 LC-PUFAs on genes involved in the main molecular mechanism and cellular processes involved in skeletal development.
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Affiliation(s)
- Leticia Luján-Amoraga
- Aquaculture Research Station (EPPO), Portuguese Institute for the Ocean and Atmosphere (IPMA), 8700-194 Olhão, Portugal; (L.L.-A.); (C.L.-M.); (P.P.-F.)
| | - Belén Delgado-Martín
- Department of Microbiology and Crop Protection, Institute of Subtropical and Mediterranean Horticulture (IHSM-UMA-CSIC), 29010 Malaga, Spain;
| | - Cátia Lourenço-Marques
- Aquaculture Research Station (EPPO), Portuguese Institute for the Ocean and Atmosphere (IPMA), 8700-194 Olhão, Portugal; (L.L.-A.); (C.L.-M.); (P.P.-F.)
- Collaborative Laboratory on Sustainable and Smart Aquaculture (S2AQUACOLAB) Av. Parque Natural da Ria Formosa s/n, 8700-194 Olhão, Portugal
| | - Paulo J. Gavaia
- Centre of Marine Sciences (CCMAR), University of Algarve (UALG), 8005-139 Faro, Portugal;
| | - Jimena Bravo
- Aquaculture Research Group (GIA), University of Las Palmas de Gran Canaria (ULPGC) Crta. Taliarte s/n, 35214 Telde, Spain; (J.B.); (D.D.); (M.S.I.)
| | - Narcisa M. Bandarra
- Division of Aquaculture, Upgrading, and Bioprospection (DivAV), Portuguese Institute for the Sea and Atmosphere (IPMA, IP), Rua Alfredo Magalhães Ramalho, 7, 1495-006 Lisbon, Portugal;
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - David Dominguez
- Aquaculture Research Group (GIA), University of Las Palmas de Gran Canaria (ULPGC) Crta. Taliarte s/n, 35214 Telde, Spain; (J.B.); (D.D.); (M.S.I.)
| | - Marisol S. Izquierdo
- Aquaculture Research Group (GIA), University of Las Palmas de Gran Canaria (ULPGC) Crta. Taliarte s/n, 35214 Telde, Spain; (J.B.); (D.D.); (M.S.I.)
| | - Pedro Pousão-Ferreira
- Aquaculture Research Station (EPPO), Portuguese Institute for the Ocean and Atmosphere (IPMA), 8700-194 Olhão, Portugal; (L.L.-A.); (C.L.-M.); (P.P.-F.)
- Collaborative Laboratory on Sustainable and Smart Aquaculture (S2AQUACOLAB) Av. Parque Natural da Ria Formosa s/n, 8700-194 Olhão, Portugal
| | - Laura Ribeiro
- Aquaculture Research Station (EPPO), Portuguese Institute for the Ocean and Atmosphere (IPMA), 8700-194 Olhão, Portugal; (L.L.-A.); (C.L.-M.); (P.P.-F.)
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