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Herrera M, Ravasi T, Laudet V. Anemonefishes: A model system for evolutionary genomics. F1000Res 2023; 12:204. [PMID: 37928172 PMCID: PMC10624958 DOI: 10.12688/f1000research.130752.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.
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Affiliation(s)
- Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Marine Research Station, Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, 23-10, Dah-Uen Rd, Jiau Shi I-Lan 262, Taiwan
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Negrete B, Esbaugh AJ. A methodological evaluation of the determination of critical oxygen threshold in an estuarine teleost. Biol Open 2019; 8:bio.045310. [PMID: 31649119 PMCID: PMC6899028 DOI: 10.1242/bio.045310] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
One measure of hypoxia tolerance is the critical oxygen threshold, Pcrit, which is the point where standard metabolism can no longer be maintained through aerobic processes. Traditionally, Pcrit was determined using closed respirometry, whereby the fish's respiration naturally lowered O2. More recently, intermittent flow techniques have been adopted, where N2 is used to displace O2, which ostensibly reduces end-product build-up. This study used a paired design on the marine teleost, red drum. Pcrit is comparable between closed (4.6±0.2 kPa; mean±s.e.m.) and intermittent flow (4.4±0.2 kPa; mean±s.e.m.) respirometry. pCO2, ammonia and pH changes within the chamber were measured prior to the onset of Pcrit and at the end of a typical Pcrit trial and revealed changes in water chemistry in both closed and intermittent flow. Pcrit values were similar in both methods of hypoxia induction regardless of subsequent water chemistry changes that occurred in both methods. Summary: The two leading methods of measuring the critical oxygen threshold in fishes are similar in their estimations, regardless of changes to water chemistry.
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Affiliation(s)
- Benjamin Negrete
- Department of Marine Science, Marine Science Institute, The University of Texas at Austin, Port Aransas, TX 78373, USA
| | - Andrew J Esbaugh
- Department of Marine Science, Marine Science Institute, The University of Texas at Austin, Port Aransas, TX 78373, USA
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Moßhammer M, Brodersen KE, Kühl M, Koren K. Nanoparticle- and microparticle-based luminescence imaging of chemical species and temperature in aquatic systems: a review. Mikrochim Acta 2019; 186:126. [PMID: 30680465 DOI: 10.1007/s00604-018-3202-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/20/2018] [Indexed: 11/25/2022]
Abstract
Most aquatic systems rely on a multitude of biogeochemical processes that are coupled with each other in a complex and dynamic manner. To understand such processes, minimally invasive analytical tools are required that allow continuous, real-time measurements of individual reactions in these complex systems. Optical chemical sensors can be used in the form of fiber-optic sensors, planar sensors, or as micro- and nanoparticles (MPs and NPs). All have their specific merits, but only the latter allow for visualization and quantification of chemical gradients over 3D structures. This review (with 147 references) summarizes recent developments mainly in the field of optical NP sensors relevant for chemical imaging in aquatic science. The review encompasses methods for signal read-out and imaging, preparation of NPs and MPs, and an overview of relevant MP/NP-based sensors. Additionally, examples of MP/NP-based sensors in aquatic systems such as corals, plant tissue, biofilms, sediments and water-sediment interfaces, marine snow and in 3D bioprinting are given. We also address current challenges and future perspectives of NP-based sensing in aquatic systems in a concluding section. Graphical abstract ᅟ.
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Affiliation(s)
- Maria Moßhammer
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark
| | - Kasper Elgetti Brodersen
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark.
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Klaus Koren
- Aarhus University Center for Water Technology, Department of Bioscience - Microbiology, Aarhus University, 8000, Aarhus, Denmark.
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Lehmann R, Lightfoot DJ, Schunter C, Michell CT, Ohyanagi H, Mineta K, Foret S, Berumen ML, Miller DJ, Aranda M, Gojobori T, Munday PL, Ravasi T. Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Mol Ecol Resour 2018; 19:570-585. [PMID: 30203521 PMCID: PMC7379943 DOI: 10.1111/1755-0998.12939] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 11/29/2022]
Abstract
The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C-based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein-coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
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Affiliation(s)
- Robert Lehmann
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Damien J Lightfoot
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Celia Schunter
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Craig T Michell
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hajime Ohyanagi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sylvain Foret
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Philip L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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