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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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2
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Roux N, Miura S, Dussenne M, Tara Y, Lee SH, de Bernard S, Reynaud M, Salis P, Barua A, Boulahtouf A, Balaguer P, Gauthier K, Lecchini D, Gibert Y, Besseau L, Laudet V. The multi-level regulation of clownfish metamorphosis by thyroid hormones. Cell Rep 2023; 42:112661. [PMID: 37347665 PMCID: PMC10467156 DOI: 10.1016/j.celrep.2023.112661] [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: 06/01/2022] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023] Open
Abstract
Most marine organisms have a biphasic life cycle during which pelagic larvae transform into radically different juveniles. In vertebrates, the role of thyroid hormones (THs) in triggering this transition is well known, but how the morphological and physiological changes are integrated in a coherent way with the ecological transition remains poorly explored. To gain insight into this question, we performed an integrated analysis of metamorphosis of a marine teleost, the false clownfish (Amphiprion ocellaris). We show how THs coordinate a change in color vision as well as a major metabolic shift in energy production, highlighting how it orchestrates this transformation. By manipulating the activity of liver X regulator (LXR), a major regulator of metabolism, we also identify a tight link between metabolic changes and metamorphosis progression. Strikingly, we observed that these regulations are at play in the wild, explaining how hormones coordinate energy needs with available resources during the life cycle.
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Affiliation(s)
- Natacha Roux
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Saori Miura
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Mélanie Dussenne
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yuki Tara
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Shu-Hua Lee
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10, Dah-Uen Rd., Jiau Shi, I-Lan 262, Taiwan
| | | | - Mathieu Reynaud
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Pauline Salis
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Agneesh Barua
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Abdelhay Boulahtouf
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, University of Montpellier, 34090 Montpellier, France
| | - Patrick Balaguer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, University of Montpellier, 34090 Montpellier, France
| | - Karine Gauthier
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, INRAE USC 1370 École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, 69007 Lyon, France
| | - David Lecchini
- PSL Research University, EPHE-UPVD-CNRS-UAR 3278 CRIOBE BP 1013, 98729 Papetoai, Moorea, French Polynesia; Laboratoire d'Excellence "CORAIL," 66100 Perpignan, France
| | - Yann Gibert
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - Laurence Besseau
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France.
| | - Vincent Laudet
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10, Dah-Uen Rd., Jiau Shi, I-Lan 262, Taiwan.
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3
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Mitchell LJ, Cortesi F, Marshall NJ, Cheney KL. Higher ultraviolet skin reflectance signals submissiveness in the anemonefish, Amphiprion akindynos. Behav Ecol 2022; 34:19-32. [PMID: 36789393 PMCID: PMC9918861 DOI: 10.1093/beheco/arac089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/14/2022] Open
Abstract
Ultraviolet (UV) vision is widespread among teleost fishes, of which many exhibit UV skin colors for communication. However, aside from its role in mate selection, few studies have examined the information UV signaling conveys in other socio-behavioral contexts. Anemonefishes (subfamily, Amphiprioninae) live in a fascinating dominance hierarchy, in which a large female and male dominate over non-breeding subordinates, and body size is the primary cue for dominance. The iconic orange and white bars of anemonefishes are highly UV-reflective, and their color vision is well tuned to perceive the chromatic contrast of skin, which we show here decreases in the amount of UV reflectance with increasing social rank. To test the function of their UV-skin signals, we compared the outcomes of staged contests over dominance between size-matched Barrier Reef anemonefish (Amphiprion akindynos) in aquarium chambers viewed under different UV-absorbing filters. Fish under UV-blocking filters were more likely to win contests, where fish under no-filter or neutral-density filter were more likely to submit. For contests between fish in no-filter and neutral density filter treatments, light treatment had no effect on contest outcome (win/lose). We also show that sub-adults were more aggressive toward smaller juveniles placed under a UV filter than a neutral density filter. Taken together, our results show that UV reflectance or UV contrast in anemonefish can modulate aggression and encode dominant and submissive cues, when changes in overall intensity are controlled for.
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Affiliation(s)
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - N Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Karen L Cheney
- School of Biological Sciences, Faculty of Science, The University of Queensland, Brisbane, QLD 4072, Australia
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Kratochwil CF, Liang Y, Gerwin J, Franchini P, Meyer A. Comparative ontogenetic and transcriptomic analyses shed light on color pattern divergence in cichlid fishes. Evol Dev 2022; 24:158-170. [PMID: 35971657 DOI: 10.1111/ede.12416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 11/27/2022]
Abstract
Stripe patterns are a striking example for a repeatedly evolved color pattern. In the African adaptive radiations of cichlid fishes, stripes evolved several times independently. Previously, it has been suggested that regulatory evolution of a single gene, agouti-related-peptide 2 (agrp2), explains the evolutionary lability of this trait. Here, using a comparative transcriptomic approach, we performed comparisons between (adult) striped and nonstriped cichlid fishes of representatives of Lake Victoria and the two major clades of Lake Malawi (mbuna and non-mbuna lineage). We identify agrp2 to be differentially expressed across all pairwise comparisons, reaffirming its association with stripe pattern divergence. We therefore also provide evidence that agrp2 is associated with the loss of the nonstereotypic oblique stripe of Mylochromis mola. Complementary ontogenetic data give insights into the development of stripe patterns as well as vertical bar patterns that both develop postembryonically. Lastly, using the Lake Victoria species pair Haplochromis sauvagei and Pundamilia nyererei, we investigated the differences between melanic and non-melanic regions to identify additional genes that contribute to the formation of stripes. Expression differences-that most importantly also do not include agrp2-are surprisingly small. This suggests, at least in this species pair, that the stripe phenotype might be caused by a combination of more subtle transcriptomic differences or cellular changes without transcriptional correlates. In summary, our comprehensive analysis highlights the ontogenetic and adult transcriptomic differences between cichlids with different color patterns and serves as a basis for further investigation of the mechanistic underpinnings of their diversification.
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Affiliation(s)
- Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yipeng Liang
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jan Gerwin
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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5
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McKinnon JS, Newsome WB, Balakrishnan CN. Gene expression in male and female stickleback from populations with convergent and divergent throat coloration. Ecol Evol 2022; 12:e8860. [PMID: 35509607 PMCID: PMC9055290 DOI: 10.1002/ece3.8860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jeffrey S. McKinnon
- Department of Biology East Carolina University Greenville North Carolina USA
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Mitchell LJ, Tettamanti V, Rhodes JS, Marshall NJ, Cheney KL, Cortesi F. CRISPR/Cas9-mediated generation of biallelic F0 anemonefish (Amphiprion ocellaris) mutants. PLoS One 2021; 16:e0261331. [PMID: 34910772 PMCID: PMC8673619 DOI: 10.1371/journal.pone.0261331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/29/2021] [Indexed: 12/02/2022] Open
Abstract
Genomic manipulation is a useful approach for elucidating the molecular pathways underlying aspects of development, physiology, and behaviour. However, a lack of gene-editing tools appropriated for use in reef fishes has meant the genetic underpinnings for many of their unique traits remain to be investigated. One iconic group of reef fishes ideal for applying this technique are anemonefishes (Amphiprioninae) as they are widely studied for their symbiosis with anemones, sequential hermaphroditism, complex social hierarchies, skin pattern development, and vision, and are raised relatively easily in aquaria. In this study, we developed a gene-editing protocol for applying the CRISPR/Cas9 system in the false clown anemonefish, Amphiprion ocellaris. Microinjection of zygotes was used to demonstrate the successful use of our CRISPR/Cas9 approach at two separate target sites: the rhodopsin-like 2B opsin encoding gene (RH2B) involved in vision, and Tyrosinase-producing gene (tyr) involved in the production of melanin. Analysis of the sequenced target gene regions in A. ocellaris embryos showed that uptake was as high as 73.3% of injected embryos. Further analysis of the subcloned mutant gene sequences combined with amplicon shotgun sequencing revealed that our approach had a 75% to 100% efficiency in producing biallelic mutations in F0 A. ocellaris embryos. Moreover, we clearly show a loss-of-function in tyr mutant embryos which exhibited typical hypomelanistic phenotypes. This protocol is intended as a useful starting point to further explore the potential application of CRISPR/Cas9 in A. ocellaris, as a platform for studying gene function in anemonefishes and other reef fishes.
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Affiliation(s)
- Laurie J. Mitchell
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
- * E-mail:
| | - Valerio Tettamanti
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Justin S. Rhodes
- Department of Psychology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana, Champaign, Urbana, IL, United States of America
| | - N. Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Karen L. Cheney
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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Yamanaka S, Okada Y, Furuta T, Kinoshita M. Establishment of culture and microinjection methods for false clownfish embryos without parental care. Dev Growth Differ 2021; 63:459-466. [PMID: 34786704 DOI: 10.1111/dgd.12759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 11/27/2022]
Abstract
Anemonefish, including the false clownfish Amphiprion ocellaris, are attractive model organisms because of their unique features, such as sex change and brilliant color patterns in mutants. However, anemonefish are not widely used to study gene function using reverse genetic approaches owing to microinjection difficulties and subsequent rearing and hatching of embryos without parental care. A. ocellaris embryos are spawned on a hard substrate and cared for by their parents until hatching. However, the eggs need to be detached from the substrate and raised without their parents to perform successful microinjection. We established a method to culture and hatch A. ocellaris embryos without spawning substrates or parental care. We found that changing water and generating water flow are critical for culturing the embryos, and that water flow (as physical stimulation) and complete darkness in the dark period are necessary for successful hatching. We further investigated the effectiveness of microinjection into the yolk sac of fertilized eggs rather than into the cytoplasm, which makes microinjection easier. A reporter RNA injected into the yolk sac was transferred to the cytoplasm and translated, indicating that yolk sac microinjection is an efficient alternative as has been used for zebrafish. These findings highlight the potential of A. ocellaris as an experimental model organism for reverse genetics, and our methods could be applied to other anemonefish species.
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Affiliation(s)
- Sakuto Yamanaka
- Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yosuke Okada
- Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takeshi Furuta
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Chiba, Japan
| | - Masato Kinoshita
- Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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8
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Salis P, Lee S, Roux N, Lecchini D, Laudet V. The real Nemo movie: Description of embryonic development in Amphiprion ocellaris from first division to hatching. Dev Dyn 2021; 250:1651-1667. [PMID: 33899313 PMCID: PMC8597122 DOI: 10.1002/dvdy.354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Amphiprion ocellaris is one of the rare reef fish species that can be reared in aquaria. It is increasingly used as a model species for Eco-Evo-Devo. Therefore, it is important to have an embryonic development table based on high quality images that will allow for standardized sampling by the scientific community. RESULTS Here we provide high-resolution time-lapse videos to accompany a detailed description of embryonic development in A ocellaris. We describe a series of developmental stages and we define six broad periods of embryogenesis: zygote, cleavage, blastula, gastrula, segmentation, and organogenesis that we further subdivide into 32 stages. These periods highlight the changing spectrum of major developmental processes that occur during embryonic development. CONCLUSIONS We provide an easy system for the determination of embryonic stages, enabling the development of A ocellaris as a coral reef fish model species. This work will facilitate evolutionary development studies, in particular studies of the relationship between climate change and developmental trajectories in the context of coral reefs. Thanks to its lifestyle, complex behavior, and ecology, A ocellaris will undoubtedly become a very attractive model in a wide range of biological fields.
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Affiliation(s)
- Pauline Salis
- Observatoire Océanologique de Banyuls‐sur‐Mer, UMR CNRS 7232 BIOMSorbonne Université ParisBanyuls‐sur‐MerFrance
- EPHE‐UPVD‐CNRS, USR 3278 CRIOBEPSL UniversityMooreaFrench Polynesia
| | - Shu‐hua Lee
- Lab of Marine Eco‐Evo‐Devo, Marine Research StationInstitute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Natacha Roux
- Observatoire Océanologique de Banyuls‐sur‐Mer, UMR CNRS 7232 BIOMSorbonne Université ParisBanyuls‐sur‐MerFrance
| | - David Lecchini
- EPHE‐UPVD‐CNRS, USR 3278 CRIOBEPSL UniversityMooreaFrench Polynesia
| | - Vincent Laudet
- Lab of Marine Eco‐Evo‐Devo, Marine Research StationInstitute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
- Marine Eco‐Evo‐Devo UnitOkinawa Institute of Science and TechnologyOnna sonOkinawaJapan
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9
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Huang D, Lewis VM, Foster TN, Toomey MB, Corbo JC, Parichy DM. Development and genetics of red coloration in the zebrafish relative Danio albolineatus. eLife 2021; 10:70253. [PMID: 34435950 PMCID: PMC8416024 DOI: 10.7554/elife.70253] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/25/2021] [Indexed: 12/11/2022] Open
Abstract
Animal pigment patterns play important roles in behavior and, in many species, red coloration serves as an honest signal of individual quality in mate choice. Among Danio fishes, some species develop erythrophores, pigment cells that contain red ketocarotenoids, whereas other species, like zebrafish (D. rerio) only have yellow xanthophores. Here, we use pearl danio (D. albolineatus) to assess the developmental origin of erythrophores and their mechanisms of differentiation. We show that erythrophores in the fin of D. albolineatus share a common progenitor with xanthophores and maintain plasticity in cell fate even after differentiation. We further identify the predominant ketocarotenoids that confer red coloration to erythrophores and use reverse genetics to pinpoint genes required for the differentiation and maintenance of these cells. Our analyses are a first step toward defining the mechanisms underlying the development of erythrophore-mediated red coloration in Danio and reveal striking parallels with the mechanism of red coloration in birds.
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Affiliation(s)
- Delai Huang
- Department of Biology, University of Virginia, Charlottesville, United States
| | - Victor M Lewis
- Department of Biology, University of Virginia, Charlottesville, United States
| | - Tarah N Foster
- Department of Biological Science, University of Tulsa, Tulsa, United States
| | - Matthew B Toomey
- Department of Biological Science, University of Tulsa, Tulsa, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States
| | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, United States.,Department of Cell Biology, University of Virginia, Charlottesville, United States
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10
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Stuckert AMM, Chouteau M, McClure M, LaPolice TM, Linderoth T, Nielsen R, Summers K, MacManes MD. The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system. Mol Ecol 2021; 30:4039-4061. [PMID: 34145931 PMCID: PMC8457190 DOI: 10.1111/mec.16024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/13/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022]
Abstract
A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defence, are excellent models to understand the link between vivid colour pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which multiple species share the same conspicuous phenotype can provide an even better model for understanding the mechanisms of colour production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which vivid colour and pattern are produced in a Müllerian mimicry complex of poison frogs. We did this by first assembling a high-quality de novo genome assembly for the mimic poison frog Ranitomeya imitator. This assembled genome is 6.8 Gbp in size, with a contig N50 of 300 Kbp R. imitator and two colour morphs from both Ranitomeya fantastica and R. variabilis which R. imitator mimics. We identified a large number of pigmentation and patterning genes that are differentially expressed throughout development, many of them related to melanocyte development, melanin synthesis, iridophore development and guanine synthesis. Polytypic differences within species may be the result of differences in expression and/or timing of expression, whereas convergence for colour pattern between species does not appear to be due to the same changes in gene expression. In addition, we identify the pteridine synthesis pathway (including genes such as qdpr and xdh) as a key driver of the variation in colour between morphs of these species. Finally, we hypothesize that genes in the keratin family are important for producing different structural colours within these frogs.
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Affiliation(s)
- Adam M. M. Stuckert
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Mathieu Chouteau
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA)Université de Guyane, CNRS, IFREMERCayenneFrance
| | - Melanie McClure
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA)Université de Guyane, CNRS, IFREMERCayenneFrance
| | - Troy M. LaPolice
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
| | - Tyler Linderoth
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Rasmus Nielsen
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Kyle Summers
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
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11
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Guo L, Bloom J, Sykes S, Huang E, Kashif Z, Pham E, Ho K, Alcaraz A, Xiao XG, Duarte-Vogel S, Kruglyak L. Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos. PLoS Genet 2021; 17:e1009580. [PMID: 34166378 PMCID: PMC8224956 DOI: 10.1371/journal.pgen.1009580] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/04/2021] [Indexed: 12/16/2022] Open
Abstract
The squamates (lizards and snakes) are close relatives of birds and mammals, with more than 10,000 described species that display extensive variation in a number of important biological traits, including coloration, venom production, and regeneration. Due to a lack of genomic tools, few genetic studies in squamates have been carried out. The leopard gecko, Eublepharis macularius, is a popular companion animal, and displays a variety of coloration patterns. We took advantage of a large breeding colony and used linkage analysis, synteny, and homozygosity mapping to investigate a spontaneous semi-dominant mutation, “Lemon Frost”, that produces white coloration and causes skin tumors (iridophoroma). We localized the mutation to a single locus which contains a strong candidate gene, SPINT1, a tumor suppressor implicated in human skin cutaneous melanoma (SKCM) and over-proliferation of epithelial cells in mice and zebrafish. Our work establishes the leopard gecko as a tractable genetic system and suggests that a tumor suppressor in melanocytes in humans can also suppress tumor development in iridophores in lizards. The squamates (lizards and snakes) comprise a diverse group of reptiles, with more than 10,000 described species that display extensive variation in a number of important biological traits, including coloration. In this manuscript, we used quantitative genetics and genomics to map the mutation underlying white coloration in the Lemon Frost morph of the common leopard gecko, Eublepharis macularius. Lemon Frost geckos have increased white body coloration with brightened yellow and orange areas. This morph also displays a high incidence of iridophoroma, a tumor of white-colored cells. We obtained phenotype information and DNA samples from geckos in a large breeding colony and used genome sequencing and genetic linkage analysis to localize the Lemon Frost mutation to a single locus. This locus contains a strong candidate gene, SPINT1, a tumor suppressor implicated in human skin cutaneous melanoma. Together with other recent advances, our work brings reptiles into the modern genetics era.
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Affiliation(s)
- Longhua Guo
- Department of Human Genetics, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, California, United States of America
- * E-mail: (LG); (LK)
| | - Joshua Bloom
- Department of Human Genetics, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, California, United States of America
| | - Steve Sykes
- Geckos Etc. Herpetoculture, Rocklin, California, United States of America
| | - Elaine Huang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
| | - Zain Kashif
- Department of Human Genetics, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, California, United States of America
| | - Elise Pham
- Department of Human Genetics, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, California, United States of America
| | - Katarina Ho
- Department of Human Genetics, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, California, United States of America
| | - Ana Alcaraz
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, United States of America
| | - Xinshu Grace Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
| | - Sandra Duarte-Vogel
- Division of Laboratory Animal Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Leonid Kruglyak
- Department of Human Genetics, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, California, United States of America
- * E-mail: (LG); (LK)
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12
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Klann M, Mercader M, Carlu L, Hayashi K, Reimer JD, Laudet V. Variation on a theme: pigmentation variants and mutants of anemonefish. EvoDevo 2021; 12:8. [PMID: 34147131 PMCID: PMC8214269 DOI: 10.1186/s13227-021-00178-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
Pigmentation patterning systems are of great interest to understand how changes in developmental mechanisms can lead to a wide variety of patterns. These patterns are often conspicuous, but their origins remain elusive for many marine fish species. Dismantling a biological system allows a better understanding of the required components and the deciphering of how such complex systems are established and function. Valuable information can be obtained from detailed analyses and comparisons of pigmentation patterns of mutants and/or variants from normal patterns. Anemonefishes have been popular marine fish in aquaculture for many years, which has led to the isolation of several mutant lines, and in particular color alterations, that have become very popular in the pet trade. Additionally, scattered information about naturally occurring aberrant anemonefish is available on various websites and image platforms. In this review, the available information on anemonefish color pattern alterations has been gathered and compiled in order to characterize and compare different mutations. With the global picture of anemonefish mutants and variants emerging from this, such as presence or absence of certain phenotypes, information on the patterning system itself can be gained.
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Affiliation(s)
- Marleen Klann
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Manon Mercader
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Lilian Carlu
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Kina Hayashi
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Molecular Invertebrate Systematics and Ecology Lab, Graduate School of the Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Lab, Graduate School of the Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 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, I-Lan, Taiwan.
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13
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Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes. Proc Natl Acad Sci U S A 2021; 118:2101634118. [PMID: 34031155 DOI: 10.1073/pnas.2101634118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Determining how plasticity of developmental traits responds to environmental conditions is a challenge that must combine evolutionary sciences, ecology, and developmental biology. During metamorphosis, fish alter their morphology and color pattern according to environmental cues. We observed that juvenile clownfish (Amphiprion percula) modulate the developmental timing of their adult white bar formation during metamorphosis depending on the sea anemone species in which they are recruited. We observed an earlier formation of white bars when clownfish developed with Stichodactyla gigantea (Sg) than with Heteractis magnifica (Hm). As these bars, composed of iridophores, form during metamorphosis, we hypothesized that timing of their development may be thyroid hormone (TH) dependent. We treated clownfish larvae with TH and found that white bars developed earlier than in control fish. We further observed higher TH levels, associated with rapid white bar formation, in juveniles recruited in Sg than in Hm, explaining the faster white bar formation. Transcriptomic analysis of Sg recruits revealed higher expression of duox, a dual oxidase implicated in TH production as compared to Hm recruits. Finally, we showed that duox is an essential regulator of iridophore pattern timing in zebrafish. Taken together, our results suggest that TH controls the timing of adult color pattern formation and that shifts in duox expression and TH levels are associated with ecological differences resulting in divergent ontogenetic trajectories in color pattern development.
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14
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Holtze S, Gorshkova E, Braude S, Cellerino A, Dammann P, Hildebrandt TB, Hoeflich A, Hoffmann S, Koch P, Terzibasi Tozzini E, Skulachev M, Skulachev VP, Sahm A. Alternative Animal Models of Aging Research. Front Mol Biosci 2021; 8:660959. [PMID: 34079817 PMCID: PMC8166319 DOI: 10.3389/fmolb.2021.660959] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Most research on mechanisms of aging is being conducted in a very limited number of classical model species, i.e., laboratory mouse (Mus musculus), rat (Rattus norvegicus domestica), the common fruit fly (Drosophila melanogaster) and roundworm (Caenorhabditis elegans). The obvious advantages of using these models are access to resources such as strains with known genetic properties, high-quality genomic and transcriptomic sequencing data, versatile experimental manipulation capabilities including well-established genome editing tools, as well as extensive experience in husbandry. However, this approach may introduce interpretation biases due to the specific characteristics of the investigated species, which may lead to inappropriate, or even false, generalization. For example, it is still unclear to what extent knowledge of aging mechanisms gained in short-lived model organisms is transferable to long-lived species such as humans. In addition, other specific adaptations favoring a long and healthy life from the immense evolutionary toolbox may be entirely missed. In this review, we summarize the specific characteristics of emerging animal models that have attracted the attention of gerontologists, we provide an overview of the available data and resources related to these models, and we summarize important insights gained from them in recent years. The models presented include short-lived ones such as killifish (Nothobranchius furzeri), long-lived ones such as primates (Callithrix jacchus, Cebus imitator, Macaca mulatta), bathyergid mole-rats (Heterocephalus glaber, Fukomys spp.), bats (Myotis spp.), birds, olms (Proteus anguinus), turtles, greenland sharks, bivalves (Arctica islandica), and potentially non-aging ones such as Hydra and Planaria.
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Affiliation(s)
- Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ekaterina Gorshkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Stan Braude
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Alessandro Cellerino
- Biology Laboratory, Scuola Normale Superiore, Pisa, Italy
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Central Animal Laboratory, University Hospital Essen, Essen, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Faculty of Veterinary Medicine, Free University of Berlin, Berlin, Germany
| | - Andreas Hoeflich
- Division Signal Transduction, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Eva Terzibasi Tozzini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maxim Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir P. Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
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15
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Parichy DM. Evolution of pigment cells and patterns: recent insights from teleost fishes. Curr Opin Genet Dev 2021; 69:88-96. [PMID: 33743392 DOI: 10.1016/j.gde.2021.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
Skin pigment patterns of vertebrates are stunningly diverse, and nowhere more so than in teleost fishes. Several species, including relatives of zebrafish, recently evolved cichlid fishes of East Africa, clownfishes, deep sea fishes, and others are providing insights into pigment pattern evolution. This overview describes recent advances in understanding periodic patterns, like stripes and spots, the loss of patterns, and the role of cell-type diversification in generating pigmentation phenotypes. Advances in this area are being facilitated by the application of modern methods of gene editing, genomics, computational analysis, and other approaches to non-traditional model organisms having interesting pigmentary phenotypes. Several topics worthy of future attention are outlined as well.
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Affiliation(s)
- David M Parichy
- Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, United States.
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16
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Roux N, Logeux V, Trouillard N, Pillot R, Magré K, Salis P, Lecchini D, Besseau L, Laudet V, Romans P. A star is born again: Methods for larval rearing of an emerging model organism, the False clownfish Amphiprion ocellaris. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:376-385. [PMID: 33539680 PMCID: PMC8248105 DOI: 10.1002/jez.b.23028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
As interest increases in ecological, evolutionary, and developmental biology (Eco‐Evo‐Devo), wild species are increasingly used as experimental models. However, we are still lacking a suitable model for marine fish species, as well as coral reef fishes that can be reared at laboratory scales. Extensive knowledge of the life cycle of anemonefishes, and the peculiarities of their biology, make them relevant marine fish models for developmental biology, ecology, and evolutionary sciences. Here, we present standard methods to maintain breeding pairs of the anemonefish Amphiprion ocellaris in captivity, obtain regular good quality spawning, and protocols to ensure larval survival throughout rearing. We provide a detailed description of the anemonefish husbandry system and life prey culturing protocols. Finally, a “low‐volume” rearing protocol useful for the pharmacological treatment of larvae is presented. Such methods are important as strict requirements for large volumes in rearing tanks often inhibit continuous treatments with expensive or rare compounds. This paper describes how to set up a rearing system for anemone fishes at the laboratory scale as this species is becoming a relevant marine fish model to tackle Eco‐Evo‐Devo questions. We detail two rearing methods, one consisting of classical rearing conditions and the other one consisting of low‐volume conditions (500 ml).
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Affiliation(s)
- Natacha Roux
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Valentin Logeux
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Nancy Trouillard
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Rémi Pillot
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Kévin Magré
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Pauline Salis
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France.,EPHE-UPVD-CNRS-USR 3278 CRIOBE BP 1013, PSL Research University, Papetoai, Moorea, French Polynesia
| | - David Lecchini
- EPHE-UPVD-CNRS-USR 3278 CRIOBE BP 1013, PSL Research University, Papetoai, Moorea, French Polynesia.,Laboratoire d'Excellence "CORAIL", Papetoai, Moorea, French Polynesia
| | - Laurence Besseau
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Vincent Laudet
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France.,Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, Okinawa, Japan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan, Taiwan
| | - Pascal Romans
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
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17
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Ahi EP, Lecaudey LA, Ziegelbecker A, Steiner O, Goessler W, Sefc KM. Expression levels of the tetratricopeptide repeat protein gene ttc39b covary with carotenoid-based skin colour in cichlid fish. Biol Lett 2020; 16:20200629. [PMID: 33236977 PMCID: PMC7728679 DOI: 10.1098/rsbl.2020.0629] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Carotenoid pigments play a major role in animal body colouration, generating strong interest in the genes involved in the metabolic processes that lead from their dietary uptake to their storage in the integument. Here, we used RNA sequencing (RNA-Seq) to test for differentially expressed genes in a taxonomically replicated design using three pairs of related cichlid fish taxa from the genera Tropheus and Aulonocara. Within each pair, taxa differed in terms of red and yellow body colouration, and high‐performance liquid chromatography (HPLC) analyses of skin extracts revealed different carotenoid profiles and concentrations across the studied taxa. Five genes were differentially expressed in all three yellow–red skin contrasts (dhrsx, nlrc3, tcaf2, urah and ttc39b), but only the tetratricopeptide repeat protein-coding gene ttc39b, whose gene product is linked to mammalian lipid metabolism, was consistently expressed more highly in the red skin samples. The RNA-Seq results were confirmed by quantitative PCR. We propose ttc39b as a compelling candidate gene for variation in animal carotenoid colouration. Since differential expression of ttc39b was correlated with the presence/absence of yellow carotenoids in a previous study, we suggest that ttc39b is more likely associated with the concentration of total carotenoids than with the metabolic formation of red carotenoids.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria.,Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, SE-75 236 Uppsala, Sweden
| | - Laurène A Lecaudey
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria.,Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | | | - Oliver Steiner
- Institute of Chemistry, University of Graz, Universitätsplatz 1, A-8010 Graz, Austria
| | - Walter Goessler
- Institute of Chemistry, University of Graz, Universitätsplatz 1, A-8010 Graz, Austria
| | - Kristina M Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
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18
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Roux N, Salis P, Lee SH, Besseau L, Laudet V. Anemonefish, a model for Eco-Evo-Devo. EvoDevo 2020; 11:20. [PMID: 33042514 PMCID: PMC7539381 DOI: 10.1186/s13227-020-00166-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/18/2020] [Indexed: 12/20/2022] Open
Abstract
Anemonefish, are a group of about 30 species of damselfish (Pomacentridae) that have long aroused the interest of coral reef fish ecologists. Combining a series of original biological traits and practical features in their breeding that are described in this paper, anemonefish are now emerging as an experimental system of interest for developmental biology, ecology and evolutionary sciences. They are small sized and relatively easy to breed in specific husbandries, unlike the large-sized marine fish used for aquaculture. Because they live in highly structured social groups in sea anemones, anemonefish allow addressing a series of relevant scientific questions such as the social control of growth and sex change, the mechanisms controlling symbiosis, the establishment and variation of complex color patterns, and the regulation of aging. Combined with the use of behavioral experiments, that can be performed in the lab or directly in the wild, as well as functional genetics and genomics, anemonefish provide an attractive experimental system for Eco-Evo-Devo.
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Affiliation(s)
- Natacha Roux
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Pauline Salis
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Shu-Hua Lee
- Lab of Marine Eco-Evo-Devo, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Laurence Besseau
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Vincent Laudet
- Lab of Marine Eco-Evo-Devo, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa, 904-0495 Japan
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19
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A "Numerical Evo-Devo" Synthesis for the Identification of Pattern-Forming Factors. Cells 2020; 9:cells9081840. [PMID: 32764501 PMCID: PMC7463486 DOI: 10.3390/cells9081840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
Animals display extensive diversity in motifs adorning their coat, yet these patterns have reproducible orientation and periodicity within species or groups. Morphological variation has been traditionally used to dissect the genetic basis of evolutionary change, while pattern conservation and stability in both mathematical and organismal models has served to identify core developmental events. Two patterning theories, namely instruction and self-organisation, emerged from this work. Combined, they provide an appealing explanation for how natural patterns form and evolve, but in vivo factors underlying these mechanisms remain elusive. By bridging developmental biology and mathematics, novel frameworks recently allowed breakthroughs in our understanding of pattern establishment, unveiling how patterning strategies combine in space and time, or the importance of tissue morphogenesis in generating positional information. Adding results from surveys of natural variation to these empirical-modelling dialogues improves model inference, analysis, and in vivo testing. In this evo-devo-numerical synthesis, mathematical models have to reproduce not only given stable patterns but also the dynamics of their emergence, and the extent of inter-species variation in these dynamics through minimal parameter change. This integrative approach can help in disentangling molecular, cellular and mechanical interaction during pattern establishment.
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20
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Liang Y, Meyer A, Kratochwil CF. Neural innervation as a potential trigger of morphological color change and sexual dimorphism in cichlid fish. Sci Rep 2020; 10:12329. [PMID: 32704058 PMCID: PMC7378239 DOI: 10.1038/s41598-020-69239-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/09/2020] [Indexed: 12/24/2022] Open
Abstract
Many species change their coloration during ontogeny or even as adults. Color change hereby often serves as sexual or status signal. The cellular and subcellular changes that drive color change and how they are orchestrated have been barely understood, but a deeper knowledge of the underlying processes is important to our understanding of how such plastic changes develop and evolve. Here we studied the color change of the Malawi golden cichlid (Melanchromis auratus). Females and subordinate males of this species are yellow and white with two prominent black stripes (yellow morph; female and non-breeding male coloration), while dominant males change their color and completely invert this pattern with the yellow and white regions becoming black, and the black stripes becoming white to iridescent blue (dark morph; male breeding coloration). A comparison of the two morphs reveals that substantial changes across multiple levels of biological organization underlie this polyphenism. These include changes in pigment cell (chromatophore) number, intracellular dispersal of pigments, and tilting of reflective platelets (iridosomes) within iridophores. At the transcriptional level, we find differences in pigmentation gene expression between these two color morphs but, surprisingly, 80% of the genes overexpressed in the dark morph relate to neuronal processes including synapse formation. Nerve fiber staining confirms that scales of the dark morph are indeed innervated by 1.3 to 2 times more axonal fibers. Our results might suggest an instructive role of nervous innervation orchestrating the complex cellular and ultrastructural changes that drive the morphological color change of this cichlid species.
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Affiliation(s)
- Yipeng Liang
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
| | - Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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21
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Volkening A. Linking genotype, cell behavior, and phenotype: multidisciplinary perspectives with a basis in zebrafish patterns. Curr Opin Genet Dev 2020; 63:78-85. [PMID: 32604031 DOI: 10.1016/j.gde.2020.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Zebrafish are characterized by dark and light stripes, but mutants display a rich variety of altered patterns. These patterns arise from the interactions of brightly colored pigment cells, making zebrafish a self-organization problem. The diversity of patterns present in zebrafish and other emerging fish models provides an excellent system for elucidating how genes, cell behavior, and visible animal characteristics are related. With the goal of highlighting how experimental and mathematical approaches can be used to link these scales, I overview current descriptions of zebrafish patterning, describe advances in the understanding of the mechanisms underlying cell communication, and discuss new work that moves beyond zebrafish to explore patterning in evolutionary relatives.
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Affiliation(s)
- Alexandria Volkening
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA; Department of Engineering Sciences and Applied Mathematics, Evanston, IL 60208, USA.
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22
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Anderson AP, Rose E, Flanagan SP, Jones AG. The Estrogen-Responsive Transcriptome of Female Secondary Sexual Traits in the Gulf Pipefish. J Hered 2020; 111:294-306. [PMID: 32124926 DOI: 10.1093/jhered/esaa008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/24/2020] [Indexed: 01/01/2023] Open
Abstract
Sexual dimorphism often results from hormonally regulated trait differences between the sexes. In sex-role-reversed vertebrates, females often have ornaments used in mating competition that are expected to be under hormonal control. Males of the sex-role-reversed Gulf pipefish (Syngnathus scovelli) develop female-typical traits when they are exposed to estrogens. We aimed to identify genes whose expression levels changed during the development and maintenance of female-specific ornaments. We performed RNA-sequencing on skin and muscle tissue in male Gulf pipefish with and without exposure to estrogen to investigate the transcriptome of the sexually dimorphic ornament of vertical iridescent bands found in females and estrogen-exposed males. We further compared differential gene expression patterns between males and females to generate a list of genes putatively involved in the female secondary sex traits of bands and body depth. A detailed analysis of estrogen-receptor binding sites demonstrates that estrogen-regulated genes tend to have nearby cis-regulatory elements. Our results identified a number of genes that differed between the sexes and confirmed that many of these were estrogen-responsive. These estrogen-regulated genes may be involved in the arrangement of chromatophores for color patterning, as well as in the growth of muscles to achieve the greater body depth typical of females in this species. In addition, anaerobic respiration and adipose tissue could be involved in the rigors of female courtship and mating competition. Overall, this study generates a number of interesting hypotheses regarding the genetic basis of a female ornament in a sex-role-reversed pipefish.
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Affiliation(s)
| | - Emily Rose
- Department of Biology, University of Tampa, Tampa, FL
| | - Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID
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23
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Ahi EP, Lecaudey LA, Ziegelbecker A, Steiner O, Glabonjat R, Goessler W, Hois V, Wagner C, Lass A, Sefc KM. Comparative transcriptomics reveals candidate carotenoid color genes in an East African cichlid fish. BMC Genomics 2020; 21:54. [PMID: 31948394 PMCID: PMC6966818 DOI: 10.1186/s12864-020-6473-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/09/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Carotenoids contribute significantly to animal body coloration, including the spectacular color pattern diversity among fishes. Fish, as other animals, derive carotenoids from their diet. Following uptake, transport and metabolic conversion, carotenoids allocated to body coloration are deposited in the chromatophore cells of the integument. The genes involved in these processes are largely unknown. Using RNA-Sequencing, we tested for differential gene expression between carotenoid-colored and white skin regions of a cichlid fish, Tropheus duboisi "Maswa", to identify genes associated with carotenoid-based integumentary coloration. To control for positional gene expression differences that were independent of the presence/absence of carotenoid coloration, we conducted the same analyses in a closely related population, in which both body regions are white. RESULTS A larger number of genes (n = 50) showed higher expression in the yellow compared to the white skin tissue than vice versa (n = 9). Of particular interest was the elevated expression level of bco2a in the white skin samples, as the enzyme encoded by this gene catalyzes the cleavage of carotenoids into colorless derivatives. The set of genes with higher expression levels in the yellow region included genes involved in xanthophore formation (e.g., pax7 and sox10), intracellular pigment mobilization (e.g., tubb, vim, kif5b), as well as uptake (e.g., scarb1) and storage (e.g., plin6) of carotenoids, and metabolic conversion of lipids and retinoids (e.g., dgat2, pnpla2, akr1b1, dhrs). Triglyceride concentrations were similar in the yellow and white skin regions. Extracts of integumentary carotenoids contained zeaxanthin, lutein and beta-cryptoxanthin as well as unidentified carotenoid structures. CONCLUSION Our results suggest a role of carotenoid cleavage by Bco2 in fish integumentary coloration, analogous to previous findings in birds. The elevated expression of genes in carotenoid-rich skin regions with functions in retinol and lipid metabolism supports hypotheses concerning analogies and shared mechanisms between these metabolic pathways. Overlaps in the sets of differentially expressed genes (including dgat2, bscl2, faxdc2 and retsatl) between the present study and previous, comparable studies in other fish species provide useful hints to potential carotenoid color candidate genes.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
- Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, SE-75 236 Uppsala, Sweden
| | - Laurène A. Lecaudey
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Angelika Ziegelbecker
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | - Oliver Steiner
- Institute of Chemistry, University of Graz, Universitätsplatz 1, A-8010, Graz, Austria
| | - Ronald Glabonjat
- Institute of Chemistry, University of Graz, Universitätsplatz 1, A-8010, Graz, Austria
| | - Walter Goessler
- Institute of Chemistry, University of Graz, Universitätsplatz 1, A-8010, Graz, Austria
| | - Victoria Hois
- Institute of Molecular Biosciences, University of Graz, Heinrichstraße 31/II, 8010, Graz, Austria
| | - Carina Wagner
- Institute of Molecular Biosciences, University of Graz, Heinrichstraße 31/II, 8010, Graz, Austria
| | - Achim Lass
- Institute of Molecular Biosciences, University of Graz, Heinrichstraße 31/II, 8010, Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Kristina M. Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
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Patterson LB, Parichy DM. Zebrafish Pigment Pattern Formation: Insights into the Development and Evolution of Adult Form. Annu Rev Genet 2019; 53:505-530. [DOI: 10.1146/annurev-genet-112618-043741] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Vertebrate pigment patterns are diverse and fascinating adult traits that allow animals to recognize conspecifics, attract mates, and avoid predators. Pigment patterns in fish are among the most amenable traits for studying the cellular basis of adult form, as the cells that produce diverse patterns are readily visible in the skin during development. The genetic basis of pigment pattern development has been most studied in the zebrafish, Danio rerio. Zebrafish adults have alternating dark and light horizontal stripes, resulting from the precise arrangement of three main classes of pigment cells: black melanophores, yellow xanthophores, and iridescent iridophores. The coordination of adult pigment cell lineage specification and differentiation with specific cellular interactions and morphogenetic behaviors is necessary for stripe development. Besides providing a nice example of pattern formation responsible for an adult trait of zebrafish, stripe-forming mechanisms also provide a conceptual framework for posing testable hypotheses about pattern diversification more broadly. Here, we summarize what is known about lineages and molecular interactions required for pattern formation in zebrafish, we review some of what is known about pattern diversification in Danio, and we speculate on how patterns in more distant teleosts may have evolved to produce a stunningly diverse array of patterns in nature.
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Affiliation(s)
| | - David M. Parichy
- Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22903, USA
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25
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The identification of genes involved in the evolution of color patterns in fish. Curr Opin Genet Dev 2019; 57:31-38. [PMID: 31421397 PMCID: PMC6838669 DOI: 10.1016/j.gde.2019.07.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/19/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022]
Abstract
The genetic basis of morphological variation, both within and between species, provides a major topic in evolutionary biology. Teleost fish produce most elaborate color patterns, and among the more than 20 000 species a number have been chosen for more detailed analyses because they are suitable to study particular aspects of color pattern evolution. In several fish species, color variants and pattern variants have been collected, transcriptome analyses have been carried out, and the recent advent of gene editing tools, such as CRISPR/Cas9, has allowed the production of mutants. Covering mostly the literature from the last three years, we discuss the cellular basis of coloration and the identification of loci involved in color pattern differences between sister species in cichlids and Danio species, in which cis-regulatory changes seem to prevail.
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26
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Lewis VM, Saunders LM, Larson TA, Bain EJ, Sturiale SL, Gur D, Chowdhury S, Flynn JD, Allen MC, Deheyn DD, Lee JC, Simon JA, Lippincott-Schwartz J, Raible DW, Parichy DM. Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores. Proc Natl Acad Sci U S A 2019; 116:11806-11811. [PMID: 31138706 PMCID: PMC6575160 DOI: 10.1073/pnas.1901021116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes, including the zebrafish Danio rerio, we identified two populations of white pigment cells-leucophores-one of which arises by transdifferentiation of adult melanophores and another of which develops from a yellow-orange xanthophore or xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical, and ultrastructural analyses of zebrafish leucophores revealed cell-type-specific chemical compositions, organelle configurations, and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching, and we showed that leucophore complement influences behavior. Together, our studies reveal independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.
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Affiliation(s)
- Victor M Lewis
- Department of Biology, University of Virginia, Charlottesville, VA 22903
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Lauren M Saunders
- Department of Biology, University of Virginia, Charlottesville, VA 22903
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195
| | - Tracy A Larson
- Department of Biology, University of Virginia, Charlottesville, VA 22903
| | - Emily J Bain
- Department of Biology, University of Virginia, Charlottesville, VA 22903
| | | | - Dvir Gur
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
- Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Sarwat Chowdhury
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Jessica D Flynn
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Michael C Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Dimitri D Deheyn
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jennifer C Lee
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Julian A Simon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | | | - David W Raible
- Department of Biology, University of Washington, Seattle, WA 98195
- Department of Biological Structure, University of Washington, Seattle, WA 98195
| | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, VA 22903;
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22903
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27
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Roux N, Salis P, Lambert A, Logeux V, Soulat O, Romans P, Frédérich B, Lecchini D, Laudet V. Staging and normal table of postembryonic development of the clownfish (Amphiprion ocellaris). Dev Dyn 2019; 248:545-568. [PMID: 31070818 PMCID: PMC6771578 DOI: 10.1002/dvdy.46] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/17/2019] [Accepted: 04/17/2019] [Indexed: 12/19/2022] Open
Abstract
Background The clownfish Amphiprion ocellaris is one of the rare coral reef fish species that can be reared in aquaria. With relatively short embryonic and larval development, it could be used as a model species to study the impact of global changes such as temperature rise or anthropogenic threats (eg, pollution) on the postembryonic development at molecular and endocrinological levels. Establishing a developmental table allows us to standardize sampling for the scientific community willing to conduct experiments on this species on different areas: ecology, evolution, and developmental biology. Results Here, we describe the postembryonic developmental stages for the clownfish A. ocellaris from hatching to juvenile stages (30 days posthatching). We quantitatively followed the postembryonic growth and described qualitative traits: head, paired and unpaired fins, notochord flexion, and pigmentation changes. The occurrence of these changes over time allowed us to define seven stages, for which we provide precise descriptions. Conclusions Our work gives an easy system to determine A. ocellaris postembryonic stages allowing, thus, to develop this species as a model species for coral reef fishes. In light of global warming, the access to the full postembryonic development stages of coral reef fish is important to determine stressors that can affect such processes. Seven developmental stages have been identified to describe the larval development of the clownfish Amphiprion ocellaris. Clownfish larvae undergo two distinct developmental growth phases that correspond to growth and metamorphosis. A dichotomous key determination has been created to assist users in identifying the various developmental stages.
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Affiliation(s)
- Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, CNRS UMR 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France.,PSL Research University, USR 3278, EPHE-CNRS-UPVD, Moorea, French Polynesia
| | - Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, CNRS UMR 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Anne Lambert
- Institut de Génomique Fonctionnelle de Lyon, Université Claude Bernard Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Valentin Logeux
- Observatoire Océanologique de Banyuls-sur-Mer, CNRS UMR 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Olivier Soulat
- Aquarium de Canet-en-Roussillon, Canet-en-Roussillon, France
| | - Pascal Romans
- Observatoire Océanologique de Banyuls-sur-Mer, CNRS UMR 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology, FOCUS, University of Liège, Liège, Belgium
| | - David Lecchini
- PSL Research University, USR 3278, EPHE-CNRS-UPVD, Moorea, French Polynesia.,Laboratoire d'Excellence CORAIL, Moorea, French Polynesia
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, CNRS UMR 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
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