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Blandon IR, DiBona E, Battenhouse A, Vargas S, Mace C, Seemann F. Analysis of the Skin and Brain Transcriptome of Normally Pigmented and Pseudo-Albino Southern Flounder ( Paralichthys lethostigma) Juveniles to Study the Molecular Mechanisms of Hypopigmentation and Its Implications for Species Survival in the Natural Environment. Int J Mol Sci 2024; 25:7775. [PMID: 39063015 PMCID: PMC11277284 DOI: 10.3390/ijms25147775] [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: 05/13/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Southern flounder skin pigmentation is a critical phenotypic characteristic for this species' survival in the natural environment. Normal pigmentation allows rapid changes of color for concealment to capture prey and UV light protection. In contrast, highly visible hypopigmented pseudo-albinos exhibit a compromised immune system and are vulnerable to predation, sensitive to UV exposure, and likely have poor survival in the wild. Skin and brain tissue samples from normally pigmented and hypopigmented individuals were analyzed with next-generation RNA sequencing. A total of 1,589,613 transcripts were used to identify 952,825 genes to assemble a de novo transcriptome, with 99.43% of genes mapped to the assembly. Differential gene expression and gene enrichment analysis of contrasting tissues and phenotypes revealed that pseudo-albino individuals appeared more susceptible to environmental stress, UV light exposure, hypoxia, and osmotic stress. The pseudo-albinos' restricted immune response showed upregulated genes linked to cancer development, signaling and response, skin tissue formation, regeneration, and healing. The data indicate that a modified skin collagen structure likely affects melanocyte differentiation and distribution, generating the pseudo-albino phenotype. In addition, the comparison of the brain transcriptome revealed changes in myelination and melanocyte stem cell activity, which may indicate modified brain function, reduced melanocyte migration, and impaired vision.
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Affiliation(s)
- Ivonne R. Blandon
- Coastal Fisheries Division CCA Marine Development Center, Texas Parks and Wildlife Department, 4300 Waldron Rd., Corpus Christi, TX 78418, USA
| | - Elizabeth DiBona
- Department of Life Sciences, College of Science, Texas A and M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Anna Battenhouse
- Center for Biochemical Research Computing Facility, University of Texas at Austin, 100 East 24th, Austin, TX 78712, USA
| | - Sean Vargas
- Genomic Core Facility, University of Texas at San Antonio, UTSA Circle, San Antonio, TX 78249, USA;
| | - Christopher Mace
- Coastal Fisheries Division CCA Marine Development Center, Texas Parks and Wildlife Department, 4300 Waldron Rd., Corpus Christi, TX 78418, USA
| | - Frauke Seemann
- Department of Life Sciences, College of Science, Texas A and M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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2
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Monteiro JPC, Pröhl H, Lyra ML, Brunetti AE, de Nardin EC, Condez TH, Haddad CFB, Rodríguez A. Expression patterns of melanin-related genes are linked to crypsis and conspicuousness in a pumpkin toadlet. Mol Ecol 2024:e17458. [PMID: 38970414 DOI: 10.1111/mec.17458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Colour signals play pivotal roles in different communication systems, and the evolution of these characters has been associated with behavioural ecology, integumentary production processes and perceptual mechanisms of the species involved. Here, we present the first insight into the molecular and histological basis of skin colour polymorphism within a miniaturized species of pumpkin toadlet, potentially representing the lowest size threshold for colour polytypism in tetrapods. Brachycephalus actaeus exhibits a coloration ranging from cryptic green to conspicuous orange skin, and our findings suggest that colour morphs differ in their capability to be detected by potential predators. We also found that the distribution and abundance of chromatophores are variable in the different colour morphs. The expression pattern of coloration related genes was predominantly associated with melanin synthesis (including dct, edn1, mlana, oca2, pmel, slc24a5, tyrp1 and wnt9a). Up-regulation of melanin genes in grey, green and brown skin was associated with higher melanophore abundance than in orange skin, where xanthophores predominate. Our findings provide a significant foundation for comparing and understanding the diverse pathways that contribute to the evolution of pigment production in the skin of amphibians.
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Affiliation(s)
- Juliane P C Monteiro
- Post-Graduate Program in Biodiversity, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Department of Biodiversity and Aquaculture Center (CAUNESP), Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Institute of Zoology, University of Veterinary Medicine of Hannover, Hannover, Lower Saxony, Germany
| | - Heike Pröhl
- Institute of Zoology, University of Veterinary Medicine of Hannover, Hannover, Lower Saxony, Germany
| | - Mariana L Lyra
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Andrés E Brunetti
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Institute of Subtropical Biology (IBS, UNaM-CONICET), Posadas, Misiones, Argentina
- Department of Insect Symbiosis, Max Planck Institute of Chemical Ecology, Jena, Thuringia, Germany
| | - Eli C de Nardin
- Department of Biodiversity and Aquaculture Center (CAUNESP), Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Thais H Condez
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Célio F B Haddad
- Department of Biodiversity and Aquaculture Center (CAUNESP), Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Ariel Rodríguez
- Institute of Zoology, University of Veterinary Medicine of Hannover, Hannover, Lower Saxony, Germany
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Rubio AO, Stuckert AMM, Geralds B, Nielsen R, MacManes MD, Summers K. What Makes a Mimic? Orange, Red, and Black Color Production in the Mimic Poison Frog (Ranitomeya imitator). Genome Biol Evol 2024; 16:evae123. [PMID: 38874406 PMCID: PMC11255871 DOI: 10.1093/gbe/evae123] [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: 09/03/2023] [Revised: 05/08/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024] Open
Abstract
Aposematic organisms rely on their conspicuous appearance to signal that they are defended and unpalatable. Such phenotypes are strongly tied to survival and reproduction. Aposematic colors and patterns are highly variable; however, the genetic, biochemical, and physiological mechanisms producing this conspicuous coloration remain largely unidentified. Here, we identify genes potentially affecting color variation in two color morphs of Ranitomeya imitator: the orange-banded Sauce and the redheaded Varadero morphs. We examine gene expression in black and orange skin patches from the Sauce morph and black and red skin patches from the Varadero morph. We identified genes differentially expressed between skin patches, including those that are involved in melanin synthesis (e.g. mlana, pmel, tyrp1), iridophore development (e.g. paics, ppat, ak1), pteridine synthesis (e.g. gch1, pax3-a, xdh), and carotenoid metabolism (e.g. dgat2, rbp1, scarb2). In addition, using weighted correlation network analysis, we identified the top 50 genes with high connectivity from the most significant network associated with gene expression differences between color morphs. Of these 50 genes, 13 were known to be related to color production (gch1, gmps, gpr143, impdh1, mc1r, pax3-a, pax7, ppat, rab27a, rlbp1, tfec, trpm1, xdh).
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Affiliation(s)
- Andrew O Rubio
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Adam M M Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - BreAnn Geralds
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Matthew D MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Kyle Summers
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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4
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Recknagel H, Leitão HG, Elmer KR. Genetic basis and expression of ventral colour in polymorphic common lizards. Mol Ecol 2024; 33:e17278. [PMID: 38268086 DOI: 10.1111/mec.17278] [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: 09/12/2022] [Revised: 12/15/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024]
Abstract
Colour is an important visual cue that can correlate with sex, behaviour, life history or ecological strategies, and has evolved divergently and convergently across animal lineages. Its genetic basis in non-model organisms is rarely known, but such information is vital for determining the drivers and mechanisms of colour evolution. Leveraging genetic admixture in a rare contact zone between oviparous and viviparous common lizards (Zootoca vivipara), we show that females (N = 558) of the two otherwise morphologically indistinguishable reproductive modes differ in their ventral colouration (from pale to vibrant yellow) and intensity of melanic patterning. We find no association between female colouration and reproductive investment, and no evidence for selection on colour. Using a combination of genetic mapping and transcriptomic evidence, we identified two candidate genes associated with ventral colour differentiation, DGAT2 and PMEL. These are genes known to be involved in carotenoid metabolism and melanin synthesis respectively. Ventral melanic spots were associated with two genomic regions, including a SNP close to protein tyrosine phosphatase (PTP) genes. Using genome re-sequencing data, our results show that fixed coding mutations in the candidate genes cannot account for differences in colouration. Taken together, our findings show that the evolution of ventral colouration and its associations across common lizard lineages is variable. A potential genetic mechanism explaining the flexibility of ventral colouration may be that colouration in common lizards, but also across squamates, is predominantly driven by regulatory genetic variation.
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Affiliation(s)
- Hans Recknagel
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Henrique G Leitão
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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5
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Ma L, Zhu Z, Zhang S, Yang R, Liu C, Yu Y, Yang X. Comparative Transcriptome Analysis of the Skin and the Peritoneal Wall Layer of Triplophysa stenura Distributed in High Elevations. BIOLOGY 2023; 13:5. [PMID: 38275726 PMCID: PMC10812932 DOI: 10.3390/biology13010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/27/2024]
Abstract
A total of 81,868 All-Unigenes were sequenced and assembled by the transcriptome in the dorsal skin, the lateral skin, and the peritoneal wall layer of Triplophysa stenura with a total assembly length of 123,827,585 bp, and 68,750 unigenes were annotated to seven functional databases. A total of 588 DEGs were screened between the dorsal and lateral skin, 17,097 DEGs were screened between the dorsal skin and the peritoneal wall layer, and 16,598 DEGs were screened between the lateral skin and the peritoneal wall layer. Most of DEGs in three tissues were annotated to GO terms related to cellular structures, binding, cellular processes, and catalytic activity. They were also annotated to KEGG pathways such as the MAPK signaling pathway, PI3K-Akt signaling pathway, Wnt signaling pathway, melanogenesis, tyrosine metabolism, and cell cycle. A total of twenty-three DEGs were found to be enriched in the melanin synthesis pathway by a local Blast comparison, of which nine DEGs were significantly upregulated in the peritoneal wall layer and six DEGs were significantly upregulated in the dorsal and lateral skin. The results suggest that these genes may be associated with the molecular mechanism of melanin synthesis in T. stenura, and the differential regulation of genes may be related to the differences in UVR intensity and tissue sites of melanin synthesis. Further investigation is needed on how these genes specifically regulate melanin synthesis.
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Affiliation(s)
- Li Ma
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.M.); (Z.Z.); (R.Y.); (C.L.); (Y.Y.)
| | - Zhen Zhu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.M.); (Z.Z.); (R.Y.); (C.L.); (Y.Y.)
- Hubei Vocational College of Bio-Technology, Wuhan 430070, China
| | - Shanzhong Zhang
- Hechuan Campus, Sichuan Fisheries School, Hechuan, Chongqing 401520, China;
| | - Ruibin Yang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.M.); (Z.Z.); (R.Y.); (C.L.); (Y.Y.)
| | - Chen Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.M.); (Z.Z.); (R.Y.); (C.L.); (Y.Y.)
| | - Yongyao Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.M.); (Z.Z.); (R.Y.); (C.L.); (Y.Y.)
| | - Xuefen Yang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.M.); (Z.Z.); (R.Y.); (C.L.); (Y.Y.)
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6
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Katkat E, Demirci Y, Heger G, Karagulle D, Papatheodorou I, Brazma A, Ozhan G. Canonical Wnt and TGF-β/BMP signaling enhance melanocyte regeneration but suppress invasiveness, migration, and proliferation of melanoma cells. Front Cell Dev Biol 2023; 11:1297910. [PMID: 38020918 PMCID: PMC10679360 DOI: 10.3389/fcell.2023.1297910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Melanoma is the deadliest form of skin cancer and develops from the melanocytes that are responsible for the pigmentation of the skin. The skin is also a highly regenerative organ, harboring a pool of undifferentiated melanocyte stem cells that proliferate and differentiate into mature melanocytes during regenerative processes in the adult. Melanoma and melanocyte regeneration share remarkable cellular features, including activation of cell proliferation and migration. Yet, melanoma considerably differs from the regenerating melanocytes with respect to abnormal proliferation, invasive growth, and metastasis. Thus, it is likely that at the cellular level, melanoma resembles early stages of melanocyte regeneration with increased proliferation but separates from the later melanocyte regeneration stages due to reduced proliferation and enhanced differentiation. Here, by exploiting the zebrafish melanocytes that can efficiently regenerate and be induced to undergo malignant melanoma, we unravel the transcriptome profiles of the regenerating melanocytes during early and late regeneration and the melanocytic nevi and malignant melanoma. Our global comparison of the gene expression profiles of melanocyte regeneration and nevi/melanoma uncovers the opposite regulation of a substantial number of genes related to Wnt signaling and transforming growth factor beta (TGF-β)/(bone morphogenetic protein) BMP signaling pathways between regeneration and cancer. Functional activation of canonical Wnt or TGF-β/BMP pathways during melanocyte regeneration promoted melanocyte regeneration but potently suppressed the invasiveness, migration, and proliferation of human melanoma cells in vitro and in vivo. Therefore, the opposite regulation of signaling mechanisms between melanocyte regeneration and melanoma can be exploited to stop tumor growth and develop new anti-cancer therapies.
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Affiliation(s)
- Esra Katkat
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Izmir, Türkiye
| | - Yeliz Demirci
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Izmir, Türkiye
| | | | - Doga Karagulle
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Izmir, Türkiye
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Türkiye
| | - Irene Papatheodorou
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Alvis Brazma
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Gunes Ozhan
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Izmir, Türkiye
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Türkiye
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7
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Bayala EX, Cisneros I, Massardo D, VanKuren NW, Kronforst MR. Divergent expression of aristaless1 and aristaless2 during embryonic appendage and pupal wing development in butterflies. BMC Biol 2023; 21:104. [PMID: 37170114 PMCID: PMC10173497 DOI: 10.1186/s12915-023-01602-5] [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: 10/20/2022] [Accepted: 04/13/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Gene duplication events are critical for the evolution of new gene functions. Aristaless is a major regulator of distinct developmental processes. It is most known for its role during appendage development across animals. However, more recently other distinct biological functions have been described for this gene and its duplicates. Butterflies and moths have two copies of aristaless, aristaless1 (al1) and aristaless2 (al2), as a result of a gene duplication event. Previous work in Heliconius has shown that both copies appear to have novel functions related to wing color patterning. Here we expand our knowledge of the expression profiles associated with both ancestral and novel functions of Al1 across embryogenesis and wing pigmentation. Furthermore, we characterize Al2 expression, providing a comparative framework between gene copies within the same species, allowing us to understand the origin of new functions following gene duplication. RESULTS Our work shows that the expression of both Al1 and Al2 is associated with the ancestral function of sensory appendage (leg, mouth, spines, and eyes) development in embryos. Interestingly, Al1 exhibits higher expression earlier in embryogenesis while the highest levels of Al2 expression are shifted to later stages of embryonic development. Furthermore, Al1 localization appears extranuclear while Al2 co-localizes tightly with nuclei earlier, and then also expands outside the nucleus later in development. Cellular expression of Al1 and Al2 in pupal wings is broadly consistent with patterns observed during embryogenesis. We also describe, for the first time, how Al1 localization appears to correlate with zones of anterior/posterior elongation of the body during embryonic growth, showcasing a possible new function related to Aristaless' previously described role in appendage extension. CONCLUSIONS Overall, our data suggest that while both gene copies play a role in embryogenesis and wing pigmentation, the duplicates have diverged temporally and mechanistically across those functions. Our study helps clarify principles behind sub-functionalization and gene expression evolution associated with developmental functions following gene duplication events.
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Affiliation(s)
- Erick X Bayala
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
| | - Isabella Cisneros
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Darli Massardo
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Nicholas W VanKuren
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Marcus R Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
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8
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Pavan ME, Movilla F, Pavan EE, Di Salvo F, López NI, Pettinari MJ. Guanine crystal formation by bacteria. BMC Biol 2023; 21:66. [PMID: 37013555 PMCID: PMC10071637 DOI: 10.1186/s12915-023-01572-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Guanine crystals are organic biogenic crystals found in many organisms. Due to their exceptionally high refractive index, they contribute to structural color and are responsible for the reflective effect in the skin and visual organs in animals such as fish, reptiles, and spiders. Occurrence of these crystals in animals has been known for many years, and they have also been observed in eukaryotic microorganisms, but not in prokaryotes. RESULTS In this work, we report the discovery of extracellular crystals formed by bacteria and reveal that they are composed of guanine monohydrate. This composition differs from that of biogenic guanine crystals found in other organisms, mostly composed of β anhydrous guanine. We demonstrate the formation of these crystals by Aeromonas and other bacteria and investigate the metabolic traits related to their synthesis. In all cases studied, the presence of the bacterial guanine crystals correlates with the absence of guanine deaminase, which could lead to guanine accumulation providing the substrate for crystal formation. CONCLUSIONS Our finding of the hitherto unknown guanine crystal occurrence in prokaryotes extends the range of organisms that produce these crystals to a new domain of life. Bacteria constitute a novel and more accessible model to study the process of guanine crystal formation and assembly. This discovery opens countless chemical and biological questions, including those about the functional and adaptive significance of their production in these microorganisms. It also paves the road for the development of simple and convenient processes to obtain biogenic guanine crystals for diverse applications.
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Affiliation(s)
- María Elisa Pavan
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Movilla
- Departamento de Química Inorgánica, Analítica y Química Física e INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Esteban E Pavan
- Biomedical Technologies Laboratory, Department of Electronics, Information and Bioengineering, Politecnico Di Milano, Milan, Italy
| | - Florencia Di Salvo
- Departamento de Química Inorgánica, Analítica y Química Física e INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nancy I López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M Julia Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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9
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Tang CY, Zhang X, Xu X, Sun S, Peng C, Song MH, Yan C, Sun H, Liu M, Xie L, Luo SJ, Li JT. Genetic mapping and molecular mechanism behind color variation in the Asian vine snake. Genome Biol 2023; 24:46. [PMID: 36895044 PMCID: PMC9999515 DOI: 10.1186/s13059-023-02887-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved. RESULTS We investigate color morph-enriched Asian vine snakes (Ahaetulla prasina), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color. Additionally, we assemble a 1.77-Gb high-quality chromosome-anchored genome of the snake. Genome-wide association study and RNA sequencing reveal a conservative amino acid substitution (p.P20S) in SMARCE1, which may be involved in the regulation of chromatophore development initiated from neural crest cells. SMARCE1 knockdown in zebrafish and immunofluorescence verify the interactions among SMARCE1, iridophores, and tfec, which may determine color variations in the Asian vine snake. CONCLUSIONS This study reveals the genetic associations of color variation in Asian vine snakes, providing insights and important resources for a deeper understanding of the molecular and genetic mechanisms related to reptilian coloration.
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Affiliation(s)
- Chen-Yang Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaohu Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Shijie Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng-Huan Song
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huaqin Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Mingfeng Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Liang Xie
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw, 05282, Myanmar.
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10
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Subkhankulova T, Camargo Sosa K, Uroshlev LA, Nikaido M, Shriever N, Kasianov AS, Yang X, Rodrigues FSLM, Carney TJ, Bavister G, Schwetlick H, Dawes JHP, Rocco A, Makeev VJ, Kelsh RN. Zebrafish pigment cells develop directly from persistent highly multipotent progenitors. Nat Commun 2023; 14:1258. [PMID: 36878908 PMCID: PMC9988989 DOI: 10.1038/s41467-023-36876-4] [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: 06/23/2021] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Neural crest cells are highly multipotent stem cells, but it remains unclear how their fate restriction to specific fates occurs. The direct fate restriction model hypothesises that migrating cells maintain full multipotency, whilst progressive fate restriction envisages fully multipotent cells transitioning to partially-restricted intermediates before committing to individual fates. Using zebrafish pigment cell development as a model, we show applying NanoString hybridization single cell transcriptional profiling and RNAscope in situ hybridization that neural crest cells retain broad multipotency throughout migration and even in post-migratory cells in vivo, with no evidence for partially-restricted intermediates. We find that leukocyte tyrosine kinase early expression marks a multipotent stage, with signalling driving iridophore differentiation through repression of fate-specific transcription factors for other fates. We reconcile the direct and progressive fate restriction models by proposing that pigment cell development occurs directly, but dynamically, from a highly multipotent state, consistent with our recently-proposed Cyclical Fate Restriction model.
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Affiliation(s)
| | - Karen Camargo Sosa
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Leonid A Uroshlev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
| | - Masataka Nikaido
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo Pref., 678-1297, Japan
| | - Noah Shriever
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
- Department of Medical and Biological Physics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia
- A.A. Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051, Russia
| | - Xueyan Yang
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- The MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | | | - Thomas J Carney
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Lee Kong Chian School of Medicine, Experimental Medicine Building, Yunnan Garden Campus, Nanyang Technological University, 59 Nanyang Drive, Yunnan Garden, 636921, Singapore
| | - Gemma Bavister
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Hartmut Schwetlick
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Jonathan H P Dawes
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Andrea Rocco
- Department of Microbial Sciences, FHMS, University of Surrey, GU2 7XH, Guildford, UK
- Department of Physics, FEPS, University of Surrey, GU2 7XH, Guildford, UK
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
- Department of Medical and Biological Physics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia
- Laboratory 'Regulatory Genomics', Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya street, Kazan, 420008, Russia
| | - Robert N Kelsh
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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11
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Mao L, Zhu Y, Yan J, Zhang L, Zhu S, An L, Meng Q, Zhang Z, Wang X. Full-length transcriptome sequencing analysis reveals differential skin color regulation in snakeheads fish Channa argus. AQUACULTURE AND FISHERIES 2023. [DOI: 10.1016/j.aaf.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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12
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Zhang L, Wan M, Tohti R, Jin D, Zhong TP. Requirement of Zebrafish Adcy3a and Adcy5 in Melanosome Dispersion and Melanocyte Stripe Formation. Int J Mol Sci 2022; 23:ijms232214182. [PMID: 36430661 PMCID: PMC9693263 DOI: 10.3390/ijms232214182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
cAMP-PKA signaling plays a pivotal role in melanin synthesis and melanosome transport by responding to the binding of the α-melanocyte-stimulating hormone (α-MSH) to melanocortin-1 receptor (MC1R). Adenylate cyclases (ADCYs) are the enzymes responsible for the synthesis of cAMP from ATP, which comprises nine transmembrane isoforms (ADCYs 1-9) and one soluble adenylate cyclase (ADCY 10) in mammals. However, little is known about which and how ADCY isoforms regulate melanocyte generation, melanin biosynthesis, and melanosome transport in vivo. In this study, we have generated a series of single and double mutants of Adcy isoforms in zebrafish. Among them, adcy3a-/- and adcy5-/- double mutants cause defects in melanosome dispersion but do not impair melanoblast differentiation and melanocyte regeneration during the embryonic or larval stages. Activation of PKA, the main effector of cAMP signaling, significantly ameliorates the defects in melanosome dispersion in adcy3a-/- and adcy5-/- double mutants. Mechanistically, Adcy3a and Adcy5 regulate melanosome dispersion by activating kinesin-1 while inhibiting cytoplasmic dynein-1. In adult zebrafish, Adcy3a and Adcy5 participate in the regulation of the expression of microphthalmia transcription factor (Mitfa) and melanin synthesis enzymes Tyr, Dct, and Trp1b. The deletion of Adcy3a and Adcy5 inhibits melanin production and reduces pigmented melanocyte numbers, causing a defect in establishing adult melanocyte stripes. Hence, our studies demonstrate that Adcy3a and Adcy5 play essential but redundant functions in mediating α-MSH-MC1R/cAMP-PKA signaling for regulating melanin synthesis and melanosome dispersion.
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13
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Neuffer SJ, Beltran-Cardona D, Jimenez-Perez K, Clancey LF, Brown A, New L, Cooper CD. AP-3 complex delta subunit gene, ap3d1, regulates melanogenesis and melanophore survival via autophagy in zebrafish (Danio rerio). Pigment Cell Melanoma Res 2022; 35:495-505. [PMID: 35816398 PMCID: PMC9450952 DOI: 10.1111/pcmr.13055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 05/18/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Zebrafish are an emerging model organism to study the syndromic albinism disorder, Hermansky–Pudlak syndrome (HPS), due to visible pigment development at 24 hours postfertilization, and conserved melanogenesis mechanisms. We describe crasher, a novel HPS type 10 (HPS10) zebrafish model, with a mutation in AP‐3 complex subunit delta gene, ap3d1. Exon 14 of ap3d1 is overexpressed in crasher mutants, while the expression of ap3d1 as a whole is reduced. ap3d1 knockout in *AB zebrafish recapitulates the mutant crasher phenotype. We show ap3d1 loss‐of‐function mutations cause significant expression changes in the melanogenesis genes, dopachrome tautomerase (dct) and tyrosinase‐related protein 1b (tyrp1b), but not tyrosinase (tyr). Last, Generally Applicable Gene‐set Enrichment (GAGE) analysis suggests autophagy pathway genes are upregulated together in crasher. Treatment with autophagy‐inhibitor, bafilomycin A1, significantly decreases melanophore number in crasher, suggesting ap3d1 promotes melanophore survival by limiting excessive autophagy. crasher is a valuable model to explore the regulation of melanogenesis gene expression and pigmentation disease.
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Affiliation(s)
- Sam J Neuffer
- School of Molecular Biosciences, Washington State University Vancouver, Vancouver, WA, USA
| | - David Beltran-Cardona
- College of Arts and Sciences, Washington State University Vancouver, Vancouver, WA, USA
| | - Kevin Jimenez-Perez
- College of Arts and Sciences, Washington State University Vancouver, Vancouver, WA, USA
| | - Lauren F Clancey
- College of Arts and Sciences, Washington State University Vancouver, Vancouver, WA, USA
| | - Alexander Brown
- College of Arts and Sciences, Washington State University Vancouver, Vancouver, WA, USA
| | - Leslie New
- College of Arts and Sciences, Washington State University Vancouver, Vancouver, WA, USA.,Department of Mathematics and Computer Science, Ursinus College, Collegeville, PA, USA
| | - Cynthia D Cooper
- School of Molecular Biosciences, Washington State University Vancouver, Vancouver, WA, USA.,College of Arts and Sciences, Washington State University Vancouver, Vancouver, WA, USA
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14
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Lin S, Zhang L, Wang G, Huang S, Wang Y. Searching and identifying pigmentation genes from Neocaridina denticulate sinensis via comparison of transcriptome in different color strains. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100977. [PMID: 35247793 DOI: 10.1016/j.cbd.2022.100977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
Aquaria species are characterized by their amazing colors and patterns. Research on the breeding molecular genetics of ornamental shrimps is surprisingly limited. We conducted a transcriptome analysis to investigate the expression of encoding genes in the integument of the strains Neocaridina denticulate sinensis. After assembled and filtered, 19,992 unigenes were annotated by aligning with public functional databases (NR, Swiss-Prot, KEGG, COG). 14,915 unigenes with significantly different expressions were found by comparing three strains integument transcriptomes. Ribosomal protein genes, ABC transporter families, calmodulin, carotenoid proteins and crustacyanin may play roles in the cytological process of pigment migration and chromatophore maintenance. Numerous color genes associated with multiple pathways including melanin, ommochrome and pteridines pathways were identified. The expression patterns of 25 candidate genes were analysis by qPCR in red, yellow, transparent and glass strains. The qPCR results in red, yellow and transparent were consistent with the level of RPKM values in the transcriptomes. The above results will advance our knowledge of integument color varieties in N. denticulate sinensis and help the genetic selection of crustaceans with consumer-favored colors. Furthermore, it also provides some candidate pigmentation genes to investigate the correlation between coloration and sympatric speciation in crustaceans.
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Affiliation(s)
- Shi Lin
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Lili Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China.
| | - Guodong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Shiyu Huang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
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15
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Jiang B, Wang L, Luo M, Fu J, Zhu W, Liu W, Dong Z. Transcriptome analysis of skin color variation during and after overwintering of Malaysian red tilapia. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:669-682. [PMID: 35419737 DOI: 10.1007/s10695-022-01073-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
The commercial value of red tilapia is hampered by variations in skin color during overwintering. In this study, three types of skin of red tilapia, including the skin remained pink color during and after overwintering (P), the skin changed from pink color to black color during overwintering and remained black color after overwintering (P-B), and the skin changed from pink color to black color during overwintering but recovered to pink color when the temperature rose after overwintering (P-B-P), were used to analyze their molecular mechanisms of color variation. The transcriptome results revealed that the P, P-B, and P-B-P libraries had 43, 42, and 43 million clean reads, respectively. The top 10 abundance mRNAs and specific mRNAs (specificity measure SPM > 0.9) were screened. After comparing intergroup gene expression levels, there were 2528, 1924, and 1939 differentially expressed genes (DEGs) between P-B-P and P-B, P-B-P and P, and P-B and P, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of color-related mRNAs showed that a number of DEGs, including tyrp1, tyr, pmel, mitf, mc1r, asip, tat, hpdb, and foxd3, might play a potential role in pigmentation. Additionally, the co-expression patterns of genes were detected within the pigment-related pathways by the PPI network from P-B vs. P group. Furthermore, DEGs from the apoptosis and autophagy pathways, such as baxα, beclin1, and atg7, might be involved in the fading of red tilapia melanocytes. The findings will aid in understanding the molecular mechanism underlying skin color variation in red tilapia during and after overwintering as well as lay a foundation for future research aimed at improving red tilapia skin color characteristics.
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Affiliation(s)
- Bingjie Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China
| | - Lanmei Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China
| | - Mingkun Luo
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China
| | - Wenbin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China
| | - Wei Liu
- AGCU ScienTech Incorporation, Wuxi, 214174, Jiangsu, China
| | - Zaijie Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China.
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16
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Paul S, Dinesh Kumar SM, Syamala SS, Balakrishnan S, Vijayan V, Arumugaswami V, Sudhakar S. Identification, tissue specific expression analysis and functional characterization of arrestin gene (ARRDC) in the earthworm Eudrilus eugeniae: a molecular hypothesis behind worm photoreception. Mol Biol Rep 2022; 49:4225-4236. [PMID: 35211863 DOI: 10.1007/s11033-022-07256-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/09/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND The arrestin domain containing proteins (ARRDCs) are crucial adaptor proteins assist in signal transduction and regulation of sensory physiology. The molecular localization of the ARRDC gene has been confined mainly to the mammalian system while in invertebrates the expression pattern was not addressed significantly. The present study reports the identification, tissue specific expression and functional characterization of an ARRDC transcript in earthworm, Eudrilus eugeniae. METHODS AND RESULTS The coding region of earthworm ARRDC transcript was 1146 bp in length and encoded a protein of 381 amino acid residues. The worm ARRDC protein consists of conserved N-terminal and C-terminal regions and showed significant homology with the ARRDC3 sequence of other species. The tissue specific expression analysis through whole mount in-situ hybridization denoted the expression of ARRDC transcript in the central nervous system of the worm which includes cerebral ganglion and ventral nerve cord. Besides, the expression of ARRDC gene was observed in the epidermal region of earthworm skin. The functional characterization of ARRDC gene was assessed through siRNA silencing and the gene was found to play key role in the light sensing ability and photophobic movement of the worm. CONCLUSIONS The neuronal and dermal expression patterns of ARRDC gene and its functional characterization hypothesized the role of the gene in assisting the photosensory cells to regulate the process of photoreception and phototransduction in the worm.
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Affiliation(s)
- Sayan Paul
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, 627012, India
- Centre for Cardiovascular Biology and Disease, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Sudalai Mani Dinesh Kumar
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, 627012, India
| | - Sandhya Soman Syamala
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, 627012, India
| | | | - Vijithkumar Vijayan
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, 627012, India
| | | | - Sivasubramaniam Sudhakar
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, 627012, India.
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17
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Cleghorn WM, Burrell AL, Giarmarco MM, Brock DC, Wang Y, Chambers ZS, Du J, Kollman JM, Brockerhoff SE. A highly conserved zebrafish IMPDH retinal isoform produces the majority of guanine and forms dynamic protein filaments in photoreceptor cells. J Biol Chem 2022; 298:101441. [PMID: 34813793 PMCID: PMC8688572 DOI: 10.1016/j.jbc.2021.101441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 12/18/2022] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is a key regulatory enzyme in the de novo synthesis of the purine base guanine. Dominant mutations in human IMPDH1 cause photoreceptor degeneration for reasons that are unknown. Here, we sought to provide some foundational information on Impdh1a in the zebrafish retina. We found that in zebrafish, gene subfunctionalization due to ancestral duplication resulted in a predominant retinal variant expressed exclusively in rod and cone photoreceptors. This variant is structurally and functionally similar to the human IMPDH1 retinal variant and shares a reduced sensitivity to GTP-mediated inhibition. We also demonstrated that Impdh1a forms prominent protein filaments in vitro and in vivo in both rod and cone photoreceptor cell bodies, synapses, and to a lesser degree, in outer segments. These filaments changed length and cellular distribution throughout the day consistent with diurnal changes in both mRNA and protein levels. The loss of Impdh1a resulted in a substantial reduction of guanine levels, although cellular morphology and cGMP levels remained normal. Our findings demonstrate a significant role for IMPDH1 in photoreceptor guanine production and provide fundamental new information on the details of this protein in the zebrafish retina.
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Affiliation(s)
- Whitney M Cleghorn
- Department of Biochemistry, University of Washington, Seattle, Washington, USA; Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Daniel C Brock
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Yekai Wang
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Department of Biochemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Zachary S Chambers
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Department of Biochemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Susan E Brockerhoff
- Department of Biochemistry, University of Washington, Seattle, Washington, USA; Department of Ophthalmology, University of Washington, Seattle, Washington, USA.
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18
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Jang HS, Chen Y, Ge J, Wilkening AN, Hou Y, Lee HJ, Choi YR, Lowdon RF, Xing X, Li D, Kaufman CK, Johnson SL, Wang T. Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish. Genome Biol 2021; 22:282. [PMID: 34607603 PMCID: PMC8489059 DOI: 10.1186/s13059-021-02493-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/09/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Zebrafish pigment cell differentiation provides an attractive model for studying cell fate progression as a neural crest progenitor engenders diverse cell types, including two morphologically distinct pigment cells: black melanophores and reflective iridophores. Nontrivial classical genetic and transcriptomic approaches have revealed essential molecular mechanisms and gene regulatory circuits that drive neural crest-derived cell fate decisions. However, how the epigenetic landscape contributes to pigment cell differentiation, especially in the context of iridophore cell fate, is poorly understood. RESULTS We chart the global changes in the epigenetic landscape, including DNA methylation and chromatin accessibility, during neural crest differentiation into melanophores and iridophores to identify epigenetic determinants shaping cell type-specific gene expression. Motif enrichment in the epigenetically dynamic regions reveals putative transcription factors that might be responsible for driving pigment cell identity. Through this effort, in the relatively uncharacterized iridophores, we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway. CONCLUSIONS Pigment cell fate is marked by substantial DNA demethylation events coupled with dynamic chromatin accessibility to potentiate gene regulation through cis-regulatory control. Here, we provide a multi-omic resource for neural crest differentiation into melanophores and iridophores. This work led to the discovery and validation of iridophore-specific alx4a transcription factor.
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Affiliation(s)
- Hyo Sik Jang
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
- Present address: Department of Epigenetics, Van Andel Institute, Grand Rapids, MI USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Jiaxin Ge
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Alicia N. Wilkening
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - You Rim Choi
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Rebecca F. Lowdon
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Charles K. Kaufman
- Department of Medicine, Division of Medical Oncology, and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO USA
| | - Stephen L. Johnson
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA
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19
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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: 17] [Impact Index Per Article: 5.7] [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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20
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de Mello PLH, Hime PM, Glor RE. Transcriptomic Analysis of Skin Color in Anole Lizards. Genome Biol Evol 2021; 13:evab110. [PMID: 33988681 PMCID: PMC8290120 DOI: 10.1093/gbe/evab110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 01/23/2023] Open
Abstract
Color and color pattern are critical for animal camouflage, reproduction, and defense. Few studies, however, have attempted to identify candidate genes for color and color pattern in squamate reptiles, a colorful group with over 10,000 species. We used comparative transcriptomic analyses between white, orange, and yellow skin in a color-polymorphic species of anole lizard to 1) identify candidate color and color-pattern genes in squamates and 2) assess if squamates share an underlying genetic basis for color and color pattern variation with other vertebrates. Squamates have three types of chromatophores that determine color pattern: guanine-filled iridophores, carotenoid- or pteridine-filled xanthophores/erythrophores, and melanin-filled melanophores. We identified 13 best candidate squamate color and color-pattern genes shared with other vertebrates: six genes linked to pigment synthesis pathways, and seven genes linked to chromatophore development and maintenance. In comparisons of expression profiles between pigment-rich and white skin, pigment-rich skin upregulated the pteridine pathway as well as xanthophore/erythrophore development and maintenance genes; in comparisons between orange and yellow skin, orange skin upregulated the pteridine and carotenoid pathways as well as melanophore maintenance genes. Our results corroborate the predictions that squamates can produce similar colors using distinct color-reflecting molecules, and that both color and color-pattern genes are likely conserved across vertebrates. Furthermore, this study provides a concise list of candidate genes for future functional verification, representing a first step in determining the genetic basis of color and color pattern in anoles.
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Affiliation(s)
- Pietro Longo Hollanda de Mello
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Paul M Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Richard E Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
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21
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Howard AGA, Baker PA, Ibarra-García-Padilla R, Moore JA, Rivas LJ, Tallman JJ, Singleton EW, Westheimer JL, Corteguera JA, Uribe RA. An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution. eLife 2021; 10:e60005. [PMID: 33591267 PMCID: PMC7886338 DOI: 10.7554/elife.60005] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 01/31/2021] [Indexed: 02/06/2023] Open
Abstract
Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme cells, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.
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Affiliation(s)
| | - Phillip A Baker
- Department of BioSciences, Rice UniversityHoustonUnited States
| | | | - Joshua A Moore
- Department of BioSciences, Rice UniversityHoustonUnited States
| | - Lucia J Rivas
- Department of BioSciences, Rice UniversityHoustonUnited States
| | - James J Tallman
- Department of BioSciences, Rice UniversityHoustonUnited States
| | | | | | | | - Rosa A Uribe
- Department of BioSciences, Rice UniversityHoustonUnited States
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22
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Petratou K, Spencer SA, Kelsh RN, Lister JA. The MITF paralog tfec is required in neural crest development for fate specification of the iridophore lineage from a multipotent pigment cell progenitor. PLoS One 2021; 16:e0244794. [PMID: 33439865 PMCID: PMC7806166 DOI: 10.1371/journal.pone.0244794] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding how fate specification of distinct cell-types from multipotent progenitors occurs is a fundamental question in embryology. Neural crest stem cells (NCSCs) generate extraordinarily diverse derivatives, including multiple neural, skeletogenic and pigment cell fates. Key transcription factors and extracellular signals specifying NCSC lineages remain to be identified, and we have only a little idea of how and when they function together to control fate. Zebrafish have three neural crest-derived pigment cell types, black melanocytes, light-reflecting iridophores and yellow xanthophores, which offer a powerful model for studying the molecular and cellular mechanisms of fate segregation. Mitfa has been identified as the master regulator of melanocyte fate. Here, we show that an Mitf-related transcription factor, Tfec, functions as master regulator of the iridophore fate. Surprisingly, our phenotypic analysis of tfec mutants demonstrates that Tfec also functions in the initial specification of all three pigment cell-types, although the melanocyte and xanthophore lineages recover later. We show that Mitfa represses tfec expression, revealing a likely mechanism contributing to the decision between melanocyte and iridophore fate. Our data are consistent with the long-standing proposal of a tripotent progenitor restricted to pigment cell fates. Moreover, we investigate activation, maintenance and function of tfec in multipotent NCSCs, demonstrating for the first time its role in the gene regulatory network forming and maintaining early neural crest cells. In summary, we build on our previous work to characterise the gene regulatory network governing iridophore development, establishing Tfec as the master regulator driving iridophore specification from multipotent progenitors, while shedding light on possible cellular mechanisms of progressive fate restriction.
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Affiliation(s)
- Kleio Petratou
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Samantha A. Spencer
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
| | - Robert N. Kelsh
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - James A. Lister
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
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23
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Yang BT, Wen B, Ji Y, Wang Q, Zhang HR, Zhang Y, Gao JZ, Chen ZZ. Comparative metabolomics analysis of pigmentary and structural coloration in discus fish (Symphysodon haraldi). J Proteomics 2020; 233:104085. [PMID: 33378721 DOI: 10.1016/j.jprot.2020.104085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/15/2022]
Abstract
Discus fish have a variety of body colors including pigmentary and structural colors, studies on specific substances and related metabolic pathways associated with body coloration, however, are scarce to the present. Here, we used single-color (blue, yellow and white) of discus for comparative metabolomics analysis of pigmentary and structural coloration. Statistical model showed significant separations between three colors of discus, suggesting the distinct metabolite profiles of discus pigmentary and structural colors. More astaxanthin was found in yellow discus, which might be the cause of yellow pigmentary color. Moreover, docosahexaenoic acid, arachidonic acid, linoleic acid, eicosapentaenoic acid, 1-stearoyl-2-oleoyl-sn-glycerol 3-phosphocholine, dodecanoic acid and myristic acid related to lipid metabolism and pathways of ABC transporters and biosynthesis of unsaturated fatty acids were more enriched in yellow discus. More adenine, xanthine and hypoxanthine were enriched in blue discus, which might account for the blue structural color. Moreover, amino acids associated with purine biosynthesis, e.g., L-alanine and L-isoleucine, were reduced but pathways of protein digestion and absorption, aminoacyl-tRNA biosynthesis, purine metabolism and glycine, serine and threonine metabolism were enriched in blue discus. Overall, these results reveal specific chromophores and related metabolic pathways involved in pigmentary and structural coloration of discus fish. SIGNIFICANCE: We detected specific chromophores present in skin of pigmentary and structural colors of discus and revealed potential metabolic pathways associated with body coloration. These results contribute to our understanding of the mechanism of body color formation in discus fish.
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Affiliation(s)
- Bo-Tian Yang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Bin Wen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Yu Ji
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Qin Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Hao-Ran Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Yuan Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jian-Zhong Gao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Zai-Zhong Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
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24
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Molecular Plasticity in Animal Pigmentation: Emerging Processes Underlying Color Changes. Integr Comp Biol 2020; 60:1531-1543. [DOI: 10.1093/icb/icaa142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synopsis
Animal coloration has been rigorously studied and has provided morphological implications for fitness with influences over social behavior, predator–prey interactions, and sexual selection. In vertebrates, its study has developed our understanding across diverse fields ranging from behavior to molecular biology. In the search for underlying molecular mechanisms, many have taken advantage of pedigree-based and genome-wide association screens to reveal the genetic architecture responsible for pattern variation that occurs in early development. However, genetic differences do not provide a full picture of the dynamic changes in coloration that are most prevalent across vertebrates at the molecular level. Changes in coloration that occur in adulthood via phenotypic plasticity rely on various social, visual, and dietary cues independent of genetic variation. Here, I will review the contributions of pigment cell biology to animal color changes and recent studies describing their molecular underpinnings and function. In this regard, conserved epigenetic processes such as DNA methylation play a role in lending plasticity to gene regulation as it relates to chromatophore function. Lastly, I will present African cichlids as emerging models for the study of pigmentation and molecular plasticity for animal color changes. I posit that these processes, in a dialog with environmental stimuli, are important regulators of variation and the selective advantages that accompany a change in coloration for vertebrate animals.
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25
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Kuriyama T, Murakami A, Brandley M, Hasegawa M. Blue, Black, and Stripes: Evolution and Development of Color Production and Pattern Formation in Lizards and Snakes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Hou Y, Lee HJ, Chen Y, Ge J, Osman FOI, McAdow AR, Mokalled MH, Johnson SL, Zhao G, Wang T. Cellular diversity of the regenerating caudal fin. SCIENCE ADVANCES 2020; 6:eaba2084. [PMID: 32851162 PMCID: PMC7423392 DOI: 10.1126/sciadv.aba2084] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 06/26/2020] [Indexed: 05/03/2023]
Abstract
Zebrafish faithfully regenerate their caudal fin after amputation. During this process, both differentiated cells and resident progenitors migrate to the wound site and undergo lineage-restricted, programmed cellular state transitions to populate the new regenerate. Until now, systematic characterizations of cells comprising the new regenerate and molecular definitions of their state transitions have been lacking. We hereby characterize the dynamics of gene regulatory programs during fin regeneration by creating single-cell transcriptome maps of both preinjury and regenerating fin tissues at 1/2/4 days post-amputation. We consistently identified epithelial, mesenchymal, and hematopoietic populations across all stages. We found common and cell type-specific cell cycle programs associated with proliferation. In addition to defining the processes of epithelial replenishment and mesenchymal differentiation, we also identified molecular signatures that could better distinguish epithelial and mesenchymal subpopulations in fish. The insights for natural cell state transitions during regeneration point to new directions for studying this regeneration model.
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Affiliation(s)
- Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jiaxin Ge
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Fujr Osman Ibrahim Osman
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Maryville University of St Louis, St. Louis, MO 63141, USA
| | - Anthony R. McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Mayssa H. Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Stephen L. Johnson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Guoyan Zhao
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63108, USA
- Corresponding author. (G.Z.); (T.W.)
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Corresponding author. (G.Z.); (T.W.)
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27
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Li K, Zhao N, Zhang B, Jia L, Liu K, Wang Q, He X, Bao B. Identification and characterization of the melanocortin 1 receptor gene (MC1R) in hypermelanistic Chinese tongue sole (Cynoglossus semilaevis). FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:881-890. [PMID: 31909442 DOI: 10.1007/s10695-019-00758-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
The Chinese tongue sole (Cynoglossus semilaevis) is a flatfish with distinctive asymmetry in its body coloration. The melanism (hyperpigmentation) in both the blind side and ocular side of C. semilaevis gives it an extremely low commercial value. However, the fundamental molecular mechanism of this melanism remains unclear. Melanocortin 1 receptor (MC1R), a GTP-binding protein-coupled receptor, is considered to play a vital role in the physiology of the vertebrate pigment system. In order to confirm the contribution of MC1R to the body coloration of C. semilaevis, the expression levels of Mc1r mRNA were measured in seven tissue types at different developmental stages of normal and melanistic C. semilaevis. The expression levels of Mc1r mRNA in the heart, brain, liver, kidney, ocular-side skin, and blind-side skin of melanistic C. semilaevis were significantly higher than that of normal C. semilaevis in all developmental stages. Moreover, the knocking down of Mc1r in the C. semilaevis liver cell line (HTLC) increased the expression of the downstream genes microphthalmia transcription factor (Mitf) and tyrosinase-related protein 1 (Tyrp1) in the pigmentation pathway. Thus, the present data suggest that MC1R might play important roles in Tyrp1- and Mitf-mediated pigment synthesis in C. semilaevis.
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Affiliation(s)
- Kunming Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Na Zhao
- Tianjin Haolingsaiao Biotechnology Co, Ltd, Tianjin, China
| | - Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
- Tianjin Fisheries Research Institute, Tianjin, China.
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Qunshan Wang
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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28
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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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29
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Rodríguez A, Mundy NI, Ibáñez R, Pröhl H. Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio). BMC Genomics 2020; 21:301. [PMID: 32293261 PMCID: PMC7158012 DOI: 10.1186/s12864-020-6719-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Animal coloration is usually an adaptive attribute, under strong local selection pressures and often diversified among species or populations. The strawberry poison frog (Oophaga pumilio) shows an impressive array of color morphs across its distribution in Central America. Here we quantify gene expression and genetic variation to identify candidate genes involved in generating divergence in coloration between populations of red, green and blue O. pumilio from the Bocas del Toro archipelago in Panama. RESULTS We generated a high quality non-redundant reference transcriptome by mapping the products of genome-guided and de novo transcriptome assemblies onto a re-scaffolded draft genome of O. pumilio. We then measured gene expression in individuals of the three color phenotypes and identified color-associated candidate genes by comparing differential expression results against a list of a priori gene sets for five different functional categories of coloration - pteridine synthesis, carotenoid synthesis, melanin synthesis, iridophore pathways (structural coloration), and chromatophore development. We found 68 candidate coloration loci with significant expression differences among the color phenotypes. Notable upregulated examples include pteridine synthesis genes spr, xdh and pts (in red and green frogs); carotenoid metabolism genes bco2 (in blue frogs), scarb1 (in red frogs), and guanine metabolism gene psat1 (in blue frogs). We detected significantly higher expression of the pteridine synthesis gene set in red and green frogs versus blue frogs. In addition to gene expression differences, we identified 370 outlier SNPs on 162 annotated genes showing signatures of diversifying selection, including eight pigmentation-associated genes. CONCLUSIONS Gene expression in the skin of the three populations of frogs with differing coloration is highly divergent. The strong signal of differential expression in pteridine genes is consistent with a major role of these genes in generating the coloration differences among the three morphs. However, the finding of differentially expressed genes across pathways and functional categories suggests that multiple mechanisms are responsible for the coloration differences, likely involving both pigmentary and structural coloration. In addition to regulatory differences, we found potential evidence of differential selection acting at the protein sequence level in several color-associated loci, which could contribute to the color polymorphism.
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Affiliation(s)
- Ariel Rodríguez
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Nicholas I. Mundy
- Department of Zoology, University of Cambridge, Downing St, Cambridge, CB2 3EJ England
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Apartado Postal, 0843-03092 Panamá, República de Panamá
- Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, Tecnología e Innovación, Apartado, 0816-02852 Panamá, República de Panamá
| | - Heike Pröhl
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559 Hannover, Germany
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30
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Twomey E, Kain M, Claeys M, Summers K, Castroviejo-Fisher S, Van Bocxlaer I. Mechanisms for Color Convergence in a Mimetic Radiation of Poison Frogs. Am Nat 2020; 195:E132-E149. [PMID: 32364784 DOI: 10.1086/708157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In animals, bright colors often evolve to mimic other species when a resemblance is selectively favored. Understanding the proximate mechanisms underlying such color mimicry can give insights into how mimicry evolves-for example, whether color convergence evolves from a shared set of mechanisms or through the evolution of novel color production mechanisms. We studied color production mechanisms in poison frogs (Dendrobatidae), focusing on the mimicry complex of Ranitomeya imitator. Using reflectance spectrometry, skin pigment analysis, electron microscopy, and color modeling, we found that the bright colors of these frogs, both within and outside the mimicry complex, are largely structural and produced by iridophores but that color production depends crucially on interactions with pigments. Color variation and mimicry are regulated predominantly by iridophore platelet thickness and, to a lesser extent, concentration of the red pteridine pigment drosopterin. Compared with each of the four morphs of model species that it resembles, R. imitator displays greater variation in both structural and pigmentary mechanisms, which may have facilitated phenotypic divergence in this species. Analyses of nonmimetic dendrobatids in other genera demonstrate that these mechanisms are widespread within the family and that poison frogs share a complex physiological "color palette" that can produce diverse and highly reflective colors.
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31
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Liang Y, Gerwin J, Meyer A, Kratochwil CF. Developmental and Cellular Basis of Vertical Bar Color Patterns in the East African Cichlid Fish Haplochromis latifasciatus. Front Cell Dev Biol 2020; 8:62. [PMID: 32117987 PMCID: PMC7026194 DOI: 10.3389/fcell.2020.00062] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
The East African adaptive radiations of cichlid fishes are renowned for their diversity in coloration. Yet, the developmental basis of pigment pattern formation remains largely unknown. One of the most common melanic patterns in cichlid fishes are vertical bar patterns. Here we describe the ontogeny of this conspicuous pattern in the Lake Kyoga species Haplochromis latifasciatus. Beginning with the larval stages we tracked the formation of this stereotypic color pattern and discovered that its macroscopic appearance is largely explained by an increase in melanophore density and accumulation of melanin during the first 3 weeks post-fertilization. The embryonal analysis is complemented with cytological quantifications of pigment cells in adult scales and the dermis beneath the scales. In adults, melanic bars are characterized by a two to threefold higher density of melanophores than in the intervening yellow interbars. We found no strong support for differences in other pigment cell types such as xanthophores. Quantitative PCRs for twelve known pigmentation genes showed that expression of melanin synthesis genes tyr and tyrp1a is increased five to sixfold in melanic bars, while xanthophore and iridophore marker genes are not differentially expressed. In summary, we provide novel insights on how vertical bars, one of the most widespread vertebrate color patterns, are formed through dynamic control of melanophore density, melanin synthesis and melanosome dispersal.
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Affiliation(s)
- 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
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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32
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Bian F, Yang X, Ou Z, Luo J, Tan B, Yuan M, Chen T, Yang R. Morphological Characteristics and Comparative Transcriptome Analysis of Three Different Phenotypes of Pristella maxillaris. Front Genet 2019; 10:698. [PMID: 31428133 PMCID: PMC6687772 DOI: 10.3389/fgene.2019.00698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/03/2019] [Indexed: 01/09/2023] Open
Abstract
Pristella maxillaris is known as the X-ray fish based on its translucent body. However, the morphological characteristics and the molecular regulatory mechanisms of these translucent bodies are still unknown. In this study, the following three phenotypes, a black-and-gray body color or wild-type (WT), a silvery-white body color defined as mutant I (MU1), and a fully transparent body with a visible visceral mass named as mutant II (MU2), were investigated to analyze their chromatophores and molecular mechanisms. The variety and distribution of pigment cells in the three phenotypes of P. maxillaris significantly differed by histological assessment. Three types of chromatophores (melanophores, iridophores, and xanthophores) were observed in the WT, whereas MU1 fish were deficient in melanophores, and MU2 fish lacked melanophores and iridophores. Transcriptome sequencing of the skin and peritoneal tissues of P. maxillaris identified a total of 166,089 unigenes. After comparing intergroup gene expression levels, more than 3,000 unigenes with significantly differential expression levels were identified among three strains. Functional annotation and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the differentially expressed genes (DEGs) identified a number of candidates melanophores and iridophores genes that influence body color. Some DEGs that were identified using transcriptome analysis were confirmed by quantitative real-time PCR. This study serves as a global survey of the morphological characteristics and molecular mechanism of different body colors observed in P. maxillaris and thus provides a valuable theoretical foundation for the molecular regulation of the transparent phenotype.
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Affiliation(s)
- Fangfang Bian
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xuefen Yang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhijie Ou
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Department of Fisheries, Guangdong Maoming Agriculture & Forestry Technical College, Maoming, China
| | - Junzhi Luo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Bozhen Tan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Mingrui Yuan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Tiansheng Chen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, China
| | - Ruibin Yang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
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33
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McLean CA, Lutz A, Rankin KJ, Elliott A, Moussalli A, Stuart-Fox D. Red carotenoids and associated gene expression explain colour variation in frillneck lizards. Proc Biol Sci 2019; 286:20191172. [PMID: 31311479 DOI: 10.1098/rspb.2019.1172] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A long-standing hypothesis in evolutionary ecology is that red-orange ornamental colours reliably signal individual quality owing to limited dietary availability of carotenoids and metabolic costs associated with their production, such as the bioconversion of dietary yellow carotenoids to red ketocarotenoids. However, in ectothermic vertebrates, these colours can also be produced by self-synthesized pteridine pigments. As a consequence, the relative ratio of pigment types and their biochemical and genetic basis have implications for the costs and information content of colour signals; yet they remain poorly known in most taxonomic groups. We tested whether red- and yellow-frilled populations of the frillneck lizard, Chlamydosaurus kingii, differ in the ratio of different biochemical classes of carotenoid and pteridine pigments, and examined associated differences in gene expression. We found that, unlike other squamate reptiles, red hues derive from a higher proportion of ketocarotenoids relative to both dietary yellow carotenoids and to pteridines. Whereas red frill skin showed higher expression of several genes associated with carotenoid metabolism, yellow frill skin showed higher expression of genes associated with steroid hormones. Based on the different mechanisms underlying red and yellow signals, we hypothesize that frill colour conveys different information in the two populations. More generally, the data expand our knowledge of the genetic and biochemical basis of colour signals in vertebrates.
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Affiliation(s)
- Claire A McLean
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Sciences Department, Museums Victoria, Carlton Gardens, Victoria 3053, Australia
| | - Adrian Lutz
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Metabolomics Australia, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Katrina J Rankin
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Adam Elliott
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Adnan Moussalli
- Sciences Department, Museums Victoria, Carlton Gardens, Victoria 3053, Australia
| | - Devi Stuart-Fox
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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Saunders LM, Mishra AK, Aman AJ, Lewis VM, Toomey MB, Packer JS, Qiu X, McFaline-Figueroa JL, Corbo JC, Trapnell C, Parichy DM. Thyroid hormone regulates distinct paths to maturation in pigment cell lineages. eLife 2019; 8:e45181. [PMID: 31140974 PMCID: PMC6588384 DOI: 10.7554/elife.45181] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
Thyroid hormone (TH) regulates diverse developmental events and can drive disparate cellular outcomes. In zebrafish, TH has opposite effects on neural crest derived pigment cells of the adult stripe pattern, limiting melanophore population expansion, yet increasing yellow/orange xanthophore numbers. To learn how TH elicits seemingly opposite responses in cells having a common embryological origin, we analyzed individual transcriptomes from thousands of neural crest-derived cells, reconstructed developmental trajectories, identified pigment cell-lineage specific responses to TH, and assessed roles for TH receptors. We show that TH promotes maturation of both cell types but in distinct ways. In melanophores, TH drives terminal differentiation, limiting final cell numbers. In xanthophores, TH promotes accumulation of orange carotenoids, making the cells visible. TH receptors act primarily to repress these programs when TH is limiting. Our findings show how a single endocrine factor integrates very different cellular activities during the generation of adult form.
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Affiliation(s)
- Lauren M Saunders
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
| | - Abhishek K Mishra
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
| | - Andrew J Aman
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
| | - Victor M Lewis
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
| | - Matthew B Toomey
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Jonathan S Packer
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Xiaojie Qiu
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | | | - Joseph C Corbo
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Cole Trapnell
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - David M Parichy
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
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35
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Stuckert AMM, Moore E, Coyle KP, Davison I, MacManes MD, Roberts R, Summers K. Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus. BMC Evol Biol 2019; 19:85. [PMID: 30995908 PMCID: PMC6472079 DOI: 10.1186/s12862-019-1410-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/15/2019] [Indexed: 12/28/2022] Open
Abstract
Background Color and pattern phenotypes have clear implications for survival and reproduction in many species. However, the mechanisms that produce this coloration are still poorly characterized, especially at the genomic level. Here we have taken a transcriptomics-based approach to elucidate the underlying genetic mechanisms affecting color and pattern in a highly polytypic poison frog. We sequenced RNA from the skin from four different color morphs during the final stage of metamorphosis and assembled a de novo transcriptome. We then investigated differential gene expression, with an emphasis on examining candidate color genes from other taxa. Results Overall, we found differential expression of a suite of genes that control melanogenesis, melanocyte differentiation, and melanocyte proliferation (e.g., tyrp1, lef1, leo1, and mitf) as well as several differentially expressed genes involved in purine synthesis and iridophore development (e.g., arfgap1, arfgap2, airc, and gart). Conclusions Our results provide evidence that several gene networks known to affect color and pattern in vertebrates play a role in color and pattern variation in this species of poison frog. Electronic supplementary material The online version of this article (10.1186/s12862-019-1410-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam M M Stuckert
- Department of Biology, East Carolina University, Greenville, North Carolina, USA. .,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA. .,Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.
| | - Emily Moore
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Kaitlin P Coyle
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Ian Davison
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Matthew D MacManes
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA.,Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Reade Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Kyle Summers
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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Colucci-Guyon E, Batista AS, Oliveira SDS, Blaud M, Bellettini IC, Marteyn BS, Leblanc K, Herbomel P, Duval R. Ultraspecific live imaging of the dynamics of zebrafish neutrophil granules by a histopermeable fluorogenic benzochalcone probe. Chem Sci 2019; 10:3654-3670. [PMID: 30996961 PMCID: PMC6432617 DOI: 10.1039/c8sc05593a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/12/2019] [Indexed: 12/13/2022] Open
Abstract
Neutrophil granules (NGs) are key components of the innate immune response and mark the development of neutrophilic granulocytes in mammals. However, there has been no specific fluorescent vital stain up to now to monitor their dynamics within a whole live organism. We rationally designed a benzochalcone fluorescent probe (HAB) featuring high tissue permeability and optimal photophysics such as elevated quantum yield, pronounced solvatochromism and target-induced fluorogenesis. Phenotypic screening identified HAB as the first cell- and organelle-specific small-molecule fluorescent tracer of NGs in live zebrafish larvae, with no labeling of other cell types or organelles. HAB staining was independent of the state of neutrophil activation, labeling NGs of both resting and phagocytically active neutrophils with equal specificity. By high-resolution live imaging, we documented the dynamics of HAB-stained NGs during phagocytosis. Upon zymosan injection, labeled NGs were rapidly recruited to the forming phagosomes. Despite being a reversible ligand, HAB could not be displaced by high concentrations of pharmacologically relevant competing chalcones, indicating that this specific labeling was the result of the HAB's precise physicochemical signature rather than a general feature of chalcones. However, one of the competitors was discovered as a promising interstitial fluorescent tracer illuminating zebrafish histology, similarly to BODIPY-ceramide. As a yellow-emitting histopermeable vital stain, HAB functionally and spectrally complements most genetically incorporated fluorescent tags commonly used in live zebrafish biology, holding promise for the study of neutrophil-dependent responses relevant to human physiopathology such as developmental defects, inflammation and infection. Furthermore, HAB intensely labeled isolated live human neutrophils at the level of granulated subcellular structures consistent with human NGs, suggesting that the labeling of NGs by HAB is not restricted to the zebrafish model but also relevant to mammalian systems.
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Affiliation(s)
- Emma Colucci-Guyon
- Institut Pasteur , Unité Macrophages et Développement de l'Immunité , Paris , 75015 , France .
- CNRS , UMR 3738 , Paris , France
| | - Ariane S Batista
- Nanotechnology Engineering Program , Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia - COPPE , Universidade Federal do Rio de Janeiro , Rio de Janeiro , 21941-972 , Brazil
| | | | - Magali Blaud
- LCRB , CNRS , Université Paris 5 , Sorbonne Paris Cité , Paris , 75006 , France
| | - Ismael C Bellettini
- Departamento de Ciências Exatas e Educaçao , Universidade Federal de Santa Catarina , Blumenau , 89036-256 , Brazil
| | - Benoit S Marteyn
- Institut Pasteur , Unité de Pathogénie Microbienne Moléculaire , Paris , 75015 , France
- INSERM , UMR 786 , Paris , France
| | - Karine Leblanc
- BioCIS , CNRS , Université Paris-Sud 11 , Châtenay-Malabry , 92290 , France
| | - Philippe Herbomel
- Institut Pasteur , Unité Macrophages et Développement de l'Immunité , Paris , 75015 , France .
- CNRS , UMR 3738 , Paris , France
| | - Romain Duval
- MERIT , IRD , Université Paris 5 , Sorbonne Paris Cité , Paris , 75006 , France .
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Martorano L, Peron M, Laquatra C, Lidron E, Facchinello N, Meneghetti G, Tiso N, Rasola A, Ghezzi D, Argenton F. The zebrafish orthologue of the human hepatocerebral disease gene MPV17 plays pleiotropic roles in mitochondria. Dis Model Mech 2019; 12:dmm.037226. [PMID: 30833296 PMCID: PMC6451431 DOI: 10.1242/dmm.037226] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/25/2019] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial DNA depletion syndromes (MDS) are a group of rare autosomal recessive disorders with early onset and no cure available. MDS are caused by mutations in nuclear genes involved in mitochondrial DNA (mtDNA) maintenance, and characterized by both a strong reduction in mtDNA content and severe mitochondrial defects in affected tissues. Mutations in MPV17, a nuclear gene encoding a mitochondrial inner membrane protein, have been associated with hepatocerebral forms of MDS. The zebrafish mpv17 null mutant lacks the guanine-based reflective skin cells named iridophores and represents a promising model to clarify the role of Mpv17. In this study, we characterized the mitochondrial phenotype of mpv17−/− larvae and found early and severe ultrastructural alterations in liver mitochondria, as well as significant impairment of the respiratory chain, leading to activation of the mitochondrial quality control. Our results provide evidence for zebrafish Mpv17 being essential for maintaining mitochondrial structure and functionality, while its effects on mtDNA copy number seem to be subordinate. Considering that a role in nucleotide availability had already been postulated for MPV17, that embryos blocked in pyrimidine synthesis do phenocopy mpv17−/− knockouts (KOs) and that mpv17−/− KOs have impaired Dihydroorotate dehydrogenase activity, we provided mpv17 mutants with the pyrimidine precursor orotic acid (OA). Treatment with OA, an easily available food supplement, significantly increased both iridophore number and mtDNA content in mpv17−/− mutants, thus linking the loss of Mpv17 to pyrimidine de novo synthesis and opening a new simple therapeutic approach for MPV17-related MDS. Summary: The zebrafish mpv17−/− mutant shows a severe mitochondrial phenotype with ultrastructural alterations and oxidative phosphorylation impairment. The pyrimidine precursor orotic acid ameliorates mpv17−/− phenotype and increases mitochondrial DNA content, linking the loss of Mpv17 to pyrimidine de novo synthesis.
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Affiliation(s)
- Laura Martorano
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
| | - Margherita Peron
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
| | - Claudio Laquatra
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
| | - Elisa Lidron
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
| | - Nicola Facchinello
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
| | - Giacomo Meneghetti
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
| | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Amadeo 42, 20133 Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Via Libero Temolo 4, 20126 Milan, Italy
| | - Francesco Argenton
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131 Padova, Italy
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Salis P, Lorin T, Lewis V, Rey C, Marcionetti A, Escande ML, Roux N, Besseau L, Salamin N, Sémon M, Parichy D, Volff JN, Laudet V. Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish. Pigment Cell Melanoma Res 2019; 32:391-402. [PMID: 30633441 DOI: 10.1111/pcmr.12766] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/11/2018] [Accepted: 12/26/2018] [Indexed: 12/18/2022]
Abstract
Actinopterygian fishes harbor at least eight distinct pigment cell types, leading to a fascinating diversity of colors. Among this diversity, the cellular origin of the white color appears to be linked to several pigment cell types such as iridophores or leucophores. We used the clownfish Amphiprion ocellaris, which has a color pattern consisting of white bars over a darker body, to characterize the pigment cells that underlie the white hue. We observe by electron microscopy that cells in white bars are similar to iridophores. In addition, the transcriptomic signature of clownfish white bars exhibits similarities with that of zebrafish iridophores. We further show by pharmacological treatments that these cells are necessary for the white color. Among the top differentially expressed genes in white skin, we identified several genes (fhl2a, fhl2b, saiyan, gpnmb, and apoD1a) and show that three of them are expressed in iridophores. Finally, we show by CRISPR/Cas9 mutagenesis that these genes are critical for iridophore development in zebrafish. Our analyses provide clues to the genomic underpinning of color diversity and allow identification of new iridophore genes in fish.
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Affiliation(s)
- Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Thibault Lorin
- IGFL, ENS de Lyon, UMR 5242 CNRS, Université Claude Bernard Lyon I, Lyon Cedex 07, France
| | - Victor Lewis
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Carine Rey
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Université Claude Bernard, Lyon, France.,LBBE, CNRS, Université Lyon 1, Villeurbanne, France
| | - Anna Marcionetti
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marie-Line Escande
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Laurence Besseau
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Nicolas Salamin
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marie Sémon
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Université Claude Bernard, Lyon, France
| | - David Parichy
- Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Jean-Nicolas Volff
- IGFL, ENS de Lyon, UMR 5242 CNRS, Université Claude Bernard Lyon I, Lyon Cedex 07, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
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Subkhankulova T, Kelsh RN. Fluorescence-Activated Cell Sorting and NanoString Profiling of Single Neural Crest Cells and Pigment Cells. Methods Mol Biol 2019; 1976:185-193. [PMID: 30977074 DOI: 10.1007/978-1-4939-9412-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Neural crest cells are an important class of multipotent stem cells, generating highly diverse derivatives. Understanding the gene regulatory networks underlying this process is of great interest, but the highly migratory and thus widely dispersed nature of the differentiating cells makes isolation of cells difficult. Fluorescence-activated cell sorting (FACS) of transgenically labelled neural crest-derived cells after disaggregation of embryos is well-suited to purifying these cells. However, their diverse differentiation means that transcriptional analysis at single cell resolution is necessary to dissect the gene regulatory networks at play. NanoString technology provides a method for highly sensitive, quantitative transcriptional profiling for a pre-defined set of genes of interest. Here we provide a detailed protocol for FACS purification of neural crest-derived cells, sorted as single cells into a multi-well plate, and their subsequent NanoString profiling, using a predetermined gene set focused on pigment cells.
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Affiliation(s)
| | - Robert Neil Kelsh
- Department of Biology and Biochemistry, University of Bath, Bath, UK.
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40
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Jiang H, Newman M, Lardelli M. The zebrafish orthologue of familial Alzheimer's disease gene PRESENILIN 2 is required for normal adult melanotic skin pigmentation. PLoS One 2018; 13:e0206155. [PMID: 30359395 PMCID: PMC6201934 DOI: 10.1371/journal.pone.0206155] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/07/2018] [Indexed: 12/25/2022] Open
Abstract
Alzheimer's disease is the most common form of age-related dementia. At least 15 mutations in the human gene PRESENILIN 2 (PSEN2) have been found to cause familial Alzheimer's disease (fAD). Zebrafish possess an orthologous gene, psen2, and present opportunities for investigation of PRESENILIN function related to Alzheimer's disease. The most prevalent and best characterized fAD mutation in PSEN2 is N141I. The equivalent codon in zebrafish psen2 is N140. We used genome editing technology in zebrafish to target generation of mutations to the N140 codon. We isolated two mutations: psen2N140fs, (hereafter "N140fs"), causing truncation of the coding sequence, and psen2T141_L142delinsMISLISV, (hereafter "T141_L142delinsMISLISV"), that deletes the two codons immediately downstream of N140 and replaces them with seven codons coding for amino acid residues MISLISV. Thus, like almost every fAD mutation in the PRESENILIN genes, this latter mutation does not truncate the gene's open reading frame. Both mutations are homozygous viable although N140fs transcripts are subject to nonsense-mediated decay and lack any possibility of coding for an active γ-secretase enzyme. N140fs homozygous larvae initially show grossly normal melanotic skin pigmentation but subsequently lose this as they grow while retaining pigmentation in the retinal pigmented epithelium. T141_L142delinsMISLISV homozygotes retain faint skin melanotic pigmentation as adults, most likely indicating that the protein encoded by this allele retains weak γ-secretase activity. Null mutations in the human PRESENILIN genes do not cause Alzheimer's disease so these two mutations may be useful for future investigation of the differential effects of null and fAD-like PRESENILIN mutations on brain aging.
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Affiliation(s)
- Haowei Jiang
- University of Adelaide, School of Biological Sciences, Alzheimer’s Disease Genetics Laboratory, North Terrace, Adelaide, South Australia, Australia
| | - Morgan Newman
- University of Adelaide, School of Biological Sciences, Alzheimer’s Disease Genetics Laboratory, North Terrace, Adelaide, South Australia, Australia
| | - Michael Lardelli
- University of Adelaide, School of Biological Sciences, Alzheimer’s Disease Genetics Laboratory, North Terrace, Adelaide, South Australia, Australia
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Petratou K, Subkhankulova T, Lister JA, Rocco A, Schwetlick H, Kelsh RN. A systems biology approach uncovers the core gene regulatory network governing iridophore fate choice from the neural crest. PLoS Genet 2018; 14:e1007402. [PMID: 30286071 PMCID: PMC6191144 DOI: 10.1371/journal.pgen.1007402] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/16/2018] [Accepted: 08/22/2018] [Indexed: 12/29/2022] Open
Abstract
Multipotent neural crest (NC) progenitors generate an astonishing array of derivatives, including neuronal, skeletal components and pigment cells (chromatophores), but the molecular mechanisms allowing balanced selection of each fate remain unknown. In zebrafish, melanocytes, iridophores and xanthophores, the three chromatophore lineages, are thought to share progenitors and so lend themselves to investigating the complex gene regulatory networks (GRNs) underlying fate segregation of NC progenitors. Although the core GRN governing melanocyte specification has been previously established, those guiding iridophore and xanthophore development remain elusive. Here we focus on the iridophore GRN, where mutant phenotypes identify the transcription factors Sox10, Tfec and Mitfa and the receptor tyrosine kinase, Ltk, as key players. Here we present expression data, as well as loss and gain of function results, guiding the derivation of an initial iridophore specification GRN. Moreover, we use an iterative process of mathematical modelling, supplemented with a Monte Carlo screening algorithm suited to the qualitative nature of the experimental data, to allow for rigorous predictive exploration of the GRN dynamics. Predictions were experimentally evaluated and testable hypotheses were derived to construct an improved version of the GRN, which we showed produced outputs consistent with experimentally observed gene expression dynamics. Our study reveals multiple important regulatory features, notably a sox10-dependent positive feedback loop between tfec and ltk driving iridophore specification; the molecular basis of sox10 maintenance throughout iridophore development; and the cooperation between sox10 and tfec in driving expression of pnp4a, a key differentiation gene. We also assess a candidate repressor of mitfa, a melanocyte-specific target of sox10. Surprisingly, our data challenge the reported role of Foxd3, an established mitfa repressor, in iridophore regulation. Our study builds upon our previous systems biology approach, by incorporating physiologically-relevant parameter values and rigorous evaluation of parameter values within a qualitative data framework, to establish for the first time the core GRN guiding specification of the iridophore lineage.
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Affiliation(s)
- Kleio Petratou
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, Faculty of Science, University of Bath, Bath, United Kingdom
| | - Tatiana Subkhankulova
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, Faculty of Science, University of Bath, Bath, United Kingdom
| | - James A. Lister
- Department of Human and Molecular Genetics and Massey Cancer Center, VCU School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Andrea Rocco
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Hartmut Schwetlick
- Department of Mathematical Sciences, Faculty of Science, University of Bath, Bath, United Kingdom
| | - Robert N. Kelsh
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, Faculty of Science, University of Bath, Bath, United Kingdom
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42
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Deane-Coe PE, Chu ET, Slavney A, Boyko AR, Sams AJ. Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies. PLoS Genet 2018; 14:e1007648. [PMID: 30286082 PMCID: PMC6171790 DOI: 10.1371/journal.pgen.1007648] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/20/2018] [Indexed: 12/30/2022] Open
Abstract
Consumer genomics enables genetic discovery on an unprecedented scale by linking very large databases of personal genomic data with phenotype information voluntarily submitted via web-based surveys. These databases are having a transformative effect on human genomics research, yielding insights on increasingly complex traits, behaviors, and disease by including many thousands of individuals in genome-wide association studies (GWAS). The promise of consumer genomic data is not limited to human research, however. Genomic tools for dogs are readily available, with hundreds of causal Mendelian variants already characterized, because selection and breeding have led to dramatic phenotypic diversity underlain by a simple genetic structure. Here, we report the results of the first consumer genomics study ever conducted in a non-human model: a GWAS of blue eyes based on more than 3,000 customer dogs with validation panels including nearly 3,000 more, the largest canine GWAS to date. We discovered a novel association with blue eyes on chromosome 18 (P = 1.3x10-68) and used both sequence coverage and microarray probe intensity data to identify the putative causal variant: a 98.6-kb duplication directly upstream of the Homeobox gene ALX4, which plays an important role in mammalian eye development. This duplication is largely restricted to Siberian Huskies, is strongly associated with the blue-eyed phenotype (chi-square P = 5.2x10-290), and is highly, but not completely, penetrant. These results underscore the power of consumer-data-driven discovery in non-human species, especially dogs, where there is intense owner interest in the personal genomic information of their pets, a high level of engagement with web-based surveys, and an underlying genetic architecture ideal for mapping studies.
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Affiliation(s)
- Petra E. Deane-Coe
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Erin T. Chu
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Andrea Slavney
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Adam R. Boyko
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Aaron J. Sams
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
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43
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Deng S, Zhang X, Li Q, Zhang J, Han F, Liu X. Comparative transcriptome analysis of Paphia undulata with different foot colors. Mar Genomics 2018; 42:25-31. [PMID: 30195478 DOI: 10.1016/j.margen.2018.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/20/2018] [Accepted: 08/28/2018] [Indexed: 12/27/2022]
Abstract
Foot color is an important trait in Paphia undulata that influences consumer selection. To elucidate the molecular basis of foot color, six transcriptome libraries of P. undulata with different foot colors were constructed: white (L2, L3 and L4) and orange (D2, D3, D4). There is a significant difference in color index (L⁎, a⁎, b⁎) between the two groups (P < 0.05). These six paired-end libraries were sequenced using the Illumina HiSeq 2500 platform. In total, 48.22 Gb of clean data were obtained and de novo assembled into 58,159 unigenes with a mean length of 889.51 bp and N50 of 1461 bp. A total of 19,070 unigenes were significantly matched to known unique proteins. The Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to determine metabolic pathways and candidate genes associated with foot color traits. Compared with white P. undulate, a total of 107 transcripts were identified as differentially expressed genes (DEGs) in orange samples using Cuffdiff, including 74 up-regulated and 33 down-regulated genes. Of these differentially expressed genes, many were involved in the synthesis and transport of carotenoids and pigment biosynthesis. Additionally, results of the transcriptome analysis were verified by quantitative real-time PCR (qRT-PCR). Overall, this experiment discovered several potential foot coloration genes and related molecular mechanisms using RNA-seq, which paves the way for further functional elucidation of color-related genes and assists selective breeding practices in P. undulata.
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Affiliation(s)
- Suzhen Deng
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, Fujian, PR China
| | - Xiaolin Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, Fujian, PR China
| | - Qingchang Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, Fujian, PR China
| | - Jing Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, Fujian, PR China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, Fujian, PR China
| | - Xiande Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, Fujian, PR China.
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44
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Hozumi S, Shirai M, Wang J, Aoki S, Kikuchi Y. The N-terminal domain of gastrulation brain homeobox 2 (Gbx2) is required for iridophore specification in zebrafish. Biochem Biophys Res Commun 2018; 502:104-109. [PMID: 29787751 DOI: 10.1016/j.bbrc.2018.05.128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 10/16/2022]
Abstract
Although body color pattern formation by pigment cells plays critical roles in animals, pigment cell specification has not yet been fully elucidated. In zebrafish, there are three chromatophores: melanophore, iridophore, and xanthophore, that are derived from neural crest cells (NCCs). A recent study has reported the differentially expressed genes between melanophores and iridophores. Based on transcriptome data, we identified that Gbx2 is required for iridophore specification during development. In support of this, iridophore formation is suppressed by gbx2 knockdown by morpholino antisense oligonucleotide, at 72 h post fertilization (hpf) in zebrafish. Moreover, gbx2 is expressed in sox10-expressing NCCs and guanine crystal plates-containing iridophores during development at 24 and 48 hpf, respectively. In gbx2 knockdown zebrafish embryos, apoptosis of sox10-expressing NCCs was detected at 24 hpf without any effect on the formation of melanophores and xanthophores at 48 hpf. We further observed that the N-terminal domain of Gbx2 is able to rescue the iridophore formation defect caused by gbx2 knockdown. Our study provides insights into the requirement of N-terminal domain of Gbx2 for iridophore specification in zebrafish.
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Affiliation(s)
- Shunya Hozumi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Masaki Shirai
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Jingxin Wang
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Shun Aoki
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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45
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Perez DE, Henle AM, Amsterdam A, Hagen HR, Lees JA. Uveal melanoma driver mutations in GNAQ/11 yield numerous changes in melanocyte biology. Pigment Cell Melanoma Res 2018; 31:604-613. [PMID: 29570931 DOI: 10.1111/pcmr.12700] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/09/2018] [Indexed: 11/27/2022]
Abstract
Uveal melanoma (UM) is the most common primary intraocular cancer and has a high incidence of metastasis, which lacks any effective treatment. Here, we present zebrafish models of UM, which are driven by melanocyte-specific expression of activating GNAQ or GNA11 alleles, GNAQ/11Q209L , the predominant initiating mutations for human UM. When combined with mutant tp53, GNAQ/11Q209L transgenics develop various melanocytic tumors, including UM, with near complete penetrance. These tumors display nuclear YAP localization and thus phenocopy human UM. We show that GNAQ/11Q209L expression induces profound melanocyte defects independent of tp53 mutation, which are apparent within 3 days of development. First, increases in melanocyte number, melanin content, and subcellular melanin distribution result in hyperpigmentation. Additionally, altered melanocyte migration, survival properties, and evasion of normal boundary cues lead to aberrant melanocyte localization and stripe patterning. Collectively, these data show that GNAQ/11Q209L is sufficient to induce numerous protumorigenic changes within melanocytes.
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Affiliation(s)
- Dahlia E Perez
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrea M Henle
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Biology Department, Carthage College, Kenosha, WI, USA
| | - Adam Amsterdam
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannah R Hagen
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacqueline A Lees
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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46
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Williams JS, Hsu JY, Rossi CC, Artinger KB. Requirement of zebrafish pcdh10a and pcdh10b in melanocyte precursor migration. Dev Biol 2018; 444 Suppl 1:S274-S286. [PMID: 29604249 DOI: 10.1016/j.ydbio.2018.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/16/2018] [Accepted: 03/25/2018] [Indexed: 01/13/2023]
Abstract
Melanocytes derive from neural crest cells, which are a highly migratory population of cells that play an important role in pigmentation of the skin and epidermal appendages. In most vertebrates, melanocyte precursor cells migrate solely along the dorsolateral pathway to populate the skin. However, zebrafish melanocyte precursors also migrate along the ventromedial pathway, in route to the yolk, where they interact with other neural crest derivative populations. Here, we demonstrate the requirement for zebrafish paralogs pcdh10a and pcdh10b in zebrafish melanocyte precursor migration. pcdh10a and pcdh10b are expressed in a subset of melanocyte precursor and somatic cells respectively, and knockdown and TALEN mediated gene disruption of pcdh10a results in aberrant migration of melanocyte precursors resulting in fully melanized melanocytes that differentiate precociously in the ventromedial pathway. Live cell imaging analysis demonstrates that loss of pchd10a results in a reduction of directed cell migration of melanocyte precursors, caused by both increased adhesion and a loss of cell-cell contact with other migratory neural crest cells. Also, we determined that the paralog pcdh10b is upregulated and can compensate for the genetic loss of pcdh10a. Disruption of pcdh10b alone by CRISPR mutagenesis results in somite defects, while the loss of both paralogs results in enhanced migratory melanocyte precursor phenotype and embryonic lethality. These results reveal a novel role for pcdh10a and pcdh10b in zebrafish melanocyte precursor migration and suggest that pcdh10 paralogs potentially interact for proper transient migration along the ventromedial pathway.
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Affiliation(s)
- Jason S Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Cell Biology, Stem Cells, and Development Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jessica Y Hsu
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Pharmacology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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47
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Cao D, Gong S, Yang J, Li W, Ge Y, Wei Y. Melanin deposition ruled out as cause of color changes in the red-eared sliders (Trachemys scripta elegans). Comp Biochem Physiol B Biochem Mol Biol 2018; 217:79-85. [DOI: 10.1016/j.cbpb.2017.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/04/2017] [Accepted: 12/12/2017] [Indexed: 11/28/2022]
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48
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Avci ME, Keskus AG, Targen S, Isilak ME, Ozturk M, Atalay RC, Adams MM, Konu O. Development of a novel zebrafish xenograft model in ache mutants using liver cancer cell lines. Sci Rep 2018; 8:1570. [PMID: 29371671 PMCID: PMC5785479 DOI: 10.1038/s41598-018-19817-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/05/2018] [Indexed: 01/09/2023] Open
Abstract
Acetylcholinesterase (AChE), an enzyme responsible for degradation of acetylcholine, has been identified as a prognostic marker in liver cancer. Although in vivo Ache tumorigenicity assays in mouse are present, no established liver cancer xenograft model in zebrafish using an ache mutant background exists. Herein, we developed an embryonic zebrafish xenograft model using epithelial (Hep3B) and mesenchymal (SKHep1) liver cancer cell lines in wild-type and ache sb55 sibling mutant larvae after characterization of cholinesterase expression and activity in cell lines and zebrafish larvae. The comparison of fluorescent signal reflecting tumor size at 3-days post-injection (dpi) revealed an enhanced tumorigenic potential and a reduced migration capacity in cancer cells injected into homozygous ache sb55 mutants when compared with the wild-type. Increased tumor load was confirmed using an ALU based tumor DNA quantification method modified for use in genotyped xenotransplanted zebrafish embryos. Confocal microscopy using the Huh7 cells stably expressing GFP helped identify the distribution of tumor cells in larvae. Our results imply that acetylcholine accumulation in the microenvironment directly or indirectly supports tumor growth in liver cancer. Use of this model system for drug screening studies holds potential in discovering new cholinergic targets for treatment of liver cancers.
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Affiliation(s)
- M Ender Avci
- Department of Molecular Biology and Genetics, Bilkent University, 06800, Ankara, Turkey.
- Izmir International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylul University, 35340, Izmir, Turkey.
| | - Ayse Gokce Keskus
- Interdisciplinary Program in Neuroscience, Bilkent University, 06800, Ankara, Turkey
| | - Seniye Targen
- Department of Molecular Biology and Genetics, Bilkent University, 06800, Ankara, Turkey
| | - M Efe Isilak
- Department of Molecular Biology and Genetics, Bilkent University, 06800, Ankara, Turkey
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Mehmet Ozturk
- Department of Molecular Biology and Genetics, Bilkent University, 06800, Ankara, Turkey
- Izmir International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylul University, 35340, Izmir, Turkey
| | - Rengul Cetin Atalay
- Medical Informatics Department, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Michelle M Adams
- Department of Psychology, Bilkent University, 06800, Ankara, Turkey
- Interdisciplinary Program in Neuroscience, Bilkent University, 06800, Ankara, Turkey
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Ozlen Konu
- Department of Molecular Biology and Genetics, Bilkent University, 06800, Ankara, Turkey.
- Interdisciplinary Program in Neuroscience, Bilkent University, 06800, Ankara, Turkey.
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey.
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49
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Ahi EP, Richter F, Sefc KM. A gene expression study of ornamental fin shape in Neolamprologus brichardi, an African cichlid species. Sci Rep 2017; 7:17398. [PMID: 29234131 PMCID: PMC5727040 DOI: 10.1038/s41598-017-17778-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/29/2017] [Indexed: 01/14/2023] Open
Abstract
The diversity of fin morphology within and across fish taxa offers great, but still largely unexplored, opportunities to investigate the proximate mechanisms underlying fin shape variation. Relying on available genetic knowledge brought forth mainly by the comprehensive study of the zebrafish caudal fin, we explored candidate molecular mechanisms for the maintenance and formation of the conspicuously elongated filaments adorning the unpaired fins of the East African "princess cichlid" Neolamprologus brichardi. Via qPCR assays, we detected expression differences of candidate genes between elongated and short regions of intact and regenerating fins. The identified genes include skeletogenic and growth factors (igf2b, fgf3, bmp2 and bmp4), components of the WNT pathway (lef1, wnt5b and wnt10) and a regulatory network determining fin ray segment size and junction (cx43, esco2 and sema3d), as well as other genes with different roles (mmp9, msxb and pea3). Interestingly, some of these genes showed fin specific expression differences which are often neglected in studies of model fish that focus on the caudal fin. Moreover, while the observed expression patterns were generally consistent with zebrafish results, we also detected deviating expression correlations and gene functions.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria.
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50
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Ahi EP, Sefc KM. Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation. PeerJ 2017; 5:e4080. [PMID: 29158996 PMCID: PMC5695249 DOI: 10.7717/peerj.4080] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/01/2017] [Indexed: 01/04/2023] Open
Abstract
Morphological differentiation among closely related species provides opportunities to study mechanisms shaping natural phenotypic variation. Here, we address variation in the orientation of melanin-colored body stripes in three cichlid species of the tribe Haplochromini. Melanochromis auratus displays a common pattern of dark, straight horizontal body stripes, whereas in Aristochromis christyi and Buccochromis rhoadesii, oblique stripes extend from the anterior dorsal to the posterior mid-lateral trunk. We first validated a stably reference gene, and then, investigated the chromatophore distribution in the skin by assessing the expression levels of the iridophore and melanophore marker genes, ltk and slc24a5, respectively, as well as pmel, a melanophore pigmentation marker gene. We found anterior-posterior differences in the expression levels of the three genes in the oblique-striped species. The higher anterior expression of ltk, indicates increased iridophore density in the anterior region, i.e., uneven horizontal distribution of iridophores, which coincides with the anterior dorsalization of melanophore stripe in these species. The obliqueness of the horizontal body stripes might be a result of distinct migratory or patterning abilities of melanophores in anterior and posterior stripe regions which could be reflected by variation in the expression of genes involved in melanophore patterning. To address this, we investigated anterior-posterior expression levels of a primary set of candidate target genes with known functions in melanophore migration and stripe patterning in the adult zebrafish, and their related gene regulatory network. Among these genes, those with differences in anterior-posterior expression showed only species-specific differential expression, e.g., sdf1a, col14a1a, ifitm5, and agpat3, with the exception of fbxw4/hagoromo (differentially expressed in an oblique-and the straight-striped species). In summary, distinct anterior-posterior gradients in iridophore density found to be more similar characteristic between the two oblique-striped species. Furthermore, the species-specific differential expression of genes involved in stripe patterning might also implicate distinct molecular processes underlying the obliqueness of body stripe in two closely related cichlid species.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Zoology, Universitätsplatz 2, Universität Graz, Graz, Austria
| | - Kristina M Sefc
- Institute of Zoology, Universitätsplatz 2, Universität Graz, Graz, Austria
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