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Mercurio S, Bozzo M, Pennati A, Candiani S, Pennati R. Serotonin Receptors and Their Involvement in Melanization of Sensory Cells in Ciona intestinalis. Cells 2023; 12:cells12081150. [PMID: 37190059 DOI: 10.3390/cells12081150] [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: 03/07/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Serotonin (5-hydroxytryptamine (5-HT)) is a biogenic monoamine with pleiotropic functions. It exerts its roles by binding to specific 5-HT receptors (5HTRs) classified into different families and subtypes. Homologs of 5HTRs are widely present in invertebrates, but their expression and pharmacological characterization have been scarcely investigated. In particular, 5-HT has been localized in many tunicate species but only a few studies have investigated its physiological functions. Tunicates, including ascidians, are the sister group of vertebrates, and data about the role of 5-HTRs in these organisms are thus important for understanding 5-HT evolution among animals. In the present study, we identified and described 5HTRs in the ascidian Ciona intestinalis. During development, they showed broad expression patterns that appeared consistent with those reported in other species. Then, we investigated 5-HT roles in ascidian embryogenesis exposing C. intestinalis embryos to WAY-100635, an antagonist of the 5HT1A receptor, and explored the affected pathways in neural development and melanogenesis. Our results contribute to unraveling the multifaceted functions of 5-HT, revealing its involvement in sensory cell differentiation in ascidians.
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Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milan, Italy
| | - Matteo Bozzo
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università degli Studi di Genova, 16132 Genoa, Italy
| | | | - Simona Candiani
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università degli Studi di Genova, 16132 Genoa, Italy
| | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milan, Italy
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2
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Duruz J, Sprecher M, Kaldun JC, Al-Soudy AS, Lischer HEL, van Geest G, Nicholson P, Bruggmann R, Sprecher SG. Molecular characterization of cell types in the squid Loligo vulgaris. eLife 2023; 12:80670. [PMID: 36594460 PMCID: PMC9839350 DOI: 10.7554/elife.80670] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Cephalopods are set apart from other mollusks by their advanced behavioral abilities and the complexity of their nervous systems. Because of the great evolutionary distance that separates vertebrates from cephalopods, it is evident that higher cognitive features have evolved separately in these clades despite the similarities that they share. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Despite significant progress in genome and transcriptome sequencing, the molecular identities of cell types in cephalopods remain largely unknown. We here combine single-cell transcriptomics with in situ gene expression analysis to uncover cell type diversity in the European squid Loligo vulgaris. We describe cell types that are conserved with other phyla such as neurons, muscles, or connective tissues but also cephalopod-specific cells, such as chromatophores or sucker cells. Moreover, we investigate major components of the squid nervous system including progenitor and developing cells, differentiated cells of the brain and optic lobes, as well as sensory systems of the head. Our study provides a molecular assessment for conserved and novel cell types in cephalopods and a framework for mapping the nervous system of L. vulgaris.
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Affiliation(s)
- Jules Duruz
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Marta Sprecher
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Jenifer C Kaldun
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Al-Sayed Al-Soudy
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
| | - Heidi EL Lischer
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | - Geert van Geest
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernBernSwitzerland
| | - Simon G Sprecher
- Department of Biology, Institute of Zoology, University of FribourgFribourgSwitzerland
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3
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De novo assembly transcriptome analysis reveals the genes associated with body color formation in the freshwater ornamental shrimps Neocaridina denticulate sinensis. Gene 2022; 806:145929. [PMID: 34461150 DOI: 10.1016/j.gene.2021.145929] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/10/2021] [Accepted: 08/25/2021] [Indexed: 12/11/2022]
Abstract
The body color of Neocaridina denticulate sinensis is a compelling phenotypic trait, in which a cascade of carotenoid metabolic processes plays an important role. The study was conducted to compare the transcriptome of cephalothoraxes among three pigmentation phenotypes (red, blue, and chocolate) of N. denticulate sinensis. The purpose of this study was to explore the candidate genes associated with different colors of N. denticulate sinensis. Nine cDNA libraries in three groups were constructed from the cephalothoraxes of shrimps. After assembly, 75022 unigenes were obtained in total with an average length of 1026 bp and N50 length of 1876 bp. There were 45977, 25284, 23605, 21913 unigenes annotated in the Nr, Swissprot, KOG, and KEGG databases, respectively. Differential expression analysis revealed that there were 829, 554, and 3194 differentially expressed genes (DEGs) in RD vs BL, RD vs CH, and BL vs CH, respectively. These DEGs may play roles in the absorption, transport, and metabolism of carotenoids. We also emphasized that electron transfer across the inner mitochondrial membrane (IMM) was a key process in pigment metabolism. In addition, a total of 6328 simple sequence repeats (SSRs) were also detected in N. denticulate sinensis. The results laid a solid foundation for further research on the molecular mechanism of integument pigmentation in the crustacean and contributed to developing more attractive aquatic animals.
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Chen H, Wang J, Du J, Mandal BK, Si Z, Xu X, Yang H, Wang C. Analysis of recently duplicated TYRP1 genes and their effect on the formation of black patches in Oujiang-color common carp (Cyprinus carpio var. color). Anim Genet 2021; 52:451-460. [PMID: 33939849 DOI: 10.1111/age.13071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2021] [Indexed: 11/29/2022]
Abstract
Tyrp1 gene, as a member of the tyrosinase family, has undergone a recent duplication event during fourth-round whole genome duplication in common carp. In this research, three Tyrp1 genes were identified in Oujiang-color common carp (Cyprinus carpio var. color). The similar expression patterns and close phylogenetic relationship indicated that Tyrp1c is homologous to Tyrp1b and possibly originated from the ancient Tyrp1b. The rates of synonymous and non-synonymous substitution (Ka /Ks ) in Tyrp1 across teleost phylogeny indicated that Tyrp1a is more likely to be in the process of purifying selection. The CRISPR/Cas9 system was used to disrupt the Tyrp1 genes in zebrafish and the WB (black patches on white skin) strain of Oujiang-color common carp. The Tyrp1 loss of function variants in zebrafish and WB carp showed severe melanin deficiency in the skin. Meanwhile, inactivation of a single Tyrp1 gene did not obstruct melanin synthesis, which proved that the functional redundancy of Tyrp1 genes existed in both zebrafish and Oujiang-color common carp. Among the mosaic individuals with Tyrp1 genes in disrupted-color common carp, various mutations in Tyrp1b gene induced gray or brown phenotypes, suggesting that it may be bifunctional in Oujiang-color common carp. In addition, the phenotype of WB variants was different from that of WW (whole white skin), suggesting that Tyrp1 genes were not the key factor that caused the difference between WB and WW.
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Affiliation(s)
- H Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China.,Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - J Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - J Du
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - B K Mandal
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Zh Si
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - X Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - H Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Ch Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
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Glover JA, Lattanzio MS. Female preferences for discrete and continuous male colour expression may help reinforce colour polymorphism in a desert lizard. BEHAVIOUR 2021. [DOI: 10.1163/1568539x-bja10068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Despite recognition that colour can vary continuously, colour expression in colour polymorphic species is usually treated as discrete. We conducted three experiments to evaluate the extent that discrete and continuous male coloration influenced female mating preferences in long-tailed brush lizards (Urosaurus graciosus). Each experiment provided females with a different social context: a dimorphic choice between a yellow and an orange male (coloration treated as discrete), and a choice between either two orange males or two yellow males (coloration treated as continuous variation). Females preferred orange males over yellow males in the first experiment, and the findings of our second experiment suggested that males with moderate orange coloration were most preferred. In contrast, females behaved randomly with respect to two yellow males. Our findings show that females in colour polymorphic species can evaluate both discrete and continuous aspects of morph coloration during mate assessment, which may help maintain their polymorphism.
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Affiliation(s)
- Jenell A. Glover
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA 23606, USA
| | - Matthew S. Lattanzio
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA 23606, USA
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6
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DeLeo DM, Bracken-Grissom HD. Illuminating the impact of diel vertical migration on visual gene expression in deep-sea shrimp. Mol Ecol 2020; 29:3494-3510. [PMID: 32748474 DOI: 10.1111/mec.15570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/19/2022]
Abstract
Diel vertical migration (DVM) of marine animals represents one of the largest migrations on our planet. Migrating fauna are subjected to a variety of light fields and environmental conditions that can have notable impacts on sensory mechanisms, including an organism's visual capabilities. Among deep-sea migrators are oplophorid shrimp that vertically migrate hundreds of metres to feed in shallow waters at night. These species also have bioluminescent light organs that emit light during migrations to aid in camouflage. The organs have recently been shown to contain visual proteins (opsins) and genes that infer light sensitivity. Knowledge regarding the impacts of vertical migratory behaviour, and fluctuating environmental conditions, on sensory system evolution is unknown. In this study, the oplophorid Systellaspis debilis was either collected during the day from deep waters or at night from relatively shallow waters to ensure sampling across the vertical distributional range. De novo transcriptomes of light-sensitive tissues (eyes/photophores) from the day/night specimens were sequenced and analysed to characterize opsin diversity and visual/light interaction genes. Gene expression analyses were also conducted to quantify expression differences associated with DVM. Our results revealed an expanded opsin repertoire among the shrimp and differential opsin expression that may be linked to spectral tuning during the migratory process. This study sheds light on the sensory systems of a bioluminescent invertebrate and provides additional evidence for extraocular light sensitivity. Our findings further suggest opsin co-expression and subsequent fluctuations in opsin expression may play an important role in diversifying the visual responses of vertical migrators.
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Affiliation(s)
- Danielle M DeLeo
- Institute of Environment, Department of Biology, Florida International University, North Miami, FL, USA.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Heather D Bracken-Grissom
- Institute of Environment, Department of Biology, Florida International University, North Miami, FL, USA
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7
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Jiang K, Jiang L, Nie H, Huo Z, Yan X. Molecular cloning and expression analysis of tyrosinases ( tyr) in four shell-color strains of Manila clam Ruditapes philippinarum. PeerJ 2020; 8:e8641. [PMID: 32110498 PMCID: PMC7032058 DOI: 10.7717/peerj.8641] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/27/2020] [Indexed: 11/27/2022] Open
Abstract
The Manila clam (Ruditapes philippinarum) is an economically important molluscan bivalve with variation in pigmentation frequently observed in the shell. In nature, tyrosinase is widely distributed in invertebrates and vertebrates, and plays a crucial role in a variety of physiological activities. In this study, a tyrosinase gene (tyr 9) was cloned and the expression level of tyr genes (tyr 6, tyr 9, tyr 10, and tyr 11) were investigated in different shell colors. Quantitative real-time PCR showed that tyr genes were significantly expressed in the mantle, a shell formation and pigmentation-related tissue. Moreover, the expression pattern of the tyr genes in the mantle of different shell-color strains was different, suggesting that tyrosinases might be involved in different shell-color formation. In addition, the expression profile of tyr 6, tyr 9, tyr 10, and tyr 11 genes were detected at different early developmental stages and the expression level varied with embryonic and larval growth. RNA interference (RNAi) results showed that the expression level of tyr 9 in the RNAi group was significantly down-regulated compared to control and negative control groups, indicating that Rptyr 9 might participate in shell-color formation. Our results indicated that tyr genes were likely to play vital roles in the formation of shell and shell-color in R. philippinarum.
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Affiliation(s)
- Kunyin Jiang
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Liwen Jiang
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Hongtao Nie
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Zhongming Huo
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Xiwu Yan
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, School of Fisheries and Life Science, Dalian Ocean University, Dalian, China
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8
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Hu Z, Song H, Yang MJ, Yu ZL, Zhou C, Wang XL, Zhang T. Transcriptome analysis of shell color-related genes in the hard clam Mercenaria mercenaria. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100598. [DOI: 10.1016/j.cbd.2019.100598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/25/2019] [Accepted: 05/27/2019] [Indexed: 01/31/2023]
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9
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Figon F, Casas J. Ommochromes in invertebrates: biochemistry and cell biology. Biol Rev Camb Philos Soc 2019; 94:156-183. [PMID: 29989284 DOI: 10.1111/brv.12441] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/09/2018] [Accepted: 06/12/2018] [Indexed: 01/24/2023]
Abstract
Ommochromes are widely occurring coloured molecules of invertebrates, arising from tryptophan catabolism through the so-called Tryptophan → Ommochrome pathway. They are mainly known to mediate compound eye vision, as well as reversible and irreversible colour patterning. Ommochromes might also be involved in cell homeostasis by detoxifying free tryptophan and buffering oxidative stress. These biological functions are directly linked to their unique chromophore, the phenoxazine/phenothiazine system. The most recent reviews on ommochrome biochemistry were published more than 30 years ago, since when new results on the enzymes of the ommochrome pathway, on ommochrome photochemistry as well as on their antiradical capacities have been obtained. Ommochromasomes are the organelles where ommochromes are synthesised and stored. Hence, they play an important role in mediating ommochrome functions. Ommochromasomes are part of the lysosome-related organelles (LROs) family, which includes other pigmented organelles such as vertebrate melanosomes. Ommochromasomes are unique because they are the only LRO for which a recycling process during reversible colour change has been described. Herein, we provide an update on ommochrome biochemistry, photoreactivity and antiradical capacities to explain their diversity and behaviour both in vivo and in vitro. We also highlight new biochemical techniques, such as quantum chemistry, metabolomics and crystallography, which could lead to major advances in their chemical and functional characterisation. We then focus on ommochromasome structure and formation by drawing parallels with the well-characterised melanosomes of vertebrates. The biochemical, genetic, cellular and microscopic tools that have been applied to melanosomes should provide important information on the ommochromasome life cycle. We propose LRO-based models for ommochromasome biogenesis and recycling that could be tested in the future. Using the context of insect compound eyes, we finally emphasise the importance of an integrated approach in understanding the biological functions of ommochromes.
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Affiliation(s)
- Florent Figon
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, Université de Tours, 37200 Tours, France
| | - Jérôme Casas
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, Université de Tours, 37200 Tours, France
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San-Jose LM, Roulin A. Genomics of coloration in natural animal populations. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0337. [PMID: 28533454 DOI: 10.1098/rstb.2016.0337] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2017] [Indexed: 12/28/2022] Open
Abstract
Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.
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Affiliation(s)
- Luis M San-Jose
- Department of Ecology and Evolution, University of Lausanne, Building Le Biophore, 1015 Lausanne, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Building Le Biophore, 1015 Lausanne, Switzerland
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Feng D, Li Q, Yu H, Zhao X, Kong L. Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation. PLoS One 2015; 10:e0145257. [PMID: 26693729 PMCID: PMC4691203 DOI: 10.1371/journal.pone.0145257] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Shell color polymorphisms of Mollusca have contributed to development of evolutionary biology and population genetics, while the genetic bases and molecular mechanisms underlying shell pigmentation are poorly understood. The Pacific oyster (Crassostrea gigas) is one of the most important farmed oysters worldwide. Through successive family selection, four shell color variants (white, golden, black and partially pigmented) of C. gigas have been developed. To elucidate the genetic mechanisms of shell coloration in C. gigas and facilitate the selection of elite oyster lines with desired coloration patterns, differentially expressed genes (DEGs) were identified among the four shell color variants by RNA-seq. RESULTS Digital gene expression generated over fifteen million reads per sample, producing expression data for 28,027 genes. A total number of 2,645 DEGs were identified from pair-wise comparisons, of which 432, 91, 43 and 39 genes specially were up-regulated in white, black, golden and partially pigmented shell of C. gigas, respectively. Three genes of Abca1, Abca3 and Abcb1 which belong to the ATP-binding cassette (ABC) transporters super-families were significantly associated with white shell formation. A tyrosinase transcript (CGI_10008737) represented consistent up-regulated pattern with golden coloration. We proposed that white shell variant of C. gigas could employ "endocytosis" to down-regulate notch level and to prevent shell pigmentation. CONCLUSION This study discovered some potential shell coloration genes and related molecular mechanisms by the RNA-seq, which would provide foundational information to further study on shell coloration and assist in selective breeding in C. gigas.
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Affiliation(s)
- Dandan Feng
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Hong Yu
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Xuelin Zhao
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
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Oakley TH, Speiser DI. How Complexity Originates: The Evolution of Animal Eyes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-110512-135907] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106;
| | - Daniel I. Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208
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13
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Esposito R, Racioppi C, Pezzotti MR, Branno M, Locascio A, Ristoratore F, Spagnuolo A. The ascidian pigmented sensory organs: structures and developmental programs. Genesis 2014; 53:15-33. [PMID: 25382437 DOI: 10.1002/dvg.22836] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 01/25/2023]
Abstract
The recent advances on ascidian pigment sensory organ development and function represent a fascinating platform to get insight on the basic programs of chordate eye formation. This review aims to summarize current knowledge, at the structural and molecular levels, on the two main building blocks of ascidian light sensory organ, i.e. pigment cells and photoreceptor cells. The unique features of these structures (e.g., simplicity and well characterized cell lineage) are indeed making it possible to dissect the developmental programs at single cell resolution and will soon provide a panel of molecular tools to be exploited for a deep developmental and comparative-evolutionary analysis.
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Affiliation(s)
- R Esposito
- Cellular and Developmental Biology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, NAPOLI, Italy
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14
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Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, Zigler KS, Crandall KA, Oakley TH. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC Bioinformatics 2014; 15:350. [PMID: 25407802 PMCID: PMC4255452 DOI: 10.1186/s12859-014-0350-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/09/2014] [Indexed: 11/10/2022] Open
Abstract
Background Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. Results We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository (http://bitbucket.org/osiris_phylogenetics/pia/) and we demonstrate PIA on a publicly-accessible web server (http://galaxy-dev.cnsi.ucsb.edu/pia/). Conclusions Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0350-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel I Speiser
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. .,Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
| | - M Sabrina Pankey
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Alexander K Zaharoff
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Barbara A Battelle
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, USA.
| | - Thomas W Cronin
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA.
| | - Anders Garm
- Department of Biology, Marine Biological Section, University of Copenhagen, Copenhagen, Denmark.
| | - Annie R Lindgren
- Department of Biology, Portland State University, Portland, OR, USA.
| | - Nipam H Patel
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Megan L Porter
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
| | - Meredith E Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, USA.
| | - Ajna S Rivera
- Department of Biology, University of the Pacific, Stockton, CA, USA.
| | - Jeanne M Serb
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Kirk S Zigler
- Department of Biology, Sewanee: The University of the South, Sewanee, TN, USA.
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA. .,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
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15
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Nasti TH, Timares L. MC1R, eumelanin and pheomelanin: their role in determining the susceptibility to skin cancer. Photochem Photobiol 2014; 91:188-200. [PMID: 25155575 DOI: 10.1111/php.12335] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 08/17/2014] [Indexed: 12/16/2022]
Abstract
Skin pigmentation is due to the accumulation of two types of melanin granules in the keratinocytes. Besides being the most potent blocker of ultraviolet radiation, the role of melanin in photoprotection is complex. This is because one type of melanin called eumelanin is UV absorbent, whereas the other, pheomelanin, is photounstable and may even promote carcinogenesis. Skin hyperpigmentation may be caused by stress or exposure to sunlight, which stimulates the release of α-melanocyte stimulating hormone (α-MSH) from damaged keratinocytes. Melanocortin 1 receptor (MC1R) is a key signaling molecule on melanocytes that responds to α-MSH by inducing expression of enzymes responsible for eumelanin synthesis. Persons with red hair have mutations in the MC1R causing its inactivation; this leads to a paucity of eumelanin production and makes red-heads more susceptible to skin cancer. Apart from its effects on melanin production, the α-MSH/MC1R signaling is also a potent anti-inflammatory pathway and has been shown to promote antimelanoma immunity. This review will focus on the role of MC1R in terms of its regulation of melanogenesis and influence on the immune system with respect to skin cancer susceptibility.
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Affiliation(s)
- Tahseen H Nasti
- The Department of Dermatology, University of Alabama at Birmingham School of Medicine, Birmingham, AL
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16
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Speiser DI, DeMartini DG, Oakley TH. The shell-eyes of the chitonAcanthopleura granulata(Mollusca, Polyplacophora) use pheomelanin as a screening pigment. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.959572] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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17
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Kimura T, Nagao Y, Hashimoto H, Yamamoto-Shiraishi YI, Yamamoto S, Yabe T, Takada S, Kinoshita M, Kuroiwa A, Naruse K. Leucophores are similar to xanthophores in their specification and differentiation processes in medaka. Proc Natl Acad Sci U S A 2014; 111:7343-8. [PMID: 24803434 PMCID: PMC4034200 DOI: 10.1073/pnas.1311254111] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Animal body color is generated primarily by neural crest-derived pigment cells in the skin. Mammals and birds have only melanocytes on the surface of their bodies; however, fish have a variety of pigment cell types or chromatophores, including melanophores, xanthophores, and iridophores. The medaka has a unique chromatophore type called the leucophore. The genetic basis of chromatophore diversity remains poorly understood. Here, we report that three loci in medaka, namely, leucophore free (lf), lf-2, and white leucophore (wl), which affect leucophore and xanthophore differentiation, encode solute carrier family 2, member 15b (slc2a15b), paired box gene 7a (pax7a), and solute carrier family 2 facilitated glucose transporter, member 11b (slc2a11b), respectively. Because lf-2, a loss-of-function mutant for pax7a, causes defects in the formation of xanthophore and leucophore precursor cells, pax7a is critical for the development of the chromatophores. This genetic evidence implies that leucophores are similar to xanthophores, although it was previously thought that leucophores were related to iridophores, as these chromatophores have purine-dependent light reflection. Our identification of slc2a15b and slc2a11b as genes critical for the differentiation of leucophores and xanthophores in medaka led to a further finding that the existence of these two genes in the genome coincides with the presence of xanthophores in nonmammalian vertebrates: birds have yellow-pigmented irises with xanthophore-like intracellular organelles. Our findings provide clues for revealing diverse evolutionary mechanisms of pigment cell formation in animals.
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Affiliation(s)
- Tetsuaki Kimura
- Interuniversity Bio-Backup Project Center, National Institute for Basic Biology, Okazaki 444-8787, Aichi, Japan;Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan;
| | - Yusuke Nagao
- Bioscience and Biotechnology Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hisashi Hashimoto
- Bioscience and Biotechnology Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yo-ichi Yamamoto-Shiraishi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shiori Yamamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Taijiro Yabe
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan;Okazaki Institute for Integrative Bioscience and National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Shinji Takada
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan;Okazaki Institute for Integrative Bioscience and National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masato Kinoshita
- Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; and
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kiyoshi Naruse
- Interuniversity Bio-Backup Project Center, National Institute for Basic Biology, Okazaki 444-8787, Aichi, Japan;Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan;Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444-8585, Aichi, Japan
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18
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Stavenga DG, Leertouwer HL, Wilts BD. Coloration principles of nymphaline butterflies - thin films, melanin, ommochromes and wing scale stacking. ACTA ACUST UNITED AC 2014; 217:2171-80. [PMID: 24675561 DOI: 10.1242/jeb.098673] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The coloration of the common butterflies Aglais urticae (small tortoiseshell), Aglais io (peacock) and Vanessa atalanta (red admiral), belonging to the butterfly subfamily Nymphalinae, is due to the species-specific patterning of differently coloured scales on their wings. We investigated the scales' structural and pigmentary properties by applying scanning electron microscopy, (micro)spectrophotometry and imaging scatterometry. The anatomy of the wing scales appears to be basically identical, with an approximately flat lower lamina connected by trabeculae to a highly structured upper lamina, which consists of an array of longitudinal, parallel ridges and transversal crossribs. Isolated scales observed at the abwing (upper) side are blue, yellow, orange, red, brown or black, depending on their pigmentation. The yellow, orange and red scales contain various amounts of 3-OH-kynurenine and ommochrome pigment, black scales contain a high density of melanin, and blue scales have a minor amount of melanin pigment. Observing the scales from their adwing (lower) side always revealed a structural colour, which is blue in the case of blue, red and black scales, but orange for orange scales. The structural colours are created by the lower lamina, which acts as an optical thin film. Its reflectance spectrum, crucially determined by the lamina thickness, appears to be well tuned to the scales' pigmentary spectrum. The colours observed locally on the wing are also due to the degree of scale stacking. Thin films, tuned pigments and combinations of stacked scales together determine the wing coloration of nymphaline butterflies.
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Affiliation(s)
- Doekele G Stavenga
- Computational Physics, Zernike Institute for Advanced Materials, University of Groningen, NL-9747 AG Groningen, The Netherlands
| | - Hein L Leertouwer
- Computational Physics, Zernike Institute for Advanced Materials, University of Groningen, NL-9747 AG Groningen, The Netherlands
| | - Bodo D Wilts
- Computational Physics, Zernike Institute for Advanced Materials, University of Groningen, NL-9747 AG Groningen, The Netherlands
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19
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Croucher PJP, Brewer MS, Winchell CJ, Oxford GS, Gillespie RG. De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes. BMC Genomics 2013; 14:862. [PMID: 24314324 PMCID: PMC3878950 DOI: 10.1186/1471-2164-14-862] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 11/25/2013] [Indexed: 12/17/2022] Open
Abstract
Background A number of spider species within the family Theridiidae exhibit a dramatic abdominal (opisthosomal) color polymorphism. The polymorphism is inherited in a broadly Mendelian fashion and in some species consists of dozens of discrete morphs that are convergent across taxa and populations. Few genomic resources exist for spiders. Here, as a first necessary step towards identifying the genetic basis for this trait we present the near complete transcriptomes of two species: the Hawaiian happy-face spider Theridion grallator and Theridion californicum. We mined the gene complement for pigment-pathway genes and examined differential expression (DE) between morphs that are unpatterned (plain yellow) and patterned (yellow with superimposed patches of red, white or very dark brown). Results By deep sequencing both RNA-seq and normalized cDNA libraries from pooled specimens of each species we were able to assemble a comprehensive gene set for both species that we estimate to be 98-99% complete. It is likely that these species express more than 20,000 protein-coding genes, perhaps 4.5% (ca. 870) of which might be unique to spiders. Mining for pigment-associated Drosophila melanogaster genes indicated the presence of all ommochrome pathway genes and most pteridine pathway genes and DE analyses further indicate a possible role for the pteridine pathway in theridiid color patterning. Conclusions Based upon our estimates, T. grallator and T. californicum express a large inventory of protein-coding genes. Our comprehensive assembly illustrates the continuing value of sequencing normalized cDNA libraries in addition to RNA-seq in order to generate a reference transcriptome for non-model species. The identification of pteridine-related genes and their possible involvement in color patterning is a novel finding in spiders and one that suggests a biochemical link between guanine deposits and the pigments exhibited by these species.
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Affiliation(s)
- Peter J P Croucher
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720-3114, USA.
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20
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Structure, biosynthesis and possible function of tunichromes and related compounds. Comp Biochem Physiol B Biochem Mol Biol 2012; 163:1-25. [PMID: 22580032 DOI: 10.1016/j.cbpb.2012.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 01/26/2023]
Abstract
Several species of ascidians (phylum Chordata, subphylum Urochordata) contain a group of oligopeptides called "tunichromes" in their blood cells. These peptides have been implicated in (a) metal chelation and accumulation/sequestration of vanadium or iron; (b) crosslinking of structural fibers in tunic formation, (c) wound healing and (d) defense reactions. However, their biosynthesis, metabolism, and biological function remain largely un-elucidated due to their extreme instability and high reactivity. Tunichromes and related compounds uniquely possess dehydrodopamine moieties, all originating from post-translational modification of peptidyl tyrosine. It is conceivable that the presence of such novel post-translationally modified groups provide attributes that are crucial for their biological roles. Therefore, we examined the chemistry and reactivity of tunichromes in light of the available knowledge of the biochemistry of simple monomeric dehydro-N-acyldopamine units. Based on the reactivity of such simple compounds, the potential biological activities of tunichromes are predicted. Their possible biosynthetic route from peptidyl tyrosine is critically evaluated to provide a better basis for unraveling their biological functions. Prevalence of dehydro-N-acyldopamine units in different tunichromes, some marine antibiotic compounds, insect cuticular sclerotizing precursors and some bioadhesive marine proteins may aid in the de novo design of unique biomaterials with potential antibiotic/adhesive properties.
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21
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Esposito R, D'Aniello S, Squarzoni P, Pezzotti MR, Ristoratore F, Spagnuolo A. New insights into the evolution of metazoan tyrosinase gene family. PLoS One 2012; 7:e35731. [PMID: 22536431 PMCID: PMC3334994 DOI: 10.1371/journal.pone.0035731] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 03/24/2012] [Indexed: 11/19/2022] Open
Abstract
Tyrosinases, widely distributed among animals, plants and fungi, are involved in the biosynthesis of melanin, a pigment that has been exploited, in the course of evolution, to serve different functions. We conducted a deep evolutionary analysis of tyrosinase family amongst metazoa, thanks to the availability of new sequenced genomes, assessing that tyrosinases (tyr) represent a distinctive feature of all the organisms included in our study and, interestingly, they show an independent expansion in most of the analyzed phyla. Tyrosinase-related proteins (tyrp), which derive from tyr but show distinct key residues in the catalytic domain, constitute an invention of chordate lineage. In addition we here reported a detailed study of the expression territories of the ascidian Ciona intestinalis tyr and tyrps. Furthermore, we put efforts in the identification of the regulatory sequences responsible for their expression in pigment cell lineage. Collectively, the results reported here enlarge our knowledge about the tyrosinase gene family as valuable resource for understanding the genetic components involved in pigment cells evolution and development.
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Affiliation(s)
| | | | | | | | | | - Antonietta Spagnuolo
- Cellular and Developmental Biology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
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22
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Abstract
Many of the features that distinguish the vertebrates from other chordates are derived from the neural crest, and it has long been argued that the emergence of this multipotent embryonic population was a key innovation underpinning vertebrate evolution. More recently, however, a number of studies have suggested that the evolution of the neural crest was less sudden than previously believed. This has exposed the fact that neural crest, as evidenced by its repertoire of derivative cell types, has evolved through vertebrate evolution. In this light, attempts to derive a typological definition of neural crest, in terms of molecular signatures or networks, are unfounded. We propose a less restrictive, embryological definition of this cell type that facilitates, rather than precludes, investigating the evolution of neural crest. While the evolutionary origin of neural crest has attracted much attention, its subsequent evolution has received almost no attention and yet it is more readily open to experimental investigation and has greater relevance to understanding vertebrate evolution. Finally, we provide a brief outline of how the evolutionary emergence of neural crest potentiality may have proceeded, and how it may be investigated.
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23
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Jeffery WR. Chordate ancestry of the neural crest: New insights from ascidians. Semin Cell Dev Biol 2007; 18:481-91. [PMID: 17509911 DOI: 10.1016/j.semcdb.2007.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 01/31/2007] [Accepted: 04/10/2007] [Indexed: 11/29/2022]
Abstract
This article reviews new insights from ascidians on the ancestry of vertebrate neural crest (NC) cells. Ascidians have neural crest-like cells (NCLC), which migrate from the dorsal midline, express some of the typical NC markers, and develop into body pigment cells. These characters suggest that primordial NC cells were already present in the common ancestor of the vertebrates and urochordates, which have been recently inferred as sister groups. The primitive role of NCLC may have been in pigment cell dispersal and development. Later, additional functions may have appeared in the vertebrate lineage, resulting in the evolution of definitive NC cells.
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Affiliation(s)
- William R Jeffery
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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24
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Braasch I, Schartl M, Volff JN. Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol 2007. [PMID: 17498288 DOI: 10.1186/1471-2148-7-74.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coloration and color patterning belong to the most diverse phenotypic traits in animals. Particularly, teleost fishes possess more pigment cell types than any other group of vertebrates. As the result of an ancient fish-specific genome duplication (FSGD), teleost genomes might contain more copies of genes involved in pigment cell development than tetrapods. No systematic genomic inventory allowing to test this hypothesis has been drawn up so far for pigmentation genes in fish, and almost nothing is known about the evolution of these genes in different fish lineages. RESULTS Using a comparative genomic approach including phylogenetic reconstructions and synteny analyses, we have studied two major pigment synthesis pathways in teleost fish, the melanin and the pteridine pathways, with respect to different types of gene duplication. Genes encoding three of the four enzymes involved in the synthesis of melanin from tyrosine have been retained as duplicates after the FSGD. In the pteridine pathway, two cases of duplicated genes originating from the FSGD as well as several lineage-specific gene duplications were observed. In both pathways, genes encoding the rate-limiting enzymes, tyrosinase and GTP-cyclohydrolase I (GchI), have additional paralogs in teleosts compared to tetrapods, which have been generated by different modes of duplication. We have also observed a previously unrecognized diversity of gchI genes in vertebrates. In addition, we have found evidence for divergent resolution of duplicated pigmentation genes, i.e., differential gene loss in divergent teleost lineages, particularly in the tyrosinase gene family. CONCLUSION Mainly due to the FSGD, teleost fishes apparently have a greater repertoire of pigment synthesis genes than any other vertebrate group. Our results support an important role of the FSGD and other types of duplication in the evolution of pigmentation in fish.
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Affiliation(s)
- Ingo Braasch
- University of Würzburg, Physiological Chemistry I, Biozentrum, Am Hubland, Würzburg, Germany.
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25
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Braasch I, Schartl M, Volff JN. Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol 2007; 7:74. [PMID: 17498288 PMCID: PMC1890551 DOI: 10.1186/1471-2148-7-74] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 05/11/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coloration and color patterning belong to the most diverse phenotypic traits in animals. Particularly, teleost fishes possess more pigment cell types than any other group of vertebrates. As the result of an ancient fish-specific genome duplication (FSGD), teleost genomes might contain more copies of genes involved in pigment cell development than tetrapods. No systematic genomic inventory allowing to test this hypothesis has been drawn up so far for pigmentation genes in fish, and almost nothing is known about the evolution of these genes in different fish lineages. RESULTS Using a comparative genomic approach including phylogenetic reconstructions and synteny analyses, we have studied two major pigment synthesis pathways in teleost fish, the melanin and the pteridine pathways, with respect to different types of gene duplication. Genes encoding three of the four enzymes involved in the synthesis of melanin from tyrosine have been retained as duplicates after the FSGD. In the pteridine pathway, two cases of duplicated genes originating from the FSGD as well as several lineage-specific gene duplications were observed. In both pathways, genes encoding the rate-limiting enzymes, tyrosinase and GTP-cyclohydrolase I (GchI), have additional paralogs in teleosts compared to tetrapods, which have been generated by different modes of duplication. We have also observed a previously unrecognized diversity of gchI genes in vertebrates. In addition, we have found evidence for divergent resolution of duplicated pigmentation genes, i.e., differential gene loss in divergent teleost lineages, particularly in the tyrosinase gene family. CONCLUSION Mainly due to the FSGD, teleost fishes apparently have a greater repertoire of pigment synthesis genes than any other vertebrate group. Our results support an important role of the FSGD and other types of duplication in the evolution of pigmentation in fish.
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Affiliation(s)
- Ingo Braasch
- University of Würzburg, Physiological Chemistry I, Biozentrum, Am Hubland, 97074 Würzburg, Germany
| | - Manfred Schartl
- University of Würzburg, Physiological Chemistry I, Biozentrum, Am Hubland, 97074 Würzburg, Germany
| | - Jean-Nicolas Volff
- University of Würzburg, Physiological Chemistry I, Biozentrum, Am Hubland, 97074 Würzburg, Germany
- Institut de Génomique Fonctionnelle, Université de Lyon, F-69003, France, INRA; CNRS, Université Lyon 1, Ecole Normale Supérieure, F-69364, France
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Jeffery WR. Ascidian neural crest-like cells: phylogenetic distribution, relationship to larval complexity, and pigment cell fate. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2006; 306:470-80. [PMID: 16619245 DOI: 10.1002/jez.b.21109] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Migratory neural crest-like cells, which express the cell surface antigen HNK-1 and develop into pigment cells, have recently been identified in the ascidian Ecteinascidia turbinata. Here we use HNK-1 expression as a marker to determine whether neural crest-like cells are responsible for pigment development in diverse ascidian species. We surveyed HNK-1 expression and tyrosinase activity in 12 ascidian species, including those with different adult organizations, developmental modes, and larval sizes and complexities. We observed HNK-1 positive cells in every species, although the timing of HNK-1 expression varied according to the extent of larval complexity. HNK-1 expression was initiated during the late tailbud stage in species in which adult features are formed precociously in large complex larvae. In contrast, HNK-1 positive cells did not appear until the swimming tadpole or juvenile stage in species with small simple larvae in which most adult features appear after metamorphosis. Double labeling experiments indicated that HNK-1 and tyrosinase are expressed in the same subset of pigment-forming mesenchymal cells in species with complex or simple larvae. In addition, the absence of HNK-1 and tyrosinase expression in albino morphs of the colonial ascidian Botryllus schlosseri suggested that the major fate of neural crest-like cells is to become pigment cells. The results suggest that ascidian neural crest-like cells and vertebrate neural crest cells had a common origin during chordate evolution and that their primitive function was to generate body pigmentation.
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Affiliation(s)
- William R Jeffery
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
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Abstract
This year is the centenary of Edward G. Conklin's signal findings in embryology: the elucidation of complete cell lineages and the discovery of localized maternal determinants. Conklin used ascidian embryos to elucidate universal principles in embryology. A century later, ascidians, or sea squirts, have not only entered the post-genome era, but in many ways are leading the way to the promise of a "systems-level" understanding of complex processes such as notochord formation, neurogenesis, and even behavior.
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Affiliation(s)
- Nori Satoh
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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