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Brandon AA, Michael C, Carmona Baez A, Moore EC, Ciccotto PJ, Roberts NB, Roberts RB, Powder KE. Distinct genetic origins of eumelanin levels and barring patterns in cichlid fishes. PLoS One 2024; 19:e0306614. [PMID: 38976656 PMCID: PMC11230561 DOI: 10.1371/journal.pone.0306614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Pigment patterns are incredibly diverse across vertebrates and are shaped by multiple selective pressures from predator avoidance to mate choice. A common pattern across fishes, but for which we know little about the underlying mechanisms, is repeated melanic vertical bars. To understand the genetic factors that modify the level or pattern of vertical barring, we generated a genetic cross of 322 F2 hybrids between two cichlid species with distinct barring patterns, Aulonocara koningsi and Metriaclima mbenjii. We identify 48 significant quantitative trait loci that underlie a series of seven phenotypes related to the relative pigmentation intensity, and four traits related to patterning of the vertical bars. We find that genomic regions that generate variation in the level of eumelanin produced are largely independent of those that control the spacing of vertical bars. Candidate genes within these intervals include novel genes and those newly-associated with vertical bars, which could affect melanophore survival, fate decisions, pigment biosynthesis, and pigment distribution. Together, this work provides insights into the regulation of pigment diversity, with direct implications for an animal's fitness and the speciation process.
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Affiliation(s)
- A. Allyson Brandon
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Cassia Michael
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Aldo Carmona Baez
- Department of Biological Sciences, Genetics and Genomics Academy, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Emily C. Moore
- Department of Biological Sciences, Genetics and Genomics Academy, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Patrick J. Ciccotto
- Department of Biology, Warren Wilson College, Swannanoa, North Carolina, United States of America
| | - Natalie B. Roberts
- Department of Biological Sciences, Genetics and Genomics Academy, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Reade B. Roberts
- Department of Biological Sciences, Genetics and Genomics Academy, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Kara E. Powder
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
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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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3
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Mandal RN, Ke J, Kanika NH, Wang F, Wang J, Wang C. Regulatory gene network for coffee-like color morph of TYRP1 mutant of oujiang color common carp. BMC Genomics 2024; 25:659. [PMID: 38956500 PMCID: PMC11218255 DOI: 10.1186/s12864-024-10550-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Neither a TYRP1-mediated highly conserved genetic network underlying skin color towards optimum defense nor the pathological tendency of its mutation is well understood. The Oujiang Color Common Carp (Cyprinus carpio var. color) as a model organism, offering valuable insights into genetics, coloration, aquaculture practices, and environmental health. Here, we performed a comparative skin transcriptome analysis on TYRP1 mutant and wild fishes by applying a conservative categorical approach considering different color phenotypes. RESULTS Our results reveal that an unusual color phenotype may be sensitized with TYRP1 mutation as a result of upregulating several genes related to an anti-inflammatory autoimmune system in response to the COMT-mediated catecholamine neurotransmitters in the skin. Particularly, catecholamines-derived red/brown, red with blue colored membrane attack complex, and brown/grey colored reduced eumelanin are expected to be aggregated in the regenerated cells. CONCLUSIONS It is, thus, concluded that the regenerated cells with catecholamines, membrane attack complex, and eumelanin altogether may contribute to the formation of the unusual (coffee-like) color phenotype in TYRP1 mutant.
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Affiliation(s)
- Roland Nathan Mandal
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated By the Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Aquaculture, National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jing Ke
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated By the Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Aquaculture, National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Nusrat Hasan Kanika
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated By the Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Aquaculture, National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Fuyan Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated By the Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Aquaculture, National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated By the Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Aquaculture, National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
- College of Fisheries and Life Sciences, Shanghai Ocean University, 999, Huchenghuan Road, Shanghai, 201306, China.
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated By the Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Aquaculture, National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
- College of Fisheries and Life Sciences, Shanghai Ocean University, 999, Huchenghuan Road, Shanghai, 201306, China.
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4
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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 2024; 33:e17438. [PMID: 38923007 DOI: 10.1111/mec.17438] [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: 07/13/2023] [Revised: 04/22/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024]
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 species share a 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 mimicry is produced in poison frogs. We assembled a 6.02-Gbp genome with a contig N50 of 310 Kbp, a scaffold N50 of 390 Kbp and 85% of expected tetrapod genes. We leveraged this genome to conduct gene expression analyses throughout development of four colour morphs of Ranitomeya imitator and two colour morphs from both R. fantastica and R. variabilis which R. imitator mimics. We identified a large number of pigmentation and patterning genes differentially expressed throughout development, many of them related to melanophores/melanin, iridophore development and guanine synthesis. We also 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, and identify several plausible candidates for colouration in vertebrates (e.g. cd36, ep-cadherin and perlwapin). Finally, we hypothesise that keratin genes (e.g. krt8) are important for producing different structural colours within these frogs.
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Affiliation(s)
- Adam M M Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Mathieu Chouteau
- Laboratoire Écologie, Évolution, Interactions Des Systèmes Amazoniens (LEEISA), CNRS, IFREMER, Université de Guyane, Cayenne, France
| | - Melanie McClure
- Laboratoire Écologie, Évolution, Interactions Des Systèmes Amazoniens (LEEISA), CNRS, IFREMER, Université de Guyane, Cayenne, France
| | - Troy M LaPolice
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tyler Linderoth
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Kyle Summers
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Matthew D MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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5
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Crowell HL, Curlis JD, Weller HI, Davis Rabosky AR. Ecological drivers of ultraviolet colour evolution in snakes. Nat Commun 2024; 15:5213. [PMID: 38890335 PMCID: PMC11189474 DOI: 10.1038/s41467-024-49506-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Ultraviolet (UV) colour patterns invisible to humans are widespread in nature. However, research bias favouring species with conspicuous colours under sexual selection can limit our assessment of other ecological drivers of UV colour, like interactions between predators and prey. Here we demonstrate widespread UV colouration across Western Hemisphere snakes and find stronger support for a predator defence function than for reproduction. We find that UV colouration has evolved repeatedly in species with ecologies most sensitive to bird predation, with no sexual dichromatism at any life stage. By modelling visual systems of potential predators, we find that snake conspicuousness correlates with UV colouration and predator cone number, providing a plausible mechanism for selection. Our results suggest that UV reflectance should not be assumed absent in "cryptically coloured" animals, as signalling beyond human visual capacities may be a key outcome of species interactions in many taxa for which UV colour is likely underreported.
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Affiliation(s)
- Hayley L Crowell
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, MI, 48109, USA
| | - John David Curlis
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hannah I Weller
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI, 02912, USA
- Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Uusimaa, 00790, Finland
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, MI, 48109, USA.
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6
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Li Z, Wang X, Guan L, Liu M, Wang H, Wu D, Yi X, Jian S, Sheng J. Molecular characterization, spatiotemporal expression, and background adaptation regulation of tyrosinase in loach (Misgurnus anguillicaudatus). JOURNAL OF FISH BIOLOGY 2024. [PMID: 38852940 DOI: 10.1111/jfb.15822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 04/29/2024] [Accepted: 05/14/2024] [Indexed: 06/11/2024]
Abstract
The Poyang Lake region is home to large-blackspot loaches (LBL), small-blackspot loaches (SBL), and non-blackspot loaches (NBL), Misgurnus anguillicaudatus. To investigate the impact of tyrosinase on spot development, the complementary DNAs (cDNA) of tyrosinase in M. anguillicaudatus (designated as Matyr) were cloned using the rapid amplification of cDNA ends (RACE)-PCR method. The full-length cDNA for Matyr was 2020 bp, and the open-reading frame comprised 1617 bp, encoding a predicted protein with 538 amino acids. Phylogenetic studies revealed that MaTyr was first grouped with Tyr of Triplophysa tibetana and Leptobotia taeniops, and then Tyr of other cyprinid fish. The quantitative reverse-transcription-PCR results show that Matyr was highly expressed in the muscle, caudal fin, and dorsal skin. The Matyr gene's messenger RNA expression pattern steadily increased from the fertilized ovum period to the somitogenesis period, and from the muscle effect stage to 6 days after fertilization, it considerably increased (p < 0.01). The Matyr hybridization signals with similar location could be found in all developmental stages of three kinds of loaches using whole-mount in situ hybridization (WISH) technology and were the strongest during the organ development period and melanin formation period. Dot hybridization signals in LBLs rapidly spread to the back of the body beginning at the period when the eyes first formed melanin, and their dimensions were larger than those of NBLs during the same time period. The body color of loaches could change reversibly with black/white background adaptation. The α-msh, mitfa, and tyr are mainly expressed in loaches adapted with a black background. Tyr gene could be involved in the development of blackspots and body color polymorphism, and contribute to organ development in the loach.
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Affiliation(s)
- Zhixiong Li
- Key Laboratory for Aquatic Germplasm Innovation and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Xinchen Wang
- Key Laboratory for Aquatic Germplasm Innovation and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Le Guan
- Key Laboratory for Aquatic Germplasm Innovation and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Muxin Liu
- Key Laboratory for Aquatic Germplasm Innovation and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Hong Wang
- Key Laboratory for Aquatic Germplasm Innovation and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Di Wu
- Key Laboratory for Aquatic Germplasm Innovation and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Xiaobing Yi
- Jiangxi Jiacheng Loach Breeding Base, Yichun, China
| | - Shaoqing Jian
- Key Laboratory for Aquatic Germplasm Innovation and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Junqing Sheng
- Key Laboratory for Aquatic Germplasm Innovation and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
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Chen J, Wang H, Wu S, Zhang A, Qiu Z, Huang P, Qu JY, Xu J. col1a2+ fibroblasts/muscle progenitors finetune xanthophore countershading by differentially expressing csf1a/1b in embryonic zebrafish. SCIENCE ADVANCES 2024; 10:eadj9637. [PMID: 38578990 PMCID: PMC10997200 DOI: 10.1126/sciadv.adj9637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/29/2024] [Indexed: 04/07/2024]
Abstract
Animals evolve diverse pigment patterns to adapt to the natural environment. Countershading, characterized by a dark-colored dorsum and a light-colored ventrum, is one of the most prevalent pigment patterns observed in vertebrates. In this study, we reveal a mechanism regulating xanthophore countershading in zebrafish embryos. We found that csf1a and csf1b mutants altered xanthophore countershading differently: csf1a mutants lack ventral xanthophores, while csf1b mutants have reduced dorsal xanthophores. Further study revealed that csf1a is expressed throughout the trunk, whereas csf1b is expressed dorsally. Ectopic expression of csf1a or csf1b in neurons attracted xanthophores into the spinal cord. Blocking csf1 signaling by csf1ra mutants disrupts spinal cord distribution and normal xanthophores countershading. Single-cell RNA sequencing identified two col1a2+ populations: csf1ahighcsf1bhigh muscle progenitors and csf1ahighcsf1blow fibroblast progenitors. Ablation of col1a2+ fibroblast and muscle progenitors abolished xanthophore patterns. Our study suggests that fibroblast and muscle progenitors differentially express csf1a and csf1b to modulate xanthophore patterning, providing insights into the mechanism of countershading.
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Affiliation(s)
- Jiahao Chen
- Department of Neurology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Honggao Wang
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Shuting Wu
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Ao Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PRC
| | - Zhongkai Qiu
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Peng Huang
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jianan Y Qu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Kowloon, China
| | - Jin Xu
- Department of Neurology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
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8
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Liu S, Wang S, Zhao L, Li T, Zhang Y, Wang H, Bao Z, Hu X. Functional Analysis of β-Carotene Oxygenase 2 ( BCO2) Gene in Yesso Scallop ( Patinopecten yessoensis). Int J Mol Sci 2024; 25:3947. [PMID: 38612756 PMCID: PMC11012205 DOI: 10.3390/ijms25073947] [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: 02/22/2024] [Revised: 03/23/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Carotenoids are essential nutrients for humans and animals, and carotenoid coloration represents an important meat quality parameter for many farmed animals. Increasingly, studies have demonstrated that vertebrate carotenoid cleavage oxygenases (CCOs) are essential enzymes in carotenoid metabolism and are therefore potential candidate genes for improving carotenoid deposition. However, our understanding of carotenoid bioavailability and CCOs functions in invertebrates, particularly marine species, is currently quite limited. We previously identified that a CCO homolog, PyBCO-like 1, was the causal gene for carotenoid coloration in the 'Haida golden scallop', a variety of Yesso scallop (Patinopecten yessoensis) characterized by carotenoid enrichment. Here, we found that another CCO-encoding gene named PyBCO2 (β-carotene oxygenase 2) was widely expressed in P. yessoensis organs/tissues, with the highest expression in striated muscle. Inhibiting BCO2 expression in P. yessoensis through RNA interference led to increased carotenoid (pectenolone and pectenoxanthin) deposition in the striated muscle, and the color of the striated muscle changed from white to light orange. Our results indicate that PyBCO2 might be a candidate gene used for improving carotenoid content in normal Yesso scallops, and also in 'Haida golden scallops'.
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Affiliation(s)
- Shiqi Liu
- MOE Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (S.L.); (S.W.); (Y.Z.)
| | - Shuyue Wang
- MOE Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (S.L.); (S.W.); (Y.Z.)
| | - Liang Zhao
- MOE Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (S.L.); (S.W.); (Y.Z.)
| | - Tingting Li
- MOE Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (S.L.); (S.W.); (Y.Z.)
| | - Yihan Zhang
- MOE Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (S.L.); (S.W.); (Y.Z.)
| | - Huizhen Wang
- MOE Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (S.L.); (S.W.); (Y.Z.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhenmin Bao
- MOE Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (S.L.); (S.W.); (Y.Z.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Xiaoli Hu
- MOE Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (S.L.); (S.W.); (Y.Z.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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9
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Gong LL, Zhang MQ, Ma YF, Feng HY, Zhao YQ, Zhou YY, He M, Smagghe G, He P. RNAi of yellow-y, required for normal cuticle pigmentation, impairs courtship behavior and oviposition in the German cockroach (Blattella germanica). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22114. [PMID: 38659314 DOI: 10.1002/arch.22114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
The insect cuticle plays a key role in maintaining the insect's physiological function and behavior. Herein, the yellow-y protein is required to produce black melanin, and is expressed in a pattern that correlates with the distribution of this pigment. However, yellow-y can also have other functions, for instance, in insect behavior, but not much is known. In this study, we have studied the yellow-y gene in one important model and pest species, namely the German cockroach (Blattella germanica), which is to our knowledge the first time reported. In essence, we identified the yellow-y gene (BgY-y) and characterized its function by using RNA interference (RNAi). Silencing of BgY-y gene led to different developmental abnormalities (body weight and wings) in both genders. Specifically, there was an abundant decrease in melanin, turning the body color in pale yellow and the cuticle softer and more transparent. Interestingly, we also observed that the knockdown of BgY-y impaired the male cockroaches to display a weaker response to female-emitted contact sex pheromones, and also that the oviposition ability was weakened in the RNAi females. This study comprehensively analyzed the biological functions of the yellow-y gene in German cockroaches from the perspectives of development, body color, courtship behavior and oviposition, and as a consequence, this may opens new avenues to explore it as a novel pest control gene.
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Affiliation(s)
- Lang-Lang Gong
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Meng-Qi Zhang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Yun-Feng Ma
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Hong-Yan Feng
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Ya-Qin Zhao
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Yang-Yuntao Zhou
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Ming He
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Guy Smagghe
- Institute Entomology, Guizhou University, Guiyang, China
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Peng He
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
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10
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Ozerov MY, Noreikiene K, Kahar S, Flajšhans M, Gross R, Vasemägi A. Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis). Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110941. [PMID: 38218377 DOI: 10.1016/j.cbpb.2024.110941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multi-tissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.
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Affiliation(s)
- M Y Ozerov
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893 Drottningholm, Sweden; Biodiversity Unit, University of Turku, 20014 Turku, Finland; Department of Biology, University of Turku, 20014 Turku, Finland
| | - K Noreikiene
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia; Department of Botany and Genetics, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania. https://twitter.com/snaudale
| | - S Kahar
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - M Flajšhans
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, 38925 Vodňany, Czech Republic
| | - R Gross
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - A Vasemägi
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893 Drottningholm, Sweden; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia.
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11
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Min Y, Li Q, Yu H, Kong L, Liu S. Comparative transcriptome elucidates key genes and pathways related to golden phenotype of Crassostrea gigas. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101197. [PMID: 38295536 DOI: 10.1016/j.cbd.2024.101197] [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: 09/26/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/02/2024]
Abstract
Marine bivalves are economically important and exhibit a remarkable diversity in shell color. The Pacific oyster Crassostrea gigas stands out as an important economic species, with the successful development of four distinct color strains through selective breeding. While previous studies have shed light on the genetic mechanism underlying color segregation, the precise molecular regulatory mechanisms responsible for shell coloration in oysters remains elusive. In this study, we confirmed that the golden phenotype is primarily attributed to pheomelanin by histological and ultrastructural observations. Additionally, we conducted a comparative transcriptome analysis of the black and golden shell color oysters to explore the potential genes and pathways contributing to the golden phenotype in C. gigas. Our results revealed a significant increase in differentially expressed genes in the golden phenotype associated with pathways such as glutathione metabolism, and calcium signaling pathway, suggesting a potential role in the synthesis of pheomelanin. Of particular note, we highlighted the potential role of two-pore channel 2 (TPC2) in modulating tyrosinase activity and melanosomal pH, ultimately determining the shade of pigmentation. Our study in this work provided a preliminary exploration of the mechanism, shedding light on the melanosome microenvironment and shell color.
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Affiliation(s)
- Yue Min
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao 266003, China; College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao 266003, China; College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao 266003, China; College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao 266003, China; College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao 266003, China; College of Fisheries, Ocean University of China, Qingdao 266003, China
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12
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Cavigliasso F, Savitsky M, Koval A, Erkosar B, Savary L, Gallart-Ayala H, Ivanisevic J, Katanaev VL, Kawecki TJ. Cis-regulatory polymorphism at fiz ecdysone oxidase contributes to polygenic evolutionary response to malnutrition in Drosophila. PLoS Genet 2024; 20:e1011204. [PMID: 38452112 PMCID: PMC10962836 DOI: 10.1371/journal.pgen.1011204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/25/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024] Open
Abstract
We investigate the contribution of a candidate gene, fiz (fezzik), to complex polygenic adaptation to juvenile malnutrition in Drosophila melanogaster. Experimental populations maintained for >250 generations of experimental evolution to a nutritionally poor larval diet (Selected populations) evolved several-fold lower fiz expression compared to unselected Control populations. Here we show that this divergence in fiz expression is mediated by a cis-regulatory polymorphism. This polymorphism, originally sampled from a natural population in Switzerland, is distinct from a second cis-regulatory SNP previously identified in non-African D. melanogaster populations, implying that two independent cis-regulatory variants promoting high fiz expression segregate in non-African populations. Enzymatic analyses of Fiz protein expressed in E. coli demonstrate that it has ecdysone oxidase activity acting on both ecdysone and 20-hydroxyecdysone. Four of five fiz paralogs annotated to ecdysteroid metabolism also show reduced expression in Selected larvae, implying that malnutrition-driven selection favored general downregulation of ecdysone oxidases. Finally, as an independent test of the role of fiz in poor diet adaptation, we show that fiz knockdown by RNAi results in faster larval growth on the poor diet, but at the cost of greatly reduced survival. These results imply that downregulation of fiz in Selected populations was favored by selection on the nutritionally poor diet because of its role in suppressing growth in response to nutrient shortage. However, they suggest that fiz downregulation is only adaptive in combination with other changes evolved by Selected populations, which ensure that the organism can sustain the faster growth promoted by fiz downregulation.
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Affiliation(s)
- Fanny Cavigliasso
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Mikhail Savitsky
- HumanaFly Facility, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Alexey Koval
- Translational Research Centre in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Berra Erkosar
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Loriane Savary
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Hector Gallart-Ayala
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Vladimir L. Katanaev
- Translational Research Centre in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Tadeusz J. Kawecki
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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Lu B, Qiu X, Yang W, Yao Z, Ma X, Deng S, Zhang Q, Fu J, Qi Y. Genetic Basis and Evolutionary Forces of Sexually Dimorphic Color Variation in a Toad-Headed Agamid Lizard. Mol Biol Evol 2024; 41:msae054. [PMID: 38466135 PMCID: PMC10963123 DOI: 10.1093/molbev/msae054] [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: 09/13/2023] [Revised: 02/17/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024] Open
Abstract
In the animal kingdom, sexually dimorphic color variation is a widespread phenomenon that significantly influences survival and reproductive success. However, the genetic underpinnings of this variation remain inadequately understood. Our investigation into sexually dimorphic color variation in the desert-dwelling Guinan population of the toad-headed agamid lizard (Phrynocephalus putjatai) utilized a multidisciplinary approach, encompassing phenotypic, ultrastructural, biochemical, genomic analyses, and behavioral experiments. Our findings unveil the association between distinct skin colorations and varying levels of carotenoid and pteridine pigments. The red coloration in males is determined by a genomic region on chromosome 14, housing four pigmentation genes: BCO2 and three 6-pyruvoyltetrahydropterin synthases. A Guinan population-specific nonsynonymous single nucleotide polymorphism in BCO2 is predicted to alter the electrostatic potential within the binding domain of the BCO2-β-carotene complex, influencing their interaction. Additionally, the gene MAP7 on chromosome 2 emerges as a potential contributor to the blue coloration in subadults and adult females. Sex-specific expression patterns point to steroid hormone-associated genes (SULT2B1 and SRD5A2) as potential upstream regulators influencing sexually dimorphic coloration. Visual modeling and field experiments support the potential selective advantages of vibrant coloration in desert environments. This implies that natural selection, potentially coupled with assortative mating, might have played a role in fixing color alleles, contributing to prevalence in the local desert habitat. This study provides novel insights into the genetic basis of carotenoid and pteridine-based color variation, shedding light on the evolution of sexually dimorphic coloration in animals. Moreover, it advances our understanding of the driving forces behind such intricate coloration patterns.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Xia Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Weizhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Zhongyi Yao
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Xiaofeng Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Shunyan Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Qi Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Yin Qi
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
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14
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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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15
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Kambal S, Tijjani A, Ibrahim SAE, Ahmed MKA, Mwacharo JM, Hanotte O. Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review. Anim Genet 2023; 54:689-708. [PMID: 37697736 DOI: 10.1111/age.13353] [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: 07/28/2023] [Revised: 07/28/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.
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Affiliation(s)
- Sumaya Kambal
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Sabah A E Ibrahim
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Mohamed-Khair A Ahmed
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Joram M Mwacharo
- Scotland's Rural College and Centre for Tropical Livestock Genetics and Health, Edinburgh, UK
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
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16
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Liao Y, Shi H, Han T, Jiang D, Lu B, Shi G, Zhu C, Li G. Pigment Identification and Gene Expression Analysis during Erythrophore Development in Spotted Scat ( Scatophagus argus) Larvae. Int J Mol Sci 2023; 24:15356. [PMID: 37895036 PMCID: PMC10607709 DOI: 10.3390/ijms242015356] [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: 09/02/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Red coloration is considered an economically important trait in some fish species, including spotted scat, a marine aquaculture fish. Erythrophores are gradually covered by melanophores from the embryonic stage. Despite studies of black spot formation and melanophore coloration in the species, little is known about erythrophore development, which is responsible for red coloration. 1-phenyl 2-thiourea (PTU) is a tyrosinase inhibitor commonly used to inhibit melanogenesis and contribute to the visualization of embryonic development. In this study, spotted scat embryos were treated with 0.003% PTU from 0 to 72 h post fertilization (hpf) to inhibit melanin. Erythrophores were clearly observed during the embryonic stage from 14 to 72 hpf, showing an initial increase (14 to 36 hpf), followed by a gradual decrease (36 to 72 hpf). The number and size of erythrophores at 36 hpf were larger than those at 24 and 72 hpf. At 36 hpf, LC-MS and absorbance spectrophotometry revealed that the carotenoid content was eight times higher than the pteridine content, and β-carotene and lutein were the main pigments related to red coloration in spotted scat larvae. Compared with their expression in the normal hatching group, rlbp1b, rbp1.1, and rpe65a related to retinol metabolism and soat2 and apoa1 related to steroid hormone biosynthesis and steroid biosynthesis were significantly up-regulated in the PTU group, and rh2 associated with phototransduction was significantly down-regulated. By qRT-PCR, the expression levels of genes involved in carotenoid metabolism (scarb1, plin6, plin2, apoda, bco1, and rep65a), pteridine synthesis (gch2), and chromatophore differentiation (slc2a15b and csf1ra) were significantly higher at 36 hpf than at 24 hpf and 72 hpf, except for bco1. These gene expression profiles were consistent with the developmental changes of erythrophores. These findings provide insights into pigment cell differentiation and gene function in the regulation of red coloration and contribute to selective breeding programs for ornamental aquatic animals.
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Affiliation(s)
- Yongguan Liao
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (H.S.); (T.H.); (D.J.); (G.S.); (C.Z.)
| | - Hongjuan Shi
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (H.S.); (T.H.); (D.J.); (G.S.); (C.Z.)
| | - Tong Han
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (H.S.); (T.H.); (D.J.); (G.S.); (C.Z.)
| | - Dongneng Jiang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (H.S.); (T.H.); (D.J.); (G.S.); (C.Z.)
| | - Baoyue Lu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China;
| | - Gang Shi
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (H.S.); (T.H.); (D.J.); (G.S.); (C.Z.)
| | - Chunhua Zhu
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (H.S.); (T.H.); (D.J.); (G.S.); (C.Z.)
| | - Guangli Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (H.S.); (T.H.); (D.J.); (G.S.); (C.Z.)
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17
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Xu Z, Lin T, Wang T, Hu Y, Shen G, Feng K, Zhang P, He L. Uridine Diphosphate Glycosyltransferases (UGTs) Involved in the Carotenoid-Based Body Color Difference between Tetranychus cinnabarinus (Red) and Tetranychus urticae (Green). INSECTS 2023; 14:823. [PMID: 37887835 PMCID: PMC10607543 DOI: 10.3390/insects14100823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
It has long been disputed whether Tetranychus cinnabarinus and Tetranychus urticae belong to the same genus, with T. cinnabarinus regarded as a red form of T. urticae. However, it is unclear why T. urticae and T. cinnabarinus have different body colors. Since carotenoids are responsible for the color of many organisms, the carotenoid profiles of T. cinnabarinus and T. urticae were compared by HPLC. There was no difference in carotenoid type, but T. cinnabarinus contained significantly more neoxanthin, astaxanthin, α-carotene, β-carotene, and γ-carotene, which may contribute to the deep red color. The transcriptome sequencing of both species identified 4079 differentially expressed genes (DEGs), of which 12 were related to carotenoid metabolism. RNA interference (RNAi) experiments demonstrated that silencing seven of these DEGs resulted in the different accumulation of carotenoid compounds in T. cinnabarinus and T. urticae. In addition, the body of T. urticae turned yellow after two days of feeding with UGT double-stranded RNAs and β-UGT small interfering RNAs. In conclusion, differences in the carotenoid profiles of T. urticae and T. cinnabarinus may be responsible for the different body colors.
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Affiliation(s)
- Zhifeng Xu
- College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
| | - Ting Lin
- College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
| | - Tongyang Wang
- College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
| | - Yuan Hu
- College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
| | - Guangmao Shen
- College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
| | - Kaiyang Feng
- College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
| | - Ping Zhang
- College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
| | - Lin He
- College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
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18
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Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. PLoS Genet 2023; 19:e1010880. [PMID: 37862332 PMCID: PMC10588866 DOI: 10.1371/journal.pgen.1010880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023] Open
Abstract
Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Audrey Brown
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Elena F. Boer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Atoosa M. Samani
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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19
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Kenyon HL, Martin PR. Color as an Interspecific Badge of Status: A Comparative Test. Am Nat 2023; 202:433-447. [PMID: 37792917 DOI: 10.1086/725916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractAnimals as diverse as cephalopods, insects, fish, and mammals signal social dominance to conspecifics to avoid costly fights. Even though between-species fights may be equally costly, the extent to which dominance signals are used between species is unknown. Here, we test the hypothesis that differences in color are associated with dominance between closely related species that aggressively interact over resources, examining between-species variation in colors that are used in within-species badges of status (black, white, and carotenoid coloration) in a comparative analysis of diverse species of birds. We found that dominant species have more black, on average, than subordinate species, particularly in regions important for aggressive signaling (face, throat, and bill). Furthermore, dominant species were more likely to have more black in comparisons in which the dominant species was similar in size or smaller than the subordinate, suggesting that black may be a more important signal when other signals of dominance (size) are missing. Carotenoid colors (i.e., red, pink, orange, and yellow) were not generally associated with dominance but may signal dominance in some taxonomic groups. White may have opposing functions: white was associated with dominance in species in which black was also associated with dominance but was associated with subordinance in species in which carotenoid-based dominance signals may be used. Overall, these results provide new evidence that colors may function broadly as signals of dominance among competing species. Such signals could help to mediate aggressive interactions among species, thereby reducing some costs of co-occurrence and facilitating coexistence in nature.
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20
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Stroupe S, Martone C, McCann B, Juras R, Kjöllerström HJ, Raudsepp T, Beard D, Davis BW, Derr JN. Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation. G3 (BETHESDA, MD.) 2023; 13:jkad156. [PMID: 37481261 PMCID: PMC10542314 DOI: 10.1093/g3journal/jkad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/24/2023]
Abstract
We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from a F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies. To demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of 3 true albino bison and 44 wild-type pelage color bison. Through the examination of genomic variants fixed in the albino cohort and absent in the controls, we identified a nonsynonymous single nucleotide polymorphism (SNP) mutation on chromosome 29 in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provides a highly robust and informative resource for genomics investigations for this iconic North American species.
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Affiliation(s)
- Sam Stroupe
- Department of Veterinary Pathobiology, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Carly Martone
- Department of Veterinary Pathobiology, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Blake McCann
- National Park Service, Theodore Roosevelt National Park, Medora, ND 58645, USA
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Helena Josefina Kjöllerström
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Donald Beard
- Texas Parks and Wildlife, Caprock Canyons State Park & Trailway, Quitaque, TX 79255, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
- Department of Small Animal Clinical Sciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - James N Derr
- Department of Veterinary Pathobiology, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
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21
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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22
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Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550625. [PMID: 37546953 PMCID: PMC10402103 DOI: 10.1101/2023.07.26.550625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Audrey Brown
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Elena F. Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Atoosa M. Samani
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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23
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Brandon AA, Michael C, Carmona Baez A, Moore EC, Ciccotto PJ, Roberts NB, Roberts RB, Powder KE. Distinct genetic origins of eumelanin intensity and barring patterns in cichlid fishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.02.547430. [PMID: 37461734 PMCID: PMC10349982 DOI: 10.1101/2023.07.02.547430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Pigment patterns are incredibly diverse across vertebrates and are shaped by multiple selective pressures from predator avoidance to mate choice. A common pattern across fishes, but for which we know little about the underlying mechanisms, is repeated melanic vertical bars. In order to understand genetic factors that modify the level or pattern of vertical barring, we generated a genetic cross of 322 F2 hybrids between two cichlid species with distinct barring patterns, Aulonocara koningsi and Metriaclima mbenjii. We identify 48 significant quantitative trait loci that underlie a series of seven phenotypes related to the relative pigmentation intensity, and four traits related to patterning of the vertical bars. We find that genomic regions that generate variation in the level of eumelanin produced are largely independent of those that control the spacing of vertical bars. Candidate genes within these intervals include novel genes and those newly-associated with vertical bars, which could affect melanophore survival, fate decisions, pigment biosynthesis, and pigment distribution. Together, this work provides insights into the regulation of pigment diversity, with direct implications for an animal's fitness and the speciation process.
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Affiliation(s)
- A. Allyson Brandon
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Cassia Michael
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Aldo Carmona Baez
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Emily C. Moore
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
- Department of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | - Natalie B. Roberts
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Reade B. Roberts
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Kara E. Powder
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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24
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Arenas-Báez P, Torres-Hernández G, Castillo-Hernández G, Hernández-Rodríguez M, Sánchez-Gutiérrez RA, Vargas-López S, González-Maldonado J, Domínguez-Martínez PA, Granados-Rivera LD, Maldonado-Jáquez JA. Coat Color in Local Goats: Influence on Environmental Adaptation and Productivity, and Use as a Selection Criterion. BIOLOGY 2023; 12:929. [PMID: 37508360 PMCID: PMC10376610 DOI: 10.3390/biology12070929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
This paper aims to review, systematically synthesize, and analyze fragmented information about the importance of coat color in local goats and its relationship with productivity and other important traits. Topics on current research on color expression are addressed, the relationship that has as a mechanism of environmental adaptation, its relationship with the production of meat, milk, and derivates, and the economic value of this characteristic. The use of this attribute as a tool to establish selection criteria in breeding programs based on results reported in the scientific literature is significant, particularly for low-income production systems, where the implementation of classic genetic improvement schemes is limited due to the lack of productive information, which is distinctive of extensive marginal or low scaled production systems around the world.
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Affiliation(s)
- Pablo Arenas-Báez
- Unidad Regional Universitaria de Zonas Áridas, Universidad Autónoma Chapingo, Bermejillo, Durango 35230, Mexico
| | | | - Gabriela Castillo-Hernández
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54714, Mexico
| | | | - Ricardo Alonso Sánchez-Gutiérrez
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Zacatecas, Calera, Zacatecas 98500, Mexico
| | | | - Juan González-Maldonado
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali 21750, Mexico
| | - Pablo Alfredo Domínguez-Martínez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Valle del Guadiana, Durango 34170, Mexico
| | - Lorenzo Danilo Granados-Rivera
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Genera Terán, General Terán 67400, Mexico
| | - Jorge Alonso Maldonado-Jáquez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental La Laguna, Matamoros 27440, Mexico
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25
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Zhang Y, Mei Y, Cao A, Li S, He C, Song L, Gao J, Zhu Y, Cao X. Transcriptome analyses of betta fish (Betta splendens) provide novel insights into fin regeneration and color-related genes. Gene 2023:147508. [PMID: 37230203 DOI: 10.1016/j.gene.2023.147508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 05/27/2023]
Abstract
The betta fish (Betta splendens), an important ornamental fish, haswell-developed and colorful fins.After fin amputation, betta fish can easily regenerate finssimilar to the originalsin terms of structureand color. The powerful fin regeneration ability and a variety of colors in the betta fish are fascinating. However, the underlying molecular mechanisms are still not fully understood. In this study, tail fin amputation and regeneration experiments were performed on two kinds of betta fish: red and white color betta fish. Then, transcriptome analyseswere conducted to screen out fin regeneration and color-relatedgenes in betta fish. Through enrichment analyses of differentially expressed genes (DEGs), we founda series of enrichment pathways and genes related to finregeneration, including cell cycle (i.e. plcg2), TGF-beta signaling pathway (i.e. bmp6), PI3K-Akt signaling pathway (i.e. loxl2aand loxl2b), Wnt signaling pathway(i.e. lef1), gap junctions (i.e. cx43), angiogenesis (i.e. foxp1), and interferon regulatory factor (i.e. irf8). Meanwhile, some fin color-related pathways and genes were identified in betta fish, especially melanogenesis (i.e. tyr, tyrp1a, tyrp1b, and mc1r) and carotenoid color genes (i.e. pax3, pax7, sox10, and ednrba). In conclusion, this studycan not only enrich the research onfish tissue regeneration, but also has a potential significance for the aquaculture and breeding of the betta fish.
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Affiliation(s)
- Yunbang Zhang
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China
| | - Yihui Mei
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Aiying Cao
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Sen Li
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Chuan He
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Liyuan Song
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Gao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China
| | - Yurong Zhu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China.
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26
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MacDonald BT, Elowe NH, Garvie CW, Kaushik VK, Ellinor PT. Identification of a new Corin atrial natriuretic peptide-converting enzyme substrate: Agouti-signaling protein (ASIP). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538495. [PMID: 37162877 PMCID: PMC10168342 DOI: 10.1101/2023.04.26.538495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Corin is a transmembrane tethered enzyme best known for processing the hormone atrial natriuretic peptide (ANP) in cardiomyocytes to control electrolyte balance and blood pressure. Loss of function mutations in Corin prevent ANP processing and lead to hypertension. Curiously, Corin loss of function variants also result in lighter coat color pigmentation in multiple species. Corin pigmentation effects are dependent on a functional Agouti locus encoding the agouti-signaling protein (ASIP) based on a genetic interaction. However, the nature of this conserved role of Corin has not been defined. Here we report that ASIP is a direct proteolytic substrate of the Corin enzyme.
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Affiliation(s)
- Bryan T. MacDonald
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Nadine H. Elowe
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Colin W. Garvie
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Virendar K. Kaushik
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA
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27
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Guo Y, Wu W, Yang X. Coordinated microRNA/mRNA Expression Profiles Reveal Unique Skin Color Regulatory Mechanisms in Chinese Giant Salamander (Andrias davidianus). Animals (Basel) 2023; 13:ani13071181. [PMID: 37048437 PMCID: PMC10093658 DOI: 10.3390/ani13071181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/18/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Chinese giant salamander (Andrias davidianus) has been increasingly popular in the aquaculture market in China in recent years. In the breeding process of Andrias davidianus, we found that some albino individuals were extremely rare and could not be inherited stably, which severely limits their commercialization in the aquaculture market. In this study, we performed transcriptome and small RNA (sRNA) sequencing analyses in the skin samples of wild-type (WT) and albino (AL) Andrias davidianus. In total, among 5517 differentially expressed genes (DEGs), 2911 DEGs were down-regulated in AL, including almost all the key genes involved in melanin formation. A total of 25 miRNAs were differentially expressed in AL compared to WT, of which 17 were up-regulated. Through the integrated analysis, no intersection was found between the target genes of the differentially expressed miRNAs and the key genes for melanin formation. Gene Ontology (GO) and KEGG pathway analyses on DEGs showed that these genes involved multiple processes relevant to melanin synthesis and the key signal pathway MAPK. Interestingly, the transcription factors SOX10 and PAX3 and the Wnt signaling pathway that play a key role in other species were not included, while the other two transcription factors in the SOX family, SOX21 and SOX7, were included. After analyzing the key genes for melanin formation, it was interesting to note an alternative splicing form of the MITF in WT and a critical mutation of the SLC24A5 gene in AL, which might be the main reason for the skin color change of Andrias davidianus. The results contributed to understanding the molecular mechanism of skin pigmentation in Andrias davidianus and accelerating the acquisition process of individuals with specific body colors by genetic means.
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28
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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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Eliason CM, Cooper JC, Hackett SJ, Zahnle E, Pequeño Saco TZ, Maddox JD, Hains T, Hauber ME, Bates JM. Interspecific hybridization explains rapid gorget colour divergence in Heliodoxa hummingbirds (Aves: Trochilidae). ROYAL SOCIETY OPEN SCIENCE 2023; 10:221603. [PMID: 36866078 PMCID: PMC9974296 DOI: 10.1098/rsos.221603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Hybridization is a known source of morphological, functional and communicative signal novelty in many organisms. Although diverse mechanisms of established novel ornamentation have been identified in natural populations, we lack an understanding of hybridization effects across levels of biological scales and upon phylogenies. Hummingbirds display diverse structural colours resulting from coherent light scattering by feather nanostructures. Given the complex relationship between feather nanostructures and the colours they produce, intermediate coloration does not necessarily imply intermediate nanostructures. Here, we characterize nanostructural, ecological and genetic inputs in a distinctive Heliodoxa hummingbird from the foothills of eastern Peru. Genetically, this individual is closely allied with Heliodoxa branickii and Heliodoxa gularis, but it is not identical to either when nuclear data are assessed. Elevated interspecific heterozygosity further suggests it is a hybrid backcross to H. branickii. Electron microscopy and spectrophotometry of this unique individual reveal key nanostructural differences underlying its distinct gorget colour, confirmed by optical modelling. Phylogenetic comparative analysis suggests that the observed gorget coloration divergence from both parentals to this individual would take 6.6-10 My to evolve at the current rate within a single hummingbird lineage. These results emphasize the mosaic nature of hybridization and suggest that hybridization may contribute to the structural colour diversity found across hummingbirds.
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Affiliation(s)
- Chad M. Eliason
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Grainger Bioinformatics Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Jacob C. Cooper
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66044, USA
- Directora de Monitoreo y Evaluacion de Recursos Naturales del Territorio, Plataforma digital única del Estado Peruano, Iquitos, Perú
| | - Shannon J. Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Erica Zahnle
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66044, USA
| | - Tatiana Z. Pequeño Saco
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú, Iquitos, Perú
| | - Joseph Dylan Maddox
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú, Iquitos, Perú
| | - Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Mark E. Hauber
- Department of Evolution, Ecology, and Behaviour, School at Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - John M. Bates
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
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Li JX, Tian Z, Liu XF, Li B, An HM, Brent CS, Wang JL, Wang XP, Liu W. Juvenile hormone regulates the photoperiodic plasticity of elytra coloration in the ladybird Harmonia axyridis. Mol Ecol 2023; 32:2884-2897. [PMID: 36811404 DOI: 10.1111/mec.16896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Many animals, including insects, exhibit plasticity of body colour in response to environmental changes. Varied expression of carotenoids, major cuticle pigments, significantly contributes to body colour flexibility. However, the molecular mechanisms by which environmental cues regulate carotenoid expression remain largely unknown. In this study, we used the ladybird Harmonia axyridis as a model to investigate the photoperiodic-responsive plasticity of elytra coloration and its endocrine regulation. It was found that H. axyridis females under long-day conditions develop elytra that are much redder than those under short-day conditions, resulting from the differential accumulation of carotenoids. Exogenous hormone application and RNAi-mediated gene knockdown indicate that carotenoid deposition was directed through the juvenile hormone (JH) receptor-mediated canonical pathway. Moreover, we characterized an SR-BI/CD36 (SCRB) gene SCRB10 as the carotenoid transporter responding to JH signalling and regulating the elytra coloration plasticity. Taken together, we propose that JH signalling transcriptionally regulates the carotenoid transporter gene for the photoperiodic coloration plasticity of elytra in the beetles, which reveals a novel role of the endocrine system in the regulation of carotenoid-associated animal body coloration under environmental stimuli.
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Affiliation(s)
- Jia-Xu Li
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhong Tian
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xing-Feng Liu
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bei Li
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hao-Min An
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Colin S Brent
- United States Department of Agriculture, Agricultural Research Service, Arid Land Agricultural Centre, Maricopa, Arizona, USA
| | - Jia-Lu Wang
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Ping Wang
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wen Liu
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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31
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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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López-Rull I, Salaberría C, Fargallo JA. Plastic plumage colouration in response to experimental humidity supports Gloger's rule. Sci Rep 2023; 13:858. [PMID: 36646811 PMCID: PMC9842646 DOI: 10.1038/s41598-023-28090-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/12/2023] [Indexed: 01/17/2023] Open
Abstract
Knowing how animals adapt their phenotype to local temperature and humidity is key to understanding not only ecogeographical rules, but also how species will manage climate change, as current models predict changes in global patterns of temperature and precipitation. In endotherms, colour adaptations in response to climate have been under investigated, and their acclimatization-the individual capacity to reversibly adjust phenotype in response to different environments-is unknown. Geographic trends can provide clues about abiotic variables involved in colouration, as postulated by Gloger's rule, which predicts darker individuals in warm and humid regions. We tested whether house sparrows (Passer domesticus) can adjust colouration when faced with varying humidity conditions. We exposed birds to either a dry (humidity 45%) or a wet environment (70%) six months before their moult, and measured colouration in newly developed feathers in five parts of the body (bib, crown, crown stripe, belly and rump). As predicted by Gloger's rule, birds in wet conditions developed darker (bib and belly) and larger (bib) melanised plumage patches, than birds in dry conditions. Our result provides the first unequivocal evidence that the ability of individual birds to adjust their colouration may be a potential adaptation to climatic changes in endotherms.
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Affiliation(s)
- Isabel López-Rull
- Departamento Biología y Geología, Física y Química Inorgánica, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, C/Tulipán s/n., 28933, Móstoles, Madrid, Spain.
| | - Concepción Salaberría
- Departamento Biología y Geología, Física y Química Inorgánica, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, C/Tulipán s/n., 28933, Móstoles, Madrid, Spain
| | - Juan Antonio Fargallo
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
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Sun Y, Wu Q, Lin R, Chen H, Zhang M, Jiang B, Wang Y, Xue P, Gan Q, Shen Y, Chen F, Liu J, Zhou C, Lan S, Pan H, Deng F, Yue W, Lu L, Jiang X, Li Y. Genome-wide association study for the primary feather color trait in a native Chinese duck. Front Genet 2023; 14:1065033. [PMID: 36936414 PMCID: PMC10020179 DOI: 10.3389/fgene.2023.1065033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Background: To reveal candidate genes and the molecular genetic mechanism underlying primary feather color trait in ducks, a genome-wide association study (GWAS) for the primary feather color trait was performed based on the genotyping-by-sequencing (GBS) technology for a native Chinese female duck, Longyan Shan-ma ducks. Methods: Blood genomic DNA from 314 female Longyan Shan-ma duck were genotyped using GBS technology. A GWAS for the primary feather color trait with genome variations was performed using an univariate linear mixed model based on all SNPs in autosomes. Results: Seven genome-wide significant single nucleotide polymorphisms (SNPs, Bonferroni-adjusted p-value <8.03 × 10-7) within the introns of the genes STARD9, ZNF106, SLC7A5, and BANP genes were associated with the primary feather color trait. Twenty-two genome-wide suggestive SNPs (Bonferroni-adjusted p-value <1.61 × 10-5) of 17 genes (besides ZNF106 and SLC7A5) were also identified. Seven SNPs were located at one 0.22 Mb region (38.65-38.87 Mb) on chromosome 5, and six SNPs were located at one 0.31 Mb region (19.53-19.84 Mb) on chromosome 11. The functions of STARD9, SLC7A5, BANP, LOC101798015, and IPMK were involved pigmentation and follicle development, especially, STARD9 upregulated expression in black feather (haplotype-CCCC) bulb tissue compared with in pockmarked feather (haplotype-TGTT) bulb tissue, implicating these genes as candidate genes for primary feather color trait. Conclusion: The preliminarily findings suggested candidate genes and regions, and the genetic basis of primary feather color trait in a female duck.
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Affiliation(s)
- Yanfa Sun
- College of Life Sciences, Longyan University, Longyan, Fujian, China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, Fujian, China
| | - Qiong Wu
- College of Life Sciences, Longyan University, Longyan, Fujian, China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, Fujian, China
| | - Rulong Lin
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, Fujian, China
| | - Hongping Chen
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, Fujian, China
| | - Min Zhang
- College of Life Sciences, Longyan University, Longyan, Fujian, China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, Fujian, China
| | - Bingbing Jiang
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaru Wang
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Pengfei Xue
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Qiuyun Gan
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Yue Shen
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Feifan Chen
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Jiantao Liu
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Chenxin Zhou
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Shishi Lan
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Haozhe Pan
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Fan Deng
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Wen Yue
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, Fujian, China
| | - Lizhi Lu
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaobing Jiang
- Fujian Provincial Animal Husbandry Headquarters, Fuzhou, Fujian, China
- *Correspondence: Xiaobing Jiang, ; Yan Li,
| | - Yan Li
- College of Life Sciences, Longyan University, Longyan, Fujian, China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, Fujian, China
- *Correspondence: Xiaobing Jiang, ; Yan Li,
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Valette T, Leitwein M, Lascaux JM, Desmarais E, Berrebi P, Guinand B. Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.). JOURNAL OF FISH BIOLOGY 2023; 102:96-118. [PMID: 36218076 DOI: 10.1111/jfb.15243] [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: 09/26/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.
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Luo W, Zhang S, Wang T, Zhang X, Zhang Y, Chen P, Guo Z, Xiong Y, Xu Z, Jiang J, Yang S, Yang S, Du Z. The background adaptation of the skin color in the loach Paramisgurnus dabryanus. Appl Anim Behav Sci 2023. [DOI: 10.1016/j.applanim.2023.105831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Wang P, Xiong G, Zeng D, Zhang J, Ge L, Liu L, Wang X, Hu Y. Comparative transcriptome and miRNA analysis of skin pigmentation during embryonic development of Chinese soft-shelled turtle (Pelodiscus sinensis). BMC Genomics 2022; 23:801. [PMID: 36471254 PMCID: PMC9721069 DOI: 10.1186/s12864-022-09029-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/21/2022] [Indexed: 12/10/2022] Open
Abstract
BACKGROUND Aquatic animals show diverse body coloration, and the formation of animal body colour is a complicated process. Increasing evidence has shown that microRNAs (miRNAs) play important regulatory roles in many life processes. The role of miRNAs in pigmentation has been investigated in some species. However, the regulatory patterns of miRNAs in reptile pigmentation remain to be elucidated. In this study, we performed an integrated analysis of miRNA and mRNA expression profiles to explore corresponding regulatory patterns in embryonic body colour formation in the soft-shelled turtle Pelodiscus sinensis. RESULTS We identified 8 866 novel genes and 9 061 mature miRNAs in the skin of Chinese soft-shelled turtles in three embryonic stages (initial period: IP, middle period: MP, final period: FP). A total of 16 563 target genes of the miRNAs were identified. Furthermore, we identified 2 867, 1 840 and 4 290 different expression genes (DEGs) and 227, 158 and 678 different expression miRNAs (DEMs) in IP vs. MP, MP vs. FP, and IP vs. FP, respectively. Among which 72 genes and 25 miRNAs may be related to turtle pigmentation in embryonic development. Further analysis of the novel miRNA families revealed that some novel miRNAs related to pigmentation belong to the miR-7386, miR-138, miR-19 and miR-129 families. Novel_miR_2622 and novel_miR_2173 belong to the miR-19 family and target Kit and Gpnmb, respectively. The quantification of novel_miR_2622 and Kit revealed negative regulation, indicating that novel_miR_2622 may participate in embryonic pigmentation in P. sinensis by negatively regulating the expression of Kit. CONCLUSIONS miRNA act as master regulators of biological processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs and their target genes in Chinese soft-shelled turtle might be useful for investigating the molecular processes involved in pigmentation. All the results of this study may aid in the improvement of P. sinensis breeding traits for aquaculture.
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Affiliation(s)
- Pei Wang
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Gang Xiong
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Dan Zeng
- grid.440778.80000 0004 1759 9670College of Life and Environmental Science, Hunan University of Arts and Science, Changde, 415000 Hunan China
| | - Jianguo Zhang
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Lingrui Ge
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China ,Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Li Liu
- grid.449642.90000 0004 1761 026XSchool of Medical Technology, Shaoyang University, Shaoyang, 422000 Hunan China
| | - Xiaoqing Wang
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Yazhou Hu
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
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Laurentino TG, Dittmer DE, Grundler MR, Pina‐Martins F, Haddock J, Hibbitts TJ, Rosenblum EB. Repeated evolution of blanched coloration in a lizard across independent white-sand habitats. Ecol Evol 2022; 12:e9555. [PMID: 36506826 PMCID: PMC9729009 DOI: 10.1002/ece3.9555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
The White Sands lizards of New Mexico are a rare and classic example of convergent evolution where three species have evolved blanched coloration on the white gypsum dunes. Until now, no geological replicate of the pattern had been described. However, one of the White Sands species, the lesser earless lizard (Holbrookia maculata), has been discovered to also inhabit the Salt Basin Dunes of Texas, where it has also evolved a blanched morph. We here present a first phenotypic and genetic description of the Salt Basin Dunes population of H. maculata. Phylogenetic inference based on a housekeeping gene (ND4) and a classic candidate gene in the melanin-synthesis pathway (Melanocortin 1 Receptor; Mc1r) shows the newly discovered population as an independent lineage, with no evidence of genetic parallelism in the coding region of Mc1r. Initial morphological data suggest that while this population displays convergent evolution in blanched coloration, there are divergent patterns in limb length and habitat use behavior between the gypsum environments. Our findings present the White Sands/Salt Basin Dunes as an exceptionally promising comparative model for studies of adaptation and convergent evolution.
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Affiliation(s)
- Telma G. Laurentino
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | | | - Maggie R. Grundler
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Francisco Pina‐Martins
- cE3c‐Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de Lisboa (ULisboa)LisbonPortugal
| | - Janey Haddock
- Division of MammalogyBiodiversity Institute, University of KansasLawrenceKansasUSA
| | - Toby J. Hibbitts
- Biodiversity Research and Teaching Collection, Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTexasUSA
- Natural Resources InstituteTexas A&M UniversityCollege StationTexasUSA
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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Song F, Shi L, Yao F, Gu Y, Zheng D, Zhang W, Liang Y, Zhang K, Yang M, Wang L, Sun J, Luo J. The Effect of Background Color on Skin Color Variation of Juvenile Plectropomus leopardus. Animals (Basel) 2022; 12:ani12233349. [PMID: 36496870 PMCID: PMC9738834 DOI: 10.3390/ani12233349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Fish skin color is usually strongly affected by the background color of their environment. The study investigated the effects of five different background colors on the skin color of leopard coral groupers (Plectropomus leopardus). More than 450 juveniles were reared in Blue, Red, Black, White, and Transparent background tanks for 56 days. The paraffin section showed that the skin melanin zone of fish in the White group was smaller, whereas the Black and Red groups (especially Black) were nearly the largest. The apparent skin color of P. leopardus was red on the white background, which darkened in response to the other color backgrounds. The Black group revealed the blackest skin color, followed by the transparent group. Moreover, the White group had the highest L*, a*, and b* values. The melanin content and tyrosinase activity in the dorsal and ventral skin of the Black group were significantly higher than those in the other groups (p < 0.05), and the serum α-MSH level was higher in the Black group as well. The carotenoid and lutein contents showed completely different trends among the experimental groups, as carotenoid content was higher in the Red and White groups, while lutein content was higher in the Transparent group. The expression level of scarb1 was highest in the Blue and White groups, followed by the Transparent group, and lowest in the Black group (p < 0.05). The expression trend of scarb1 was similar to the skin color in different backgrounds, indicating that the background color regulated scarb1 expression level through visual center, then influenced the uptake and transport of carotenoids, then influenced the skin color formation of P. leopardus. Moreover, lighter colors inhibited the formation of melanocytes and had a significant effect on carotenoid and lutein contents. Pigment-related genes were involved in the regulation of fish skin color, and they were affected by background color in P. leopardus. These results indicate that a white background is more conducive to maintaining red skin color in juvenile P. leopardus.
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Rosvall KA. Evolutionary endocrinology and the problem of Darwin's tangled bank. Horm Behav 2022; 146:105246. [PMID: 36029721 DOI: 10.1016/j.yhbeh.2022.105246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/20/2022] [Accepted: 08/10/2022] [Indexed: 11/04/2022]
Abstract
Like Darwin's tangled bank of biodiversity, the endocrine mechanisms that give rise to phenotypic diversity also exhibit nearly endless forms. This tangled bank of mechanistic diversity can prove problematic as we seek general principles on the role of endocrine mechanisms in phenotypic evolution. A key unresolved question is therefore: to what degree are specific endocrine mechanisms re-used to bring about replicated phenotypic evolution? Related areas of inquiry are booming in molecular ecology, but behavioral traits are underrepresented in this literature. Here, I leverage the rich comparative tradition in evolutionary endocrinology to evaluate whether and how certain mechanisms may be repeated hotspots of behavioral evolutionary change. At one extreme, mechanisms may be parallel, such that evolution repeatedly uses the same gene or pathway to arrive at multiple independent (or, convergent) origins of a particular behavioral trait. At the other extreme, the building blocks of behavior may be unique, such that outwardly similar phenotypes are generated via lineage-specific mechanisms. This review synthesizes existing case studies, phylogenetic analyses, and experimental evolutionary research on mechanistic parallelism in animal behavior. These examples show that the endocrine building blocks of behavior have some elements of parallelism across replicated evolutionary events. However, support for parallelism is variable among studies, at least some of which relates to the level of complexity at which we consider sameness (i.e. pathway vs. gene level). Moving forward, we need continued experimentation and better testing of neutral models to understand whether, how - and critically, why - mechanism A is used in one lineage and mechanism B is used in another. We also need continued growth of large-scale comparative analyses, especially those that can evaluate which endocrine parameters are more or less likely to undergo parallel evolution alongside specific behavioral traits. These efforts will ultimately deepen understanding of how and why hormone-mediated behaviors are constructed the way that they are.
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Affiliation(s)
- Kimberly A Rosvall
- Indiana University, Bloomington, USA; Department of Biology, USA; Center for the Integrative Study of Animal Behavior, USA.
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40
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Identification, characterization and differential expression analysis of a pteridine synthesis related gene, Ccptps, in koi carp (Cyprinus carpio L.). Comp Biochem Physiol B Biochem Mol Biol 2022; 264:110814. [DOI: 10.1016/j.cbpb.2022.110814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
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41
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Campagna L, Toews DP. The genomics of adaptation in birds. Curr Biol 2022; 32:R1173-R1186. [DOI: 10.1016/j.cub.2022.07.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Transcriptome Analysis Reveals the Complex Regulatory Pathway of Background Color in Juvenile Plectropomus leopardus Skin Color Variation. Int J Mol Sci 2022; 23:ijms231911186. [PMID: 36232493 PMCID: PMC9569894 DOI: 10.3390/ijms231911186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Fish skin color is often strongly affected by background color. We hypothesized that the regulatory mechanism of variations in skin color in P. leopardus is linked to the background color. In this study, we conducted transcriptome analysis of Plectropomus leopardus cultured under different background colors to compare gene expression levels and the important signaling pathways. The RNA-seq analysis yielded 26,675 known mRNAs, 3278 novel mRNAs, and 3179 differentially expressed genes (DEGs). The DEGs related to melanin synthesis were screened out. Some key melanin-related genes were identified, specifically tyr, slc7a11, mc1r, ednrb, dct, tat, and wnt1. These DEGs were mainly involved in melanogenesis, including tyrosine metabolism, the Wnt signaling pathway, and the cAMP signaling pathway. The expression levels of some key genes were upregulated when background color deepened, such as α-msh, wnt, and gf. The α-MSH/cAMP-dependent, Wnt/β-catenin, and PI3K/Akt signaling pathways were activated, resulting in the accumulation of intracellular mitf. mitf promoted melanin production by binding to the tyr/tyrp1/dct promoter region. In the present study, we explored the molecular mechanism underlying the darkened skin color pattern of P. leopardus, providing a theoretical basis for the molecular mechanism underlying pigmentation in P. leopardus.
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Seven Shades of Grey: A Follow-Up Study on the Molecular Basis of Coat Colour in Indicine Grey Cattle Using Genome-Wide SNP Data. Genes (Basel) 2022; 13:genes13091601. [PMID: 36140768 PMCID: PMC9498432 DOI: 10.3390/genes13091601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Shades of grey and brown are a dominant component in mammal coat colours, representing a fundamental trait involved in a great number of processes including cryptism, sexual selection and signalling. The genetic mechanisms of the grey colouration in mammals are very complex and controlled by hundreds of genes whose effects and interactions are still largely unclear. In this study, we adopted a robust multi-cohort Fst outlier approach based on pairwise contrasts between seven grey indicine cattle breeds and both taurine and indicine non-grey cattle breeds in order to find genomic regions potentially related to the grey colouration. On the basis of three main drawn settings, built in order to control both the effect of the sample size and the genetic structure, we have identified some signals common to those obtained in a previous work employing only taurine cattle. In particular, using the top 1% Fst approach, we detected a candidate region (22.6–23.8 megabases) on chromosome 14 in which genes related to pigmentation have been already documented. In addition, when we constructed a phylogenetic tree using the significant markers identified in this study and including also the genotyping data at these loci of both the grey taurine and the extinct wild auroch, we found a topological repartition consistent with breed colour pattern rather than with the known bovine evolutionary history. Thus, on the basis of this evidence, together with the geographical distribution of the current taurine grey cattle, an ancestral indicine origin for the grey phenotype would seem to be a conceivable interpretation. In this context, a higher thermo-tolerance and less UV-induced damage of the grey phenotype might have favoured the retention of advantageous genes into the taurine genome during the post-Neolithic human-mediated cattle expansions.
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Lu X, Zhang L, Wang G, Huang S, Zhang Y, Xie Y. The occurrence process of chromatophores in three body color strains of the ornamental shrimp Neocaridina denticulata sinensis. ZOOMORPHOLOGY 2022. [DOI: 10.1007/s00435-022-00563-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Evaluating different metrics to study small color differences: the red bill and plumage of common waxbills as a case study. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03236-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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46
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Kratochwil CF, Liang Y, Gerwin J, Franchini P, Meyer A. Comparative ontogenetic and transcriptomic analyses shed light on color pattern divergence in cichlid fishes. Evol Dev 2022; 24:158-170. [PMID: 35971657 DOI: 10.1111/ede.12416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 11/27/2022]
Abstract
Stripe patterns are a striking example for a repeatedly evolved color pattern. In the African adaptive radiations of cichlid fishes, stripes evolved several times independently. Previously, it has been suggested that regulatory evolution of a single gene, agouti-related-peptide 2 (agrp2), explains the evolutionary lability of this trait. Here, using a comparative transcriptomic approach, we performed comparisons between (adult) striped and nonstriped cichlid fishes of representatives of Lake Victoria and the two major clades of Lake Malawi (mbuna and non-mbuna lineage). We identify agrp2 to be differentially expressed across all pairwise comparisons, reaffirming its association with stripe pattern divergence. We therefore also provide evidence that agrp2 is associated with the loss of the nonstereotypic oblique stripe of Mylochromis mola. Complementary ontogenetic data give insights into the development of stripe patterns as well as vertical bar patterns that both develop postembryonically. Lastly, using the Lake Victoria species pair Haplochromis sauvagei and Pundamilia nyererei, we investigated the differences between melanic and non-melanic regions to identify additional genes that contribute to the formation of stripes. Expression differences-that most importantly also do not include agrp2-are surprisingly small. This suggests, at least in this species pair, that the stripe phenotype might be caused by a combination of more subtle transcriptomic differences or cellular changes without transcriptional correlates. In summary, our comprehensive analysis highlights the ontogenetic and adult transcriptomic differences between cichlids with different color patterns and serves as a basis for further investigation of the mechanistic underpinnings of their diversification.
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Affiliation(s)
- Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yipeng Liang
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jan Gerwin
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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Voß K, Blaj I, Tetens JL, Thaller G, Becker D. Roan coat color in livestock. Anim Genet 2022; 53:549-556. [PMID: 35811453 DOI: 10.1111/age.13240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022]
Abstract
Since domestication, a wide variety of phenotypes including coat color variation has developed in livestock. This variation is mostly based on selective breeding. During the beginning of selective breeding, potential negative consequences did not become immediately evident due to low frequencies of homozygous animals and have been occasionally neglected. However, numerous studies of coat color genetics have been carried out over more than a century and, meanwhile, pleiotropic effects for several coat color genes, including disorders of even lethal impact, were described. Similar coat color phenotypes can often be found across species, caused either by conserved genes or by different genes. Even in the same species, more than one gene could cause the same or similar coat color phenotype. The roan coat color in livestock species is characterized by a mixture of white and colored hair in cattle, pig, sheep, goat, alpaca, and horse. So far, the genetic background of this phenotype is not fully understood, but KIT and its ligand KITLG (MGF) are major candidate genes in livestock species. For some of these species, pleiotropic effects such as subfertility in homozygous roan cattle or homozygous embryonic lethality in certain horse breeds have been described. This review aims to point out the similarities and differences of the roan phenotype across the following livestock species: cattle, pig, sheep, goat, alpaca, and horse; and provides the current state of knowledge on genetic background and pleiotropic effects.
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Affiliation(s)
- Katharina Voß
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, Germany
| | - Iulia Blaj
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, Germany
| | - Julia L Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, Germany
| | - Doreen Becker
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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Manzo E, Bartolommei P, Dell’Agnello F, Cozzolino R. Anomalous coloration in European pine marten
Martes martes
in Elba Island, Central Italy. Ecol Evol 2022; 12:e8980. [PMID: 35784087 PMCID: PMC9170521 DOI: 10.1002/ece3.8980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022] Open
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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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Portillo A, Sibille S, Panaifo N. Record of melanism in Tamandua tetradactyla (Pilosa: Myrmecophagidae) in Perú. REVISTA PERUANA DE BIOLOGÍA 2022. [DOI: 10.15381/rpb.v29i2.22106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
A case of melanism in Tamandua tetradactyla (Myrmecophagidae) is recorded, based on an individual observed in the Huánuco Department, Peru. Two previous records are found in the iNaturalist database. With this record, the number of melanistic mammal species in Peru increases to four. It should be noted that cases of melanism in this species have already been reported in the Neotropics.
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