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Ding Y, Zou M, Guo B. Genomic signatures associated with recurrent scale loss in cyprinid fish. Integr Zool 2024. [PMID: 38816909 DOI: 10.1111/1749-4877.12851] [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] [Indexed: 06/01/2024]
Abstract
Scale morphology represents a fundamental feature of fish and a key evolutionary trait underlying fish diversification. Despite frequent and recurrent scale loss throughout fish diversification, comprehensive genome-wide analyses of the genomic signatures associated with scale loss in divergent fish lineages remain scarce. In the current study, we investigated genome-wide signatures, specifically convergent protein-coding gene loss, amino acid substitutions, and cis-regulatory sequence changes, associated with recurrent scale loss in two divergent Cypriniformes lineages based on large-scale genomic, transcriptomic, and epigenetic data. Results demonstrated convergent changes in many genes related to scale formation in divergent scaleless fish lineages, including loss of P/Q-rich scpp genes (e.g. scpp6 and scpp7), accelerated evolution of non-coding elements adjacent to the fgf and fgfr genes, and convergent amino acid changes in genes (e.g. snap29) under relaxed selection. Collectively, these findings highlight the existence of a shared genetic architecture underlying recurrent scale loss in divergent fish lineages, suggesting that evolutionary outcomes may be genetically repeatable and predictable in the convergence of scale loss in fish.
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Affiliation(s)
- Yongli Ding
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
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Zhang JH, Long R, Jing YY, Zhang P, Xu Y, Xiong W, Zhu YQ, Luo YP. Loss of behavioral stress response in blind cavefish reduces energy expenditure. Zool Res 2023; 44:678-692. [PMID: 37147886 PMCID: PMC10415775 DOI: 10.24272/j.issn.2095-8137.2022.354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023] Open
Abstract
The stress response is essential for animal self-defense and survival. However, species may exhibit stress response variation depending on their specific environmental and selection pressures. Blind cavefish dwell in cave environments, which differ markedly in stressors and resource availability compared to surface aquatic environments. However, whether blind cavefish exhibit differences in stress response as an adaptation to their cave environments remains unclear. Here, we investigated differences in stress response in six closely related Triplophysa species, including three blind cavefish (T. longibarbata, T. jiarongensis, and T. rosa) and three normal-sighted river fish (T. nasobarbatula, T. dongsaiensis, and T. bleekeri). Results showed that blind cavefish exhibited a range of distinct behavioral responses compared to sighted river fish, including greater levels of activity, shorter duration of freezing, absence of erratic movements or thrashing behavior, and opposite behavioral trends over time. Furthermore, the cavefish species demonstrated attenuated increases in metabolic rate in response to stressors related to novel environments. Cave-dwelling T. rosa also exhibited lower basal hypothalamic-pituitary-inter-renal (HPI) axis-related gene expression levels and stress hormone concentrations compared to river-dwelling T. bleekeri. These results suggest that blind cavefish may have lost their behavioral stress response, potentially mediated by a reduction in basal activity of the HPI axis, thus enabling the conservation of energy by reducing unnecessary expenditure in energy-limited caves.
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Affiliation(s)
- Jiang-Hui Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Rui Long
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yang-Yang Jing
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Pan Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yuan Xu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wei Xiong
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yan-Qiu Zhu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yi-Ping Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China. E-mail:
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Liang ZW, Li SY, Zhang XL, Chen CY, Sun WJ, Gu ZQ, Huang J, He JY, Qi PZ, Guo BY, Liao Z, Yan XJ. Morphological change and differential proteomics analysis of gill in Mytilus coruscus under starvation. Front Physiol 2023; 14:1150521. [PMID: 37064882 PMCID: PMC10097965 DOI: 10.3389/fphys.2023.1150521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/03/2023] [Indexed: 04/01/2023] Open
Abstract
Mytilus coruscus is a dominant shellfish in the Yangtze estuary and its adjacent sea area. Food deprivation often occurs during their growth due to fluctuations in algal abundance caused by seasonal freshwater flushing and high-density aquaculture mode. To investigate the coping strategies of M. coruscus to starvation stress, electron microscopy and differential proteomic analysis were performed on the critical feeding organ gill of the mussels after 9 days of starvation. The electron microscopy results showed that the cilia of the mussel gills were dissolved, and the gaps between gill filaments widened under starvation. Differential proteomic analysis revealed that phagocytosis-related proteins such as ATPeV1E, ATPeV1C, LAMP1_2 and CTSL were significantly upregulated, and the phagocytosis pathway was significantly enriched (p < 0.05). In addition, the corin content in gill and myeloperoxidase level as well as the number of dead cells in blood were both significantly increased (p < 0.05). What’s more, proteomic data suggested that immune maintenance, cellular transport and metabolism related pathways were significantly enriched, which illustrated an immune and metabolism responses under starvation. This study reveals for the first time that phagocytosis functions as an essential strategy for M. coruscus to cope with starvation, which provides new scientific knowledge and a theoretical basis for understanding the adaptation mechanisms of mussel to starvation and for rational optimization of mussel culture patterns.
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Affiliation(s)
- Ze-Wei Liang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Si-Yuan Li
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Xiao-Lin Zhang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- *Correspondence: Xiao-Lin Zhang, ; Xiao-Jun Yan,
| | - Chuan-Yue Chen
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Wen-Jing Sun
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Zhong-Qi Gu
- China Bureau of Science and Technology Shengsi, Zhoushan, Zhejiang, China
| | - Ji Huang
- China Bureau of Science and Technology Shengsi, Zhoushan, Zhejiang, China
| | - Jian-Yu He
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- Donghai Laboratory, Zhoushan, Zhejiang, China
| | - Peng-Zhi Qi
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Bao-Ying Guo
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Zhi Liao
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Xiao-Jun Yan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- *Correspondence: Xiao-Lin Zhang, ; Xiao-Jun Yan,
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Zhao Q, Shao F, Li Y, Yi SV, Peng Z. Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes. Mol Ecol 2022; 31:5831-5845. [PMID: 36125323 PMCID: PMC9828065 DOI: 10.1111/mec.16700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Department of Laboratory Animal Science, College of Basic Medical SciencesArmy Medical University (Third Military Medical University)ChongqingChina
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Key Laboratory of Sichuan Province for Fish Conservation and Utilization in the Upper Reaches of the Yangtze RiverNeijiang Normal University College of Life SciencesNeijiangChina
| | - Soojin V. Yi
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Academy of Plateau Science and SustainabilityQinghai Normal UniversityXiningChina
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Jin L, Li Z, Wang C, Wang Y, Li X, Yang J, Zhao Y, Guo B. Contrasting population differentiation in two sympatric Triplophysa loaches on the Qinghai-Tibet Plateau. Front Genet 2022; 13:958076. [PMID: 36092882 PMCID: PMC9452750 DOI: 10.3389/fgene.2022.958076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Genetic differentiation in aquatic organisms is usually shaped by drainage connectivity. Sympatric aquatic species are thus expected to show similar population differentiation patterns and similar genetic responses to their habitats. Water bodies on the Qinghai-Tibet Plateau (QTP) have recently experienced dramatic physicochemical changes, threatening the biodiversity of aquatic organisms on the "roof of the world." To uncover ecological genetics in Tibetan loaches (Triplophysa)-the largest component of the QTP ichthyofauna-we characterized population differentiation patterns and adaptive mechanisms to salinity change in two sympatric and phylogenetically closely related Tibetan loaches, T. stewarti and T. stenura, by integrating population genomic, transcriptomic, and electron probe microanalysis approaches. Based on millions of genome-wide SNPs, the two Tibetan loach species show contrasting population differentiation patterns, with highly geographically structured and clear genetic differentiation among T. stewarti populations, whereas there is no such observation in T. stenura, which is also supported by otolith microchemistry mapping. While limited genetic signals of parallel adaption to salinity changes between the two species are found from either genetic or gene expression variation perspective, a catalog of genes involved in ion transport, energy metabolism, structural reorganization, immune response, detoxification, and signal transduction is identified to be related to adaptation to salinity change in Triplophysa loaches. Together, our findings broaden our understanding of the population characteristics and adaptive mechanisms in sympatric Tibetan loach species and would contribute to biodiversity conservation and management of aquatic organisms on the QTP.
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Affiliation(s)
- Ling Jin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zitong Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Chongnv Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jian Yang
- Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
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Wang C, Xu J, Kocher TD, Li M, Wang D. CRISPR knockouts of pmela and pmelb engineered a golden tilapia by regulating relative pigment cell abundance. J Hered 2022; 113:398-413. [PMID: 35385582 DOI: 10.1093/jhered/esac018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Premelanosome protein (pmel) is a key gene for melanogenesis. Mutations in this gene are responsible for white plumage in chicken, but its role in pigmentation of fish remains to be demonstrated. In this study we found that most fishes have two pmel genes arising from the teleost-specific whole genome duplication. Both pmela and pmelb were expressed at high levels in the eyes and skin of Nile tilapia. We mutated both genes in tilapia using CRISPR/Cas9. Homozygous mutation of pmela resulted in yellowish body color with weak vertical bars and a hypo-pigmented retinal pigment epithelium (RPE) due to significantly reduced number and size of melanophores. In contrast, we observed an increased number and size of xanthophores in mutants compared to wild-type fish. Homozygous mutation of pmelb resulted in a similar, but milder phenotype than pmela-/- mutants. Double mutation of pmela and pmelb resulted in loss of additional melanophores compared to the pmela-/- mutants, and also an increase in the number and size of xanthophores, producing a golden body color. The RPE pigmentation of pmela-/-;pmelb-/- was similar to pmela-/- mutants, with much less pigmentation than pmelb-/- mutants and wild-type fish. Taken together, our results indicate that, while both pmel genes are important for the formation of body color in tilapia, pmela plays a more important role than pmelb. To our knowledge, this is the first report on mutation of pmelb or both pmela;pmelb in fish. Studies on these mutants suggest new strategies for breeding golden tilapia, and also provide a new model for studies of pmel function in vertebrates.
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Affiliation(s)
- Chenxu Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Jia Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland College Park, Maryland, USA
| | - Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
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