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Wang C, Yang L, Lu Y, Fang C, Gan X, Chen Y, He S. Genomic features for adaptation and evolutionary dynamics of four major Asian domestic carps. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1308-1310. [PMID: 38240907 DOI: 10.1007/s11427-023-2479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 06/07/2024]
Affiliation(s)
- Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Yongrui Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengchi Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yiyu Chen
- National Natural Science Foundation of China, Beijing, 100085, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
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Feng C, Wang K, Xu W, Yang L, Wanghe K, Sun N, Wu B, Wu F, Yang L, Qiu Q, Gan X, Chen Y, He S. Monsoon boosted radiation of the endemic East Asian carps. SCIENCE CHINA. LIFE SCIENCES 2023; 66:563-578. [PMID: 36166180 DOI: 10.1007/s11427-022-2141-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 10/14/2022]
Abstract
Major historical events often trigger the rapid flourishing of a few lineages, which in turn shape established biodiversity patterns. How did this process occur and develop? This study provides a window into this issue. The endemic East Asian carps (EEAC) dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems. A series of evidence, including ecogeography, phylogenetics, and macroevolution, suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities. We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting (e.g., marine transgression and regression and glacial-interglacial cycle) have further reshaped the distribution patterns of EEAC's members. Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting, which boosted radiation. Overall, this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.
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Affiliation(s)
- Chenguang Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau Biota of Chinese Academy of Sciences, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Feixiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yiyu Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Natural Science Foundation of China, Beijing, 100085, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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Policarpo M, Bemis KE, Laurenti P, Legendre L, Sandoz JC, Rétaux S, Casane D. Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes. BMC Biol 2022; 20:195. [PMID: 36050670 PMCID: PMC9438307 DOI: 10.1186/s12915-022-01397-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction. Anatomical diversity of the olfactory organ suggests that olfaction is differentially important among species. To explore this topic, we studied the evolutionary dynamics of the four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) coding for olfactory receptors in 185 species of ray-finned fishes. Results The large variation in the number of functional genes, between 28 in the ocean sunfish Mola mola and 1317 in the reedfish Erpetoichthys calabaricus, is the result of parallel expansions and contractions of the four main gene families. Several ancient and independent simplifications of the olfactory organ are associated with massive gene losses. In contrast, Polypteriformes, which have a unique and complex olfactory organ, have almost twice as many olfactory receptor genes as any other ray-finned fish. Conclusions We document a functional link between morphology of the olfactory organ and richness of the olfactory receptor repertoire. Further, our results demonstrate that the genomic underpinning of olfaction in ray-finned fishes is heterogeneous and presents a dynamic pattern of evolutionary expansions, simplifications, and reacquisitions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01397-x.
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Affiliation(s)
- Maxime Policarpo
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Katherine E Bemis
- NOAA National Systematics Laboratory, National Museum of Natural History, Smithsonian Institution, Washington, D.C, 20560, USA
| | - Patrick Laurenti
- Université Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75013, Paris, France
| | - Laurent Legendre
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jean-Christophe Sandoz
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Sylvie Rétaux
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400, Saclay, France.
| | - Didier Casane
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France. .,Université Paris Cité, UFR Sciences du Vivant, 75013, Paris, France.
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Remarkable diversity of vomeronasal type 2 receptor (OlfC) genes of basal ray-finned fish and its evolutionary trajectory in jawed vertebrates. Sci Rep 2022; 12:6455. [PMID: 35440756 PMCID: PMC9018814 DOI: 10.1038/s41598-022-10428-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 04/01/2022] [Indexed: 11/08/2022] Open
Abstract
The vomeronasal type 2 receptor (V2R, also called OlfC) multigene family is found in a broad range of jawed vertebrates from cartilaginous fish to tetrapods. V2Rs encode receptors for food-related amino acids in teleost fish, whereas for peptide pheromones in mammals. In addition, V2Rs of teleost fish are phylogenetically distinct from those of tetrapods, implying a drastic change in the V2R repertoire during terrestrial adaptation. To understand the process of diversification of V2Rs in vertebrates from "fish-type" to "tetrapod-type", we conducted an exhaustive search for V2Rs in cartilaginous fish (chimeras, sharks, and skates) and basal ray-finned fish (reedfish, sterlet, and spotted gar), and compared them with those of teleost, coelacanth, and tetrapods. Phylogenetic and synteny analyses on 1897 V2Rs revealed that basal ray-finned fish possess unexpectedly higher number of V2Rs compared with cartilaginous fish, implying that V2R gene repertoires expanded in the common ancestor of Osteichthyes. Furthermore, reedfish and sterlet possessed various V2Rs that belonged to both "fish-type" and "tetrapod-type", suggesting that the common ancestor of Osteichthyes possess "tetrapod-type" V2Rs although they inhabited underwater environments. Thus, the unexpected diversity of V2Rs in basal ray-finned fish may provide insight into how the olfaction of osteichthyan ancestors adapt from water to land.
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The Chemosensory Repertoire of the Eastern Diamondback Rattlesnake (Crotalus adamanteus) Reveals Complementary Genetics of Olfactory and Vomeronasal-Type Receptors. J Mol Evol 2021; 89:313-328. [PMID: 33881604 DOI: 10.1007/s00239-021-10007-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/22/2021] [Indexed: 01/14/2023]
Abstract
Pitviper sensory perception incorporates diverse stimuli through the integration of trichromatic color vision, bifocal heat-sensing, and dual-system chemoperception. Chemoperception, or olfaction, is mediated by chemoreceptors in the olfactory bulb and the vomeronasal organ, but the true genomic complexity of the gene families and their relative contributions is unknown. A full genomic accounting of pitviper chemoperception directly complements our current understanding of their venoms by generating a more complete polyphenic representation of their predatory arsenal. To characterize the genetic repertoire of pitviper chemoperception, we analyzed a full-genome assembly for Crotalus adamanteus, the eastern diamondback rattlesnake. We identified hundreds of genes encoding both olfactory receptors (ORs; 362 full-length genes) and type-2 vomeronasal receptors (V2Rs; 430 full-length genes). Many chemoreceptor genes are organized into large tandem repeat arrays. Comparative analysis of V2R orthologs across squamates demonstrates how gene array expansion and contraction underlies the evolution of the chemoreceptor repertoire, which likely reflects shifts in life history traits. Chromosomal assignments of chemosensory genes identified sex chromosome specific chemoreceptor genes, providing gene candidates underlying observed sex-specific chemosensory-based behaviors. We detected widespread episodic evolution in the extracellular, ligand-binding domains of both ORs and V2Rs, suggesting the diversification of chemoreceptors is driven by transient periods of positive selection. We provide a robust genetic framework for studying pitviper chemosensory ecology and evolution.
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Kushwaha B, Pandey M, Das P, Joshi CG, Nagpure NS, Kumar R, Kumar D, Agarwal S, Srivastava S, Singh M, Sahoo L, Jayasankar P, Meher PK, Shah TM, Hinsu AT, Patel N, Koringa PG, Das SP, Patnaik S, Bit A, Iquebal MA, Jaiswal S, Jena J. The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes. DNA Res 2021; 28:6070145. [PMID: 33416875 PMCID: PMC7934567 DOI: 10.1093/dnares/dsaa031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.
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Affiliation(s)
- Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Manmohan Pandey
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Naresh S Nagpure
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Suyash Agarwal
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Shreya Srivastava
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Prem K Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Tejas M Shah
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Namrata Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Sofia P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Siddhi Patnaik
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Mir A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Joykrushna Jena
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
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Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes. Genes (Basel) 2020; 11:genes11111271. [PMID: 33126655 PMCID: PMC7692064 DOI: 10.3390/genes11111271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
The solute carrier 4 (SLC4) family is a class of cell membranes transporters involved in base transport that plays crucial roles in diverse physiological processes. In our study, 15 slc4 genes were identified and annotated in spotted sea bass, including five members of Cl−/HCO3− exchangers, eight genes coding Na+-dependent HCO3− transporters, and two copies of Na+-coupled borate transporters. The gene sequence and structure, chromosomal and syntenic arrangement, phylogenetic and evolution profiles were analyzed. Results showed that the slc4 gene in teleosts obviously expanded compared with higher vertebrates, arising from teleost-specific whole genome duplication event. Most gene sites of slc4 in spotted sea bass were under strong purifying selection during evolution, while positive selection sites were only detected in slc4a1b, slc4a8, and slc4a10b. Additionally, qRT-PCR results showed that different slc4 genes exhibited distinct branchial expression patterns after alkalinity and salinity stresses, of which the strongly responsive members may play essential roles during these physiological processes. Our study provides the systemic overview of the slc4 gene family in spotted sea bass and enables a better understanding for the evolution of this family and further deciphering the biological roles in maintaining ion and acid–base homeostasis in teleosts.
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Wang Y, Jiang H, Yang L. Transcriptome Analysis of Zebrafish Olfactory Epithelium Reveal Sexual Differences in Odorant Detection. Genes (Basel) 2020; 11:genes11060592. [PMID: 32471067 PMCID: PMC7349279 DOI: 10.3390/genes11060592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 01/04/2023] Open
Abstract
Animals have evolved a large number of olfactory receptor genes in their genome to detect numerous odorants in their surrounding environments. However, we still know little about whether males and females possess the same abilities to sense odorants, especially in fish. In this study, we used deep RNA sequencing to examine the difference of transcriptome between male and female zebrafish olfactory epithelia. We found that the olfactory transcriptomes between males and females are highly similar. We also found evidence of some genes showing differential expression or alternative splicing, which may be associated with odorant-sensing between sexes. Most chemosensory receptor genes showed evidence of expression in the zebrafish olfactory epithelium, with a higher expression level in males than in females. Taken together, our results provide a comprehensive catalog of the genes mediating olfactory perception and pheromone-evoked behavior in fishes.
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Affiliation(s)
- Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan 430056, Hubei, China;
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China;
- Correspondence: ; Tel.: +86-27-6878-0281
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Yang L, Jiang H, Chen J, Lei Y, Sun N, Lv W, Near TJ, He S. Comparative Genomics Reveals Accelerated Evolution of Fright Reaction Genes in Ostariophysan Fishes. Front Genet 2019; 10:1283. [PMID: 31921316 PMCID: PMC6936194 DOI: 10.3389/fgene.2019.01283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
The ostariophysian fishes are the most species-rich clade in freshwaters. This diversification has been suggested to be associated with the fright reaction presented in most ostariophysians. However, the genetic forces that underlie fright reaction remains poorly understood. In the present study, through integrating behavioral, physiological, transcriptomic, and evolutionary genomic analyses, we found that the fright reaction has a broad impact on zebrafish at multiple levels, including changes in swimming behaviors, cortisol levels, and gene expression patterns. In total, 1,555 and 1,599 differentially expressed genes were identified in olfactory mucosae and brain of zebrafish, respectively, with a greater number upregulated after the fright reaction. Functional annotation showed that response to stress and signal transduction were strongly represented, which is directly associated with the fright reaction. These differentially expressed genes were shown to be evolved accelerated under the influence of positive selection, indicating that protein-coding evolution has played a major role in fright reaction. We found the basal vomeronasal type 2 receptors (v2r) gene, v2rl1, displayed significantly decrease expression after fright reaction, which suggests that v2rs may be important to detect the alarm substance and induce the fright reaction. Collectively, based on our transcriptome and evolutionary genomics analyses, we suggest that transcriptional plasticity of gene may play an important role in fright reaction in ostariophysian fishes.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, United States
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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