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Liao K, Xiang Y, Huang F, Huang M, Xu W, Lin Y, Liao P, Wang Z, Yang L, Tian X, Chen D, Wang Z, Liu S, Zhuang Z. Spatial and single-nucleus transcriptomics decoding the molecular landscape and cellular organization of avian optic tectum. iScience 2024; 27:109009. [PMID: 38333704 PMCID: PMC10850779 DOI: 10.1016/j.isci.2024.109009] [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: 09/30/2023] [Revised: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
The avian optic tectum (OT) has been studied for its diverse functions, yet a comprehensive molecular landscape at the cellular level has been lacking. In this study, we applied spatial transcriptome sequencing and single-nucleus RNA sequencing (snRNA-seq) to explore the cellular organization and molecular characteristics of the avian OT from two species: Columba livia and Taeniopygia guttata. We identified precise layer structures and provided comprehensive layer-specific signatures of avian OT. Furthermore, we elucidated diverse functions in different layers, with the stratum griseum periventriculare (SGP) potentially playing a key role in advanced functions of OT, like fear response and associative learning. We characterized detailed neuronal subtypes and identified a population of FOXG1+ excitatory neurons, resembling those found in the mouse neocortex, potentially involved in neocortex-related functions and expansion of avian OT. These findings could contribute to our understanding of the architecture of OT, shedding light on visual perception and multifunctional association.
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Affiliation(s)
- Kuo Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI Research, Hangzhou 310030, China
| | - Ya Xiang
- BGI Research, Hangzhou 310030, China
- College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Fubaoqian Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI Research, Hangzhou 310030, China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wenbo Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Youning Lin
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Pingfang Liao
- BGI Research, Hangzhou 310030, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zishi Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lin Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinmao Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Duoyuan Chen
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shiping Liu
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Zhenkun Zhuang
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
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2
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Alexandrovich YV, Antonov EV, Shikhevich SG, Kharlamova AV, Meister LV, Makovka YV, Shepeleva DV, Gulevich RG, Herbeck YE. The expression profile of genes associated with behavior, stress, and adult neurogenesis along the hippocampal dorsoventral axis in tame and aggressive foxes. Vavilovskii Zhurnal Genet Selektsii 2023; 27:651-661. [PMID: 38213464 PMCID: PMC10782033 DOI: 10.18699/vjgb-23-76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/18/2022] [Accepted: 06/30/2023] [Indexed: 01/13/2024] Open
Abstract
The hippocampus plays the key role in stress response regulation, and stress response appears to be weakened in domesticated animals compared to their wild relatives. The hippocampus is functionally heterogeneous along its dorsoventral axis, with its ventral compartment being more closely involved in stress regulation. An earlier series of experiments was conducted with a unique breeding model of animal domestication, the farm silver fox (Vulpes vulpes), which included tame, aggressive, and unselected animals. A decrease in many indices of the hypothalamic-pituitary-adrenal activity was observed in tame animals. Also, adult hippocampal neurogenesis was more intense in tame foxes, and this fact may relate to reduced stress levels in this experimental population of foxes. Nevertheless, the molecular mechanisms responsible for the reduced stress response in tame animals remain obscure. In this study, serum cortisol levels and the mRNA levels of 13 genes in the dorsal and ventral hippocampus have been measured and compared in tame, aggressive, and unselected foxes. At the current stage of domestication, stress-induced cortisol levels in tame, aggressive, and unselected animals differ significantly from each other: tame foxes show the lowest levels, and aggressive ones, the highest. Twelve genes tested demonstrate significant gene expression differences between the dorsal and ventral hippocampi. These differences are mainly consistent with those found in rodents and humans. In tame foxes, significantly elevated mRNA levels were recorded for several genes: CYP26B1 for cytochrome P450 26B1 and ADRA1A for α1A adrenergic receptor in the dorsal hippocampus, whereas the level of NR3C2 mRNA for mineralocorticoid receptor was higher in the ventral. It is presumed that these genes constitute an important part of the mechanism reducing stress induced by contacts with humans and contribute to linking stress regulation with adult neurogenesis in tame foxes and domesticated animals in general.
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Affiliation(s)
- Yu V Alexandrovich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E V Antonov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Sirius University of Science and Technology, Scientific Center for Translational Medicine, Sochi, Russia
| | - S G Shikhevich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Kharlamova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - L V Meister
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Y V Makovka
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D V Shepeleva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - R G Gulevich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu E Herbeck
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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3
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Boeckx C. What made us "hunter-gatherers of words". Front Neurosci 2023; 17:1080861. [PMID: 36845441 PMCID: PMC9947416 DOI: 10.3389/fnins.2023.1080861] [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: 10/26/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
This paper makes three interconnected claims: (i) the "human condition" cannot be captured by evolutionary narratives that reduce it to a recent 'cognitive modernity', nor by narratives that eliminates all cognitive differences between us and out closest extinct relatives, (ii) signals from paleogenomics, especially coming from deserts of introgression but also from signatures of positive selection, point to the importance of mutations that impact neurodevelopment, plausibly leading to temperamental differences, which may impact cultural evolutionary trajectories in specific ways, and (iii) these trajectories are expected to affect the language phenotypes, modifying what is being learned and how it is put to use. In particular, I hypothesize that these different trajectories influence the development of symbolic systems, the flexible ways in which symbols combine, and the size and configurations of the communities in which these systems are put to use.
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Affiliation(s)
- Cedric Boeckx
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Institute of Complex Systems, Universitat de Barcelona, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
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4
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Theofanopoulou C, Andirkó A, Boeckx C, Jarvis ED. Oxytocin and vasotocin receptor variation and the evolution of human prosociality. COMPREHENSIVE PSYCHONEUROENDOCRINOLOGY 2022; 11:100139. [PMID: 35757177 PMCID: PMC9227999 DOI: 10.1016/j.cpnec.2022.100139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/04/2022] Open
Abstract
Modern human lifestyle strongly depends on complex social traits like empathy, tolerance and cooperation. These diverse facets of social cognition have been associated with variation in the oxytocin receptor (OTR) and its sister genes, the vasotocin/vasopressin receptors (VTR1A/AVPR1A and AVPR1B/VTR1B). Here, we compared the available genomic sequences of these receptors between modern humans, archaic humans, and 12 non-human primate species, and identified sites that show heterozygous variation in modern humans and archaic humans distinct from variation in other primates, and for which we could find association studies with clinical implications. On these sites, we performed a range of analyses (variant clustering, pathogenicity prediction, regulation, linkage disequilibrium frequency), and reviewed the literature on selection data in different modern-human populations. We found five sites with modern human specific variation, where the modern human allele is the major allele in the global population (OTR: rs1042778, rs237885, rs6770632; VTR1A: rs10877969; VTR1B: rs33985287). Among them, variation in the OTR-rs6770632 site was predicted to be the most functional. Two alleles (OTR: rs59190448 and rs237888) present only in modern humans and archaic humans were putatively under positive selection in modern humans, with rs237888 predicted to be a highly functional site. Three sites showed convergent evolution between modern humans and bonobos (OTR: rs2228485 and rs237897; VTR1A: rs1042615), with OTR-rs2228485 ranking highly in terms of functionality and reported to be under balancing selection in modern humans (Schaschl, 2015) [1]. Our findings have implications for understanding hominid prosociality, as well as the similarities between modern human and bonobo social behavior. We compared the oxytocin/vasotocin receptors in modern humans, archaic humans, and non-human primates. We found 5 sites with modern human specific variation. In these sites, the modern human allele is the major allele in the global population. Several sites were predicted to be functional and with selection signatures in modern humans. We also identified 3 sites of convergent evolution in modern humans and bonobos.
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Zhou QJ, Liu X, Zhang L, Wang R, Yin T, Li X, Li G, He Y, Ding Z, Ma P, Wang SZ, Mao B, Zhang S, Wang GD. A single-nucleus transcriptomic atlas of the dog hippocampus reveals the potential relationship between specific cell types and domestication. Natl Sci Rev 2022; 9:nwac147. [PMID: 36569494 PMCID: PMC9772819 DOI: 10.1093/nsr/nwac147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/28/2022] [Accepted: 07/09/2022] [Indexed: 12/27/2022] Open
Abstract
The process of domestication has led to dramatic differences in behavioral traits between domestic dogs and gray wolves. Whole-genome research found that a class of putative positively selected genes were related to various aspects of learning and memory, such as long-term potentiation and long-term depression. In this study, we constructed a single-nucleus transcriptomic atlas of the dog hippocampus to illustrate its cell types, cell lineage and molecular features. Using the transcriptomes of 105 057 nuclei from the hippocampus of a Beagle dog, we identified 26 cell clusters and a putative trajectory of oligodendrocyte development. Comparative analysis revealed a significant convergence between dog differentially expressed genes (DEGs) and putative positively selected genes (PSGs). Forty putative PSGs were DEGs in glutamatergic neurons, especially in Cluster 14, which is related to the regulation of nervous system development. In summary, this study provides a blueprint to understand the cellular mechanism of dog domestication.
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Affiliation(s)
| | | | | | - Rong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China,College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Tingting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaolu Li
- Genomic Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Guimei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yuqi He
- Genomic Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zhaoli Ding
- Genomic Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shi-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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6
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Anastasiadi D, Piferrer F, Wellenreuther M, Benítez Burraco A. Fish as Model Systems to Study Epigenetic Drivers in Human Self-Domestication and Neurodevelopmental Cognitive Disorders. Genes (Basel) 2022; 13:genes13060987. [PMID: 35741749 PMCID: PMC9222608 DOI: 10.3390/genes13060987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022] Open
Abstract
Modern humans exhibit phenotypic traits and molecular events shared with other domesticates that are thought to be by-products of selection for reduced aggression. This is the human self-domestication hypothesis. As one of the first types of responses to a novel environment, epigenetic changes may have also facilitated early self-domestication in humans. Here, we argue that fish species, which have been recently domesticated, can provide model systems to study epigenetic drivers in human self-domestication. To test this, we used in silico approaches to compare genes with epigenetic changes in early domesticates of European sea bass with genes exhibiting methylation changes in anatomically modern humans (comparison 1), and neurodevelopmental cognitive disorders considered to exhibit abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome, and autism spectrum disorders (comparison 2). Overlapping genes in comparison 1 were involved in processes like limb morphogenesis and phenotypes like abnormal jaw morphology and hypopigmentation. Overlapping genes in comparison 2 affected paralogue genes involved in processes such as neural crest differentiation and ectoderm differentiation. These findings pave the way for future studies using fish species as models to investigate epigenetic changes as drivers of human self-domestication and as triggers of cognitive disorders.
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Affiliation(s)
- Dafni Anastasiadi
- Seafood Technologies, The New Zealand Institute for Plant and Food Research, Nelson 7010, New Zealand;
- Correspondence:
| | - Francesc Piferrer
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), 08003 Barcelona, Spain;
| | - Maren Wellenreuther
- Seafood Technologies, The New Zealand Institute for Plant and Food Research, Nelson 7010, New Zealand;
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Antonio Benítez Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, 41004 Seville, Spain;
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7
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Eusebi PG, Sevane N, O'Rourke T, Pizarro M, Boeckx C, Dunner S. Age Effects Aggressive Behavior: RNA-Seq Analysis in Cattle with Implications for Studying Neoteny Under Domestication. Behav Genet 2022; 52:141-153. [PMID: 35032285 PMCID: PMC8860811 DOI: 10.1007/s10519-021-10097-1] [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: 01/23/2021] [Accepted: 12/18/2021] [Indexed: 11/30/2022]
Abstract
The reactive type of aggression is regulated mostly by the brain's prefrontal cortex; however, the molecular changes underlying aggressiveness in adults have not been fully characterized. We used an RNA-seq approach to investigate differential gene expression in the prefrontal cortex of bovines from the aggressive Lidia breed at different ages: young three-year old and adult four-year-old bulls. A total of 50 up and 193 down-regulated genes in the adult group were identified. Furthermore, a cross-species comparative analysis retrieved 29 genes in common with previous studies on aggressive behaviors, representing an above-chance overlap with the differentially expressed genes in adult bulls. We detected changes in the regulation of networks such as synaptogenesis, involved in maintenance and refinement of synapses, and the glutamate receptor pathway, which acts as excitatory driver in aggressive responses. The reduced reactive aggression typical of domestication has been proposed to form part of a retention of juvenile traits as adults (neoteny).
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Affiliation(s)
- Paulina G Eusebi
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain.
| | - Natalia Sevane
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Thomas O'Rourke
- Universitat de Barcelona, Gran Vía de les Corts Catalanes 585, 08007, Barcelona, Spain.,UBICS, Carrer Martí Franqués 1, 08028, Barcelona, Spain
| | - Manuel Pizarro
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Cedric Boeckx
- Universitat de Barcelona, Gran Vía de les Corts Catalanes 585, 08007, Barcelona, Spain.,UBICS, Carrer Martí Franqués 1, 08028, Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Susana Dunner
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
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8
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Wellband K, Roth D, Linnansaari T, Curry RA, Bernatchez L. Environment-driven reprogramming of gamete DNA methylation occurs during maturation and is transmitted intergenerationally in Atlantic Salmon. G3 (BETHESDA, MD.) 2021; 11:jkab353. [PMID: 34849830 PMCID: PMC8664423 DOI: 10.1093/g3journal/jkab353] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/24/2021] [Indexed: 02/06/2023]
Abstract
An epigenetic basis for transgenerational plasticity in animals is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally induced intergenerational effects, but solely in the context of early life environmental differences. Using whole-genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Some genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.
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Affiliation(s)
- Kyle Wellband
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - David Roth
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Tommi Linnansaari
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - R Allen Curry
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
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Wilkins AS, Wrangham R, Fitch WT. The neural crest/domestication syndrome hypothesis, explained: reply to Johnsson, Henriksen, and Wright. Genetics 2021; 219:iyab098. [PMID: 34849912 PMCID: PMC8633094 DOI: 10.1093/genetics/iyab098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/29/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Adam S Wilkins
- Institute of Theoretical Biology, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Richard Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - W Tecumseh Fitch
- Department of Behavioral and Cognitive Biology, University of Vienna, 1090 Vienna, Austria
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10
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Zhang S, Liu W, Liu X, Du X, Zhang K, Zhang Y, Song Y, Zi Y, Qiu Q, Lenstra JA, Liu J. Structural Variants Selected during Yak Domestication Inferred from Long-Read Whole-Genome Sequencing. Mol Biol Evol 2021; 38:3676-3680. [PMID: 33944937 PMCID: PMC8382902 DOI: 10.1093/molbev/msab134] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Structural variants (SVs) represent an important genetic resource for both natural and artificial selection. Here we present a chromosome-scale reference genome for domestic yak (Bos grunniens) that has longer contigs and scaffolds (N50 44.72 and 114.39 Mb, respectively) than reported for any other ruminant genome. We further obtained long-read resequencing data for 6 wild and 23 domestic yaks and constructed a genetic SV map of 372,220 SVs that covers the geographic range of the yaks. The majority of the SVs contains repetitive sequences and several are in or near genes. By comparing SVs in domestic and wild yaks, we identified genes that are predominantly related to the nervous system, behavior, immunity, and reproduction and may have been targeted by artificial selection during yak domestication. These findings provide new insights in the domestication of animals living at high altitude and highlight the importance of SVs in animal domestication.
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Affiliation(s)
- Shangzhe Zhang
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Wenyu Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Xinfeng Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Ke Zhang
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Yang Zhang
- The Supercomputing Center, Lanzhou University, Lanzhou, China
| | - Yongwu Song
- Animal Disease Prevention and Control Center of Gangcha County, Haibei Tibetan Autonomous Prefecture, China
| | - Yunnan Zi
- Animal Husbandry Workstation of Xiahe County, Gannan Tibetan Autonomous Prefecture, China
| | - Qiang Qiu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianquan Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
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11
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Benítez-Burraco A, Chekalin E, Bruskin S, Tatarinova T, Morozova I. Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis. Ann Hum Biol 2021; 48:313-320. [PMID: 34241552 DOI: 10.1080/03014460.2021.1936634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND AND AIM Human evolution resulted from changes in our biology, behaviour, and culture. One source of these changes has been hypothesised to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times. METHODS In this paper, we compare whole-genome data between the Late Neolithic/Bronze Age individuals and modern Europeans. RESULTS We show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups. CONCLUSION We hypothesise that these changes might account for the increased features of self-domestication in modern humans and, ultimately, for subtle recent changes in human cognition and behaviour, including language.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, Faculty of Philology, University of Seville, Seville, Spain
| | - Evgeny Chekalin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Bruskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Tatarinova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Department of Biology, University of La Verne, La Verne, CA, USA.,A. A. Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Department of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
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12
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Trut LN, Kharlamova AV, Pilipenko AS, Herbeck YE. The Fox Domestication Experiment and Dog Evolution: A View Based on Modern Molecular, Genetic, and Archaeological Data. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421070140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Epigenetic mapping of the somatotropic axis in Nile tilapia reveals differential DNA hydroxymethylation marks associated with growth. Genomics 2021; 113:2953-2964. [PMID: 34214627 PMCID: PMC7611323 DOI: 10.1016/j.ygeno.2021.06.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/02/2021] [Accepted: 06/25/2021] [Indexed: 12/29/2022]
Abstract
In vertebrates, the somatotropic axis comprising the pituitary gland, liver and muscle plays a major role in myogenesis. Its output in terms of muscle growth is highly affected by nutritional and environmental cues, and thus likely epigenetically regulated. Hydroxymethylation is emerging as a DNA modification that modulates gene expression but a holistic characterization of the hydroxymethylome of the somatotropic axis has not been investigated to date. Using reduced representation 5-hydroxymethylcytosine profiling we demonstrate tissue-specific localization of 5-hydroxymethylcytosines at single nucleotide resolution. Their abundance within gene bodies and promoters of several growth-related genes supports their pertinent role in gene regulation. We propose that cytosine hydroxymethylation may contribute to the phenotypic plasticity of growth through epigenetic regulation of the somatotropic axis.
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14
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa. Genome Biol Evol 2021; 13:6261762. [PMID: 34009300 PMCID: PMC8214406 DOI: 10.1093/gbe/evab090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/22/2022] Open
Abstract
Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.
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Affiliation(s)
- Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Ling Kui
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Yong-Wang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Nada M Eltayeb
- Department of Animal breeding and Reproduction Technology, College of Animal Production, University of Bahri, Khartoum, Sudan
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture Livestock Fisheries and Irrigation, Nairobi, Kenya
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Erica Gorla
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture, Makurdi, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria
| | - John Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Peter Njoroge
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | | | - Rana Pedar
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Ming-Min Xu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yuan Du
- Nowbio Biotechnology Company, Kunming, China
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, California, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Sheila C Ommeh
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya.,Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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15
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Franco R, Rivas-Santisteban R, Lillo J, Camps J, Navarro G, Reyes-Resina I. 5-Hydroxytryptamine, Glutamate, and ATP: Much More Than Neurotransmitters. Front Cell Dev Biol 2021; 9:667815. [PMID: 33937270 PMCID: PMC8083958 DOI: 10.3389/fcell.2021.667815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/17/2021] [Indexed: 01/08/2023] Open
Abstract
5-hydroxytryptamine (5-HT) is derived from the essential amino acid L-tryptophan. Although the compound has been studied extensively for its neuronal handling and synaptic actions, serotonin 5-HT receptors can be found extra-synaptically and not only in neurons but in many types of mammalian cells, inside and outside the central nervous system (CNS). In sharp contrast, glutamate (Glu) and ATP are better known as metabolism-related molecules, but they also are neurotransmitters, and their receptors are expressed on almost any type of cell inside and outside the nervous system. Whereas 5-hydroxytryptamine and Glu are key regulators of the immune system, ATP actions are more general. 5-hydroxytryptamine, ATP and Glu act through both G protein-coupled receptors (GPCRs), and ionotropic receptors, i.e., ligand gated ion channels. These are the three examples of neurotransmitters whose actions as holistic regulatory molecules are briefly put into perspective here.
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Affiliation(s)
- Rafael Franco
- Department Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain,Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIberNed), Instituto de Salud Carlos III, Madrid, Spain,*Correspondence: Rafael Franco, ;
| | - Rafael Rivas-Santisteban
- Department Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain,Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIberNed), Instituto de Salud Carlos III, Madrid, Spain
| | - Jaume Lillo
- Department Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain,Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIberNed), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Camps
- Department Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain
| | - Gemma Navarro
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIberNed), Instituto de Salud Carlos III, Madrid, Spain,Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Irene Reyes-Resina
- Department Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain,Irene Reyes-Resina,
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16
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Eusebi PG, Sevane N, O'Rourke T, Pizarro M, Boeckx C, Dunner S. Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle. BMC Genomics 2021; 22:245. [PMID: 33827428 PMCID: PMC8028707 DOI: 10.1186/s12864-021-07505-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Aggressive behavior is an ancient and conserved trait, habitual for most animals in order to eat, protect themselves, compete for mating and defend their territories. Genetic factors have been shown to play an important role in the development of aggression both in animals and humans, displaying moderate to high heritability estimates. Although such types of behaviors have been studied in different animal models, the molecular architecture of aggressiveness remains poorly understood. This study compared gene expression profiles of 16 prefrontal cortex (PFC) samples from aggressive and non-aggressive cattle breeds: Lidia, selected for agonistic responses, and Wagyu, selected for tameness. RESULTS A total of 918 up-regulated and 278 down-regulated differentially expressed genes (DEG) were identified, representing above-chance overlap with genes previously identified in studies of aggression across species, as well as those implicated in recent human evolution. The functional interpretation of the up-regulated genes in the aggressive cohort revealed enrichment of pathways such as Alzheimer disease-presenilin, integrins and the ERK/MAPK signaling cascade, all implicated in the development of abnormal aggressive behaviors and neurophysiological disorders. Moreover, gonadotropins, are up-regulated as natural mechanisms enhancing aggression. Concomitantly, heterotrimeric G-protein pathways, associated with low reactivity mental states, and the GAD2 gene, a repressor of agonistic reactions associated with PFC activity, are down-regulated, promoting the development of the aggressive responses selected for in Lidia cattle. We also identified six upstream regulators, whose functional activity fits with the etiology of abnormal behavioral responses associated with aggression. CONCLUSIONS These transcriptional correlates of aggression, resulting, at least in part, from controlled artificial selection, can provide valuable insights into the complex architecture that underlies naturally developed agonistic behaviors. This analysis constitutes a first important step towards the identification of the genes and metabolic pathways that promote aggression in cattle and, providing a novel model species to disentangle the mechanisms underlying variability in aggressive behavior.
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Affiliation(s)
- Paulina G Eusebi
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain.
| | - Natalia Sevane
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Thomas O'Rourke
- Universitat de Barcelona, Gran Vía de les Corts Catalanes 585, 08007, Barcelona, Spain.,UBICS, Carrer Martí Franqués 1, 08028, Barcelona, Spain
| | - Manuel Pizarro
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Cedric Boeckx
- Universitat de Barcelona, Gran Vía de les Corts Catalanes 585, 08007, Barcelona, Spain.,UBICS, Carrer Martí Franqués 1, 08028, Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Susana Dunner
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
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17
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Wrangham RW. Targeted conspiratorial killing, human self-domestication and the evolution of groupishness. EVOLUTIONARY HUMAN SCIENCES 2021; 3:e26. [PMID: 37588548 PMCID: PMC10427284 DOI: 10.1017/ehs.2021.20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Groupishness is a set of tendencies to respond to group members with prosociality and cooperation in ways that transcend apparent self-interest. Its evolution is puzzling because it gives the impression of breaking the ordinary rules of natural selection. Boehm's solution is that moral elements of groupishness originated and evolved as a result of group members becoming efficient executioners of antisocial individuals, and he noted that self-domestication would have proceeded from the same dynamic. Self-domestication is indicated first at ~300,000 years ago and has probably gathered pace ever since, suggesting selection for self-domestication and groupishness for at least 12,000 generations. Here I propose that a specifically human style of violence, targeted conspiratorial killing, contributed importantly to both self-domestication and to promoting groupishness. Targeted conspiratorial killing is unknown in chimpanzees or any other vertebrate, and is significant because it permits coalitions to kill antisocial individuals cheaply. The hypothesis that major elements of groupishness are due to targeted conspiratorial killing helps explain why they are much more elaborated in humans than in other species.
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Affiliation(s)
- Richard W. Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
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18
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O'Rourke T, Martins PT, Asano R, Tachibana RO, Okanoya K, Boeckx C. Capturing the Effects of Domestication on Vocal Learning Complexity. Trends Cogn Sci 2021; 25:462-474. [PMID: 33810982 DOI: 10.1016/j.tics.2021.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 11/28/2022]
Abstract
Domesticated and vocal learning species can serve as informative model organisms for the reduction of reactive aggression and emergence of speech in our lineage. Amidst mounting evidence that domestication modifies vocal repertoires across different species, we focus on the domesticated Bengalese finch, which has a more complex song than the wild-type white-rumped munia. Our explanation for this effect revolves around the glutamate neurotransmitter system. Glutamate signaling (i) is implicated in birdsong learning, (ii) controls dopamine activity in neural circuits crucial for vocal learning, (iii) is disproportionately targeted in the evolution of domesticates, and (iv) regulates stress responses and aggressive behaviors attenuated under domestication. We propose that attenuated excitation of stress-related neural circuits potentiates vocal learning via altered dopaminergic signaling.
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Affiliation(s)
- Thomas O'Rourke
- Section of General Linguistics, University of Barcelona, 08007 Barcelona, Spain; University of Barcelona Institute for Complex Systems (UBICS), 08028 Barcelona, Spain
| | - Pedro Tiago Martins
- Section of General Linguistics, University of Barcelona, 08007 Barcelona, Spain; University of Barcelona Institute for Complex Systems (UBICS), 08028 Barcelona, Spain
| | - Rie Asano
- Department of Systematic Musicology, University of Cologne, 50923 Cologne, Germany
| | - Ryosuke O Tachibana
- Center for Evolutionary Cognitive Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 153-8902 Tokyo, Japan
| | - Kazuo Okanoya
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 153-8902 Tokyo, Japan
| | - Cedric Boeckx
- Section of General Linguistics, University of Barcelona, 08007 Barcelona, Spain; University of Barcelona Institute for Complex Systems (UBICS), 08028 Barcelona, Spain; Catalan Institute for Advanced Studies and Research (ICREA), 08010 Barcelona, Spain.
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19
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Niu F, Zhang B, Feng J, Mao X, Xu XJ, Dong JQ, Liu BY. Protein profiling identified mitochondrial dysfunction and synaptic abnormalities after dexamethasone intervention in rats with traumatic brain injury. Neural Regen Res 2021; 16:2438-2445. [PMID: 33907032 PMCID: PMC8374556 DOI: 10.4103/1673-5374.313047] [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] [Indexed: 11/19/2022] Open
Abstract
Dexamethasone has been widely used after various neurosurgical procedures due to its anti-inflammatory property and the abilities to restore vascular permeability, inhibit free radicals, and reduce cerebrospinal fluid production. According to the latest guidelines for the treatment of traumatic brain injury in the United States, high-dose glucocorticoids cause neurological damage. To investigate the reason why high-dose glucocorticoids after traumatic brain injury exhibit harmful effect, rat controlled cortical impact models of traumatic brain injury were established. At 1 hour and 2 days after surgery, rat models were intraperitoneally administered dexamethasone 10 mg/kg. The results revealed that 31 proteins were significantly upregulated and 12 proteins were significantly downregulated in rat models of traumatic brain injury after dexamethasone treatment. The Ingenuity Pathway Analysis results showed that differentially expressed proteins were enriched in the mitochondrial dysfunction pathway and synaptogenesis signaling pathway. Western blot analysis and immunohistochemistry results showed that Ndufv2, Maob and Gria3 expression and positive cell count in the dexamethasone-treated group were significantly greater than those in the model group. These findings suggest that dexamethasone may promote a compensatory increase in complex I subunits (Ndufs2 and Ndufv2), increase the expression of mitochondrial enzyme Maob, and upregulate synaptic-transmission-related protein Gria3. These changes may be caused by nerve injury after traumatic brain injury treatment by dexamethasone. The study was approved by Institutional Ethics Committee of Beijing Neurosurgical Institute (approval No. 201802001) on June 6, 2018.
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Affiliation(s)
- Fei Niu
- Department of Neurotrauma, Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Bin Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jie Feng
- Key Laboratory of Central Nervous System Injury Research, Center for Brain Tumor, Beijing Institute of Brain Disorders, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xiang Mao
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Xiao-Jian Xu
- Department of Neurotrauma, Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jin-Qian Dong
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bai-Yun Liu
- Department of Neurotrauma, Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University; Center for Nerve Injury and Repair, Beijing Institute of Brain Disorders; China National Clinical Research Center for Neurological Diseases, Beijing, China
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20
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Bertolotti AC, Layer RM, Gundappa MK, Gallagher MD, Pehlivanoglu E, Nome T, Robledo D, Kent MP, Røsæg LL, Holen MM, Mulugeta TD, Ashton TJ, Hindar K, Sægrov H, Florø-Larsen B, Erkinaro J, Primmer CR, Bernatchez L, Martin SAM, Johnston IA, Sandve SR, Lien S, Macqueen DJ. The structural variation landscape in 492 Atlantic salmon genomes. Nat Commun 2020; 11:5176. [PMID: 33056985 PMCID: PMC7560756 DOI: 10.1038/s41467-020-18972-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022] Open
Abstract
Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species. This study presents and validates a novel approach to reliably identify structural variations (SVs) in non-model genomes using whole genome sequencing, which was used to detect 15,483 SVs in 492 Atlantic salmon, shedding light on their roles in genome evolution and the genetic architecture of domestication.
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Affiliation(s)
- Alicia C Bertolotti
- School of Biological Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, UK.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ryan M Layer
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA.,Department of Computer Science, University of Colorado, Boulder, CO, USA
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Michael D Gallagher
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ege Pehlivanoglu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Torfinn Nome
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Matthew P Kent
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Line L Røsæg
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Matilde M Holen
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Teshome D Mulugeta
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | | | - Bjørn Florø-Larsen
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway
| | - Jaakko Erkinaro
- Natural Resources Institute Finland (Luke), P.O. Box 413, FI-90014, Oulu, Finland
| | - Craig R Primmer
- Institute for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS) Pavillon Charles-Eugène Marchand, Université Laval Québec, Québec, QC, Canada
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, UK
| | | | - Simen R Sandve
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
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