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Poirier AC, Melin AD. Smell throughout the life course. Evol Anthropol 2024; 33:e22030. [PMID: 38704704 DOI: 10.1002/evan.22030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]
Abstract
The sense of smell is an important mediator of health and sociality at all stages of life, yet it has received limited attention in our lineage. Olfaction starts in utero and participates in the establishment of social bonds in children, and of romantic and sexual relationships after puberty. Smell further plays a key role in food assessment and danger avoidance; in modern societies, it also guides our consumer behavior. Sensory abilities typically decrease with age and can be impacted by diseases, with repercussions on health and well-being. Here, we critically review our current understanding of human olfactory communication to refute outdated notions that our sense of smell is of low importance. We provide a summary of the biology of olfaction, give a prospective overview of the importance of the sense of smell throughout the life course, and conclude with an outline of the limitations and future directions in this field.
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Affiliation(s)
- Alice C Poirier
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
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2
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Perry EB, Handlos GC, Fenton JM. Impacts of olfactory cues on equine feeding behavior. J Equine Vet Sci 2024; 138:105096. [PMID: 38750945 DOI: 10.1016/j.jevs.2024.105096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 06/03/2024]
Abstract
Anise has demonstrated equine palatability but its olfactory effect is underexplored. The objective was to investigate the effect of the aroma of anise on consumptive behavior. Stock-type horses (n = 8) were used in a crossover 6-day preference test. Palatability stocks were utilized. Bowls containing oats were situated on plates holding gauze soaked with 0.375 ml of anise or corn oil (control). Variables included first diet sniffed (FS), first consumed (FC), first action (FA), and amount consumed (AC). Each trial was video-recorded. Behavior data were analyzed using chi square and Kruskal-Wallis tests. FS and FC were elevated for anise treatment (P = 0.02; P = 0.04). For FA, sniffing was more frequent versus consuming (P < 0.01). AC for anise was twice the daily average of control (P < 0.01). Data represents an important relationship between olfactory stimuli and feeding in horses. To determine thresholds, more work is needed.
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Affiliation(s)
- Erin B Perry
- Department of Animal Science Food & Nutrition, School of Agricultural, Life, and Physical Sciences, Southern Illinois University, 1205 Lincoln Dr., Carbondale, Illinois 62901, United States.
| | - Grace C Handlos
- Department of Animal Science Food & Nutrition, School of Agricultural, Life, and Physical Sciences, Southern Illinois University, 1205 Lincoln Dr., Carbondale, Illinois 62901, United States
| | - Jesse M Fenton
- Department of Animal Science Food & Nutrition, School of Agricultural, Life, and Physical Sciences, Southern Illinois University, 1205 Lincoln Dr., Carbondale, Illinois 62901, United States
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3
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Sampson JM, Morrissey KA, Douek DC, Miller RD. A family of olfactory receptors uniquely expanded in marsupial and monotreme genomes are expressed by a T cell subset also unique to marsupials and monotremes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105149. [PMID: 38340883 PMCID: PMC10926957 DOI: 10.1016/j.dci.2024.105149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Olfactory receptors (OR), expressed on olfactory neurons, mediate the sense of smell. Recently, OR have also been shown to be expressed in non-olfactory tissues, including cells of the immune system. An analysis of single-cell transcriptomes of splenocytes of the grey short-tailed opossum (Monodelphis domestica) found OR are expressed on a subset of T cells, the γμ T cells, that are unique to marsupials and monotremes. A majority of opossum γμ T cells transcriptomes contain OR family 14 transcripts, specifically, from the OR14C subfamily. Amongst the mammals, the OR14 gene family is expanded in the genomes of marsupials and monotremes, and rarer or absent in placental mammals. In summary, here we demonstrate the intriguing correlation that a family of OR genes, abundant in the genomes of marsupials and monotremes, are ectopically expressed in a particular subset of T cells unique to the marsupials and monotremes.
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Affiliation(s)
- Jordan M Sampson
- Center for Evolutionary & Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Kimberly A Morrissey
- Center for Evolutionary & Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert D Miller
- Center for Evolutionary & Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, USA.
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4
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Niimura Y, Biswa BB, Kishida T, Toyoda A, Fujiwara K, Ito M, Touhara K, Inoue-Murayama M, Jenkins SH, Adenyo C, Kayang BB, Koide T. Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents. Mol Biol Evol 2024; 41:msae071. [PMID: 38649162 PMCID: PMC11035023 DOI: 10.1093/molbev/msae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/02/2024] [Accepted: 03/03/2024] [Indexed: 04/25/2024] Open
Abstract
Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.
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Affiliation(s)
- Yoshihito Niimura
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Bhim B Biswa
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Shizuoka, Japan
| | - Takushi Kishida
- Curatorial Division, Museum of Natural and Environmental History, Shizuoka, Japan
- Present address: College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Kazumichi Fujiwara
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
| | - Masato Ito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Scott H Jenkins
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Present address: Biosphere Informatics Laboratory, Department of Social Informatics, Graduate School of Informatics, Kyoto, Japan
| | - Christopher Adenyo
- Livestock and Poultry Research Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Boniface B Kayang
- Department of Animal Science, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Tsuyoshi Koide
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Shizuoka, Japan
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5
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Raja R, Dumontier E, Phen A, Cloutier JF. Insertion of a neomycin selection cassette in the Amigo1 locus alters gene expression in the olfactory epithelium leading to region-specific defects in olfactory receptor neuron development. Genesis 2024; 62:e23594. [PMID: 38590146 DOI: 10.1002/dvg.23594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/10/2024]
Abstract
During development of the nervous system, neurons connect to one another in a precisely organized manner. Sensory systems provide a good example of this organization, whereby the composition of the outside world is represented in the brain by neuronal maps. Establishing correct patterns of neural circuitry is crucial, as inaccurate map formation can lead to severe disruptions in sensory processing. In rodents, olfactory stimuli modulate a wide variety of behaviors essential for survival. The formation of the olfactory glomerular map is dependent on molecular cues that guide olfactory receptor neuron axons to broad regions of the olfactory bulb and on cell adhesion molecules that promote axonal sorting into specific synaptic units in this structure. Here, we demonstrate that the cell adhesion molecule Amigo1 is expressed in a subpopulation of olfactory receptor neurons, and we investigate its role in the precise targeting of olfactory receptor neuron axons to the olfactory bulb using a genetic loss-of-function approach in mice. While ablation of Amigo1 did not lead to alterations in olfactory sensory neuron axonal targeting, our experiments revealed that the presence of a neomycin resistance selection cassette in the Amigo1 locus can lead to off-target effects that are not due to loss of Amigo1 expression, including unexpected altered gene expression in olfactory receptor neurons and reduced glomerular size in the ventral region of the olfactory bulb. Our results demonstrate that insertion of a neomycin selection cassette into the mouse genome can have specific deleterious effects on the development of the olfactory system and highlight the importance of removing antibiotic resistance cassettes from genetic loss-of-function mouse models when studying olfactory system development.
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Affiliation(s)
- Reesha Raja
- The Neuro (Montreal Neurological Institute-Hospital), Montréal, Québec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Québec, Canada
| | - Emilie Dumontier
- The Neuro (Montreal Neurological Institute-Hospital), Montréal, Québec, Canada
| | - Alina Phen
- The Neuro (Montreal Neurological Institute-Hospital), Montréal, Québec, Canada
| | - Jean-François Cloutier
- The Neuro (Montreal Neurological Institute-Hospital), Montréal, Québec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Québec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
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6
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Hirose A, Nakamura G, Nikaido M, Fujise Y, Kato H, Kishida T. Localized Expression of Olfactory Receptor Genes in the Olfactory Organ of Common Minke Whales. Int J Mol Sci 2024; 25:3855. [PMID: 38612665 PMCID: PMC11012115 DOI: 10.3390/ijms25073855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Baleen whales (Mysticeti) possess the necessary anatomical structures and genetic elements for olfaction. Nevertheless, the olfactory receptor gene (OR) repertoire has undergone substantial degeneration in the cetacean lineage following the divergence of the Artiodactyla and Cetacea. The functionality of highly degenerated mysticete ORs within their olfactory epithelium remains unknown. In this study, we extracted total RNA from the nasal mucosae of common minke whales (Balaenoptera acutorostrata) to investigate ORs' localized expression. All three sections of the mucosae examined in the nasal chamber displayed comparable histological structure. However, the posterior portion of the frontoturbinal region exhibited notably high OR expression. Neither the olfactory bulb nor the external skin exhibited the expression of these genes. Although this species possesses four intact non-class-2 ORs, all the ORs expressed in the nasal mucosae belong to class-2, implying the loss of aversion to specific odorants. These anatomical and genomic analyses suggest that ORs are still responsible for olfaction within the nasal region of baleen whales, enabling them to detect desirable scents such as prey and potential mating partners.
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Affiliation(s)
- Ayumi Hirose
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan;
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Gen Nakamura
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan;
| | | | - Hidehiro Kato
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
- The Institute of Cetacean Research, Tokyo 104-0055, Japan
| | - Takushi Kishida
- Museum of Natural and Environmental History, Shizuoka 422-8017, Japan;
- College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Japan
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7
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Fritzsch B, Glover JC. Gene networks and the evolution of olfactory organs, eyes, hair cells and motoneurons: a view encompassing lancelets, tunicates and vertebrates. Front Cell Dev Biol 2024; 12:1340157. [PMID: 38533086 PMCID: PMC10963430 DOI: 10.3389/fcell.2024.1340157] [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: 11/17/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Key developmental pathways and gene networks underlie the formation of sensory cell types and structures involved in chemosensation, vision and mechanosensation, and of the efferents these sensory inputs can activate. We describe similarities and differences in these pathways and gene networks in selected species of the three main chordate groups, lancelets, tunicates, and vertebrates, leading to divergent development of olfactory receptors, eyes, hair cells and motoneurons. The lack of appropriately posited expression of certain transcription factors in lancelets and tunicates prevents them from developing vertebrate-like olfactory receptors and eyes, although they generate alternative structures for chemosensation and vision. Lancelets and tunicates lack mechanosensory cells associated with the sensation of acoustic stimuli, but have gravisensitive organs and ciliated epidermal sensory cells that may (and in some cases clearly do) provide mechanosensation and thus the capacity to respond to movement relative to surrounding water. Although functionally analogous to the vertebrate vestibular apparatus and lateral line, homology is questionable due to differences in the expression of the key transcription factors Neurog and Atoh1/7, on which development of vertebrate hair cells depends. The vertebrate hair cell-bearing inner ear and lateral line thus likely represent major evolutionary advances specific to vertebrates. Motoneurons develop in vertebrates under the control of the ventral signaling molecule hedgehog/sonic hedgehog (Hh,Shh), against an opposing inhibitory effect mediated by dorsal signaling molecules. Many elements of Shh-signaling and downstream genes involved in specifying and differentiating motoneurons are also exhibited by lancelets and tunicates, but the repertoire of MNs in vertebrates is broader, indicating greater diversity in motoneuron differentiation programs.
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Affiliation(s)
- Bernd Fritzsch
- Department of Biological Sciences, University of Nebraska Medical Center, Omaha, NE, United States
| | - Joel C. Glover
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Laboratory of Neural Development and Optical Recording (NDEVOR), Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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8
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Liao BY, Weng MP, Chang TY, Chang AYF, Ching YH, Wu CH. Degeneration of the Olfactory System in a Murid Rodent that Evolved Diurnalism. Mol Biol Evol 2024; 41:msae037. [PMID: 38376543 PMCID: PMC10906987 DOI: 10.1093/molbev/msae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/03/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
In mammalian research, it has been debated what can initiate an evolutionary tradeoff between different senses, and the phenomenon of sensory tradeoff in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this model provides an opportunity for a cross-species investigation where comparative morphological and multi-omic analyses of the Nile rat are made with its closely related nocturnal species, e.g. the mouse (Mus musculus) and the rat (Rattus norvegicus). Thus, morphological examinations were performed, and evolutionary reductions in relative sizes of turbinal bone surfaces, the cribriform plate, and the olfactory bulb were discovered in Nile rats. Subsequently, we compared multiple murid genomes, and profiled olfactory epithelium transcriptomes of mice and Nile rats at various ages with RNA sequencing. The results further demonstrate that, in comparison with mouse olfactory receptor (OR) genes, Nile rat OR genes have experienced less frequent gain, more frequent loss, and more frequent expression reduction during their evolution. Furthermore, functional degeneration of coding sequences in the Nile rat lineage was found in OR genes, yet not in other genes. Taken together, these results suggest that acquisition of improved vision in the Nile rat has been accompanied by degeneration of both olfaction-related anatomical structures and OR gene repertoires, consistent with the hypothesis of an olfaction-vision tradeoff initiated by the switch from a nocturnal to a diurnal lifestyle in mammals.
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Affiliation(s)
- Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Ting-Yan Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Andrew Ying-Fei Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Taiwan, Republic of China
| | - Chia-Hwa Wu
- Laboratory Animal Center, National Health Research Institutes, Taiwan, Republic of China
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9
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Policarpo M, Baldwin MW, Casane D, Salzburger W. Diversity and evolution of the vertebrate chemoreceptor gene repertoire. Nat Commun 2024; 15:1421. [PMID: 38360851 PMCID: PMC10869828 DOI: 10.1038/s41467-024-45500-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Chemoreception - the ability to smell and taste - is an essential sensory modality of most animals. The number and type of chemical stimuli that animals can perceive depends primarily on the diversity of chemoreceptors they possess and express. In vertebrates, six families of G protein-coupled receptors form the core of their chemosensory system, the olfactory/pheromone receptor gene families OR, TAAR, V1R and V2R, and the taste receptors T1R and T2R. Here, we study the vertebrate chemoreceptor gene repertoire and its evolutionary history. Through the examination of 1,527 vertebrate genomes, we uncover substantial differences in the number and composition of chemoreceptors across vertebrates. We show that the chemoreceptor gene families are co-evolving, highly dynamic, and characterized by lineage-specific expansions (for example, OR in tetrapods; TAAR, T1R in teleosts; V1R in mammals; V2R, T2R in amphibians) and losses. Overall, amphibians, followed by mammals, are the vertebrate clades with the largest chemoreceptor repertoires. While marine tetrapods feature a convergent reduction of chemoreceptor numbers, the number of OR genes correlates with habitat in mammals and birds and with migratory behavior in birds, and the taste receptor repertoire correlates with diet in mammals and with aquatic environment in fish.
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Affiliation(s)
- Maxime Policarpo
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Didier Casane
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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10
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Martinez Q, Amson E, Laska M. Does the number of functional olfactory receptor genes predict olfactory sensitivity and discrimination performance in mammals? J Evol Biol 2024; 37:238-247. [PMID: 38297391 DOI: 10.1093/jeb/voae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 12/05/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
The number of functional genes coding for olfactory receptors differs markedly between species and has repeatedly been suggested to be predictive of a species' olfactory capabilities. To test this assumption, we compiled a database of all published olfactory detection threshold values in mammals and used three sets of data on olfactory discrimination performance that employed the same structurally related monomolecular odour pairs with different mammal species. We extracted the number of functional olfactory receptor genes of the 20 mammal species for which we found data on olfactory sensitivity and/or olfactory discrimination performance from the Chordata Olfactory Receptor Database. We found that the overall olfactory detection thresholds significantly correlate with the number of functional olfactory receptor genes. Similarly, the overall proportion of successfully discriminated monomolecular odour pairs significantly correlates with the number of functional olfactory receptor genes. These results provide the first statistically robust evidence for the relationship between olfactory capabilities and their genomics correlates. However, when analysed individually, of the 44 monomolecular odourants for which data on olfactory sensitivity from at least five mammal species are available, only five yielded a significant correlation between olfactory detection thresholds and the number of functional olfactory receptors genes. Also, for the olfactory discrimination performance, no significant correlation was found for any of the 74 relationships between the proportion of successfully discriminated monomolecular odour pairs and the number of functional olfactory receptor genes. While only a rather limited amount of data on olfactory detection thresholds and olfactory discrimination scores in a rather limited number of mammal species is available so far, we conclude that the number of functional olfactory receptor genes may be a predictor of olfactory sensitivity and discrimination performance in mammals.
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Affiliation(s)
| | - Eli Amson
- Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
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11
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Park SJ, Greer PL, Lee N. From odor to oncology: non-canonical odorant receptors in cancer. Oncogene 2024; 43:304-318. [PMID: 38087050 DOI: 10.1038/s41388-023-02908-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 01/31/2024]
Abstract
Odorant receptors, traditionally associated with olfaction as chemoreceptors, have been increasingly recognized for their presence and diverse functions in various non-nasal tissues throughout the body. Beyond their roles in sensory perception, emerging evidence suggests a compelling interplay between odorant receptors and cancer progression as well. Alongside the canonical GPCR odorant receptors, dysregulation of non-canonical odorant receptors such as trace amine-associated receptors (TAARs), formyl peptide receptors (FPRs), and membrane-spanning 4A family (MS4As) has been observed in various cancer types, suggesting their contributions to cancer progression. The roles of these non-canonical chemoreceptors in cancer are complex, with some receptors promoting tumorigenesis and others acting as tumor-suppressing factors upon activation, depending on the cancer type. These findings shed light on the potential of non-canonical odorant receptors as therapeutic targets and prognostic markers in cancer, inviting further exploration to unravel their precise mechanisms of action and implications in cancer biology. In this review, we provide a comprehensive overview of the intricate relationships between these chemoreceptors and various types of cancer, potentially paving the way for innovative odor-based therapeutics. Ultimately, this review discusses the potential development of novel therapeutic strategies targeting these non-canonical chemoreceptors.
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Affiliation(s)
- Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Paul L Greer
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Namgyu Lee
- Department of Biomedical Science and Engineering, Dankook University, Cheonan, 31116, Republic of Korea.
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12
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Nakamuta S, Itoh M, Mori M, Kurita M, Zhang Z, Nikaido M, Miyazaki M, Yokoyama T, Yamamoto Y, Nakamuta N. In situ hybridization analysis of odorant receptor expression in the olfactory organ of the pig-nosed turtle Carettochelys insculpta. Tissue Cell 2023; 85:102255. [PMID: 37922676 DOI: 10.1016/j.tice.2023.102255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
The turtle olfactory organ consists of upper (UCE) and lower (LCE) chamber epithelium, which send axons to the ventral and dorsal portions of the olfactory bulbs, respectively. Generally, the UCE is associated with glands and contains ciliated olfactory receptor neurons (ORNs), while the LCE is devoid of glands and contains microvillous ORNs. However, the olfactory organ of the pig-nosed turtle Carettochelys insculpta appears to be a single olfactory system morphologically: there are no associated glands; ciliated ORNs are distributed throughout the olfactory organ; and the olfactory bulb is not divided into ventral and dorsal portions. In this study, we analyzed the expression of odorant receptors (ORs), the major olfactory receptors in turtles, in the pig-nosed turtle olfactory organ, via in situ hybridization. Of 690 ORs, 375 were classified as class I and 315 as class II. Some class II ORs were expressed predominantly in the posterior dorsomedial walls of the nasal cavity, while other class II ORs and all class I ORs examined were expressed in the remaining region. These results suggest that the pig-nosed turtle olfactory organ can be divided into two regions according to the expression of ORs.
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Affiliation(s)
- Shoko Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Miho Itoh
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi 455-0033, Japan
| | - Masanori Mori
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi 455-0033, Japan
| | - Masanori Kurita
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi 455-0033, Japan
| | - Zicong Zhang
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masao Miyazaki
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Takuya Yokoyama
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Yoshio Yamamoto
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Nobuaki Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
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13
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Ferreira JS, Bruschi DP. Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species. J Mol Evol 2023; 91:793-805. [PMID: 37906255 DOI: 10.1007/s00239-023-10135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Olfaction is a crucial capability for most vertebrates and is realized through olfactory receptors in the nasal cavity. The enormous diversity of olfactory receptors has been created by gene duplication, following a birth-and-death model of evolution. The olfactory receptor genes of the amphibians have received relatively little attention up to now, although recent studies have increased the number of species for which data are available. This study analyzed the diversity and chromosomal distribution of the OR genes of three anuran species (Engystomops pustulosus, Bufo bufo and Hymenochirus boettgeri). The OR genes were identified through searches for homologies, and sequence filtering and alignment using bioinformatic tools and scripts. A high diversity of OR genes was found in all three species, ranging from 917 in B. bufo to 1194 in H. boettgeri, and a total of 2076 OR genes in E. pustulosus. Six OR groups were recognized using an evolutionary gene tree analysis. While E. pustulosus has one of the highest numbers of genes of the gamma group (which detect airborne odorants) yet recorded in an anuran, B. bufo presented the smallest number of pseudogene sequences ever identified, with no pseudogenes in either the beta or epsilon groups. Although H. boettgeri shares many morphological adaptations for an aquatic lifestyle with Xenopus, and presented a similar number of genes related to the detection of water-soluble odorants, it had comparatively far fewer genes related to the detection of airborne odorants. This study is the first to describe the complete OR repertoire of the three study species and represents an important contribution to the understanding of the evolution and function of the sense of smell in vertebrates.
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Affiliation(s)
- Johnny Sousa Ferreira
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil
| | - Daniel Pacheco Bruschi
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil.
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14
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Courcelle M, Fabre PH, Douzery EJP. Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents. Genome Biol Evol 2023; 15:evad197. [PMID: 37972291 PMCID: PMC10653590 DOI: 10.1093/gbe/evad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2023] [Indexed: 11/19/2023] Open
Abstract
Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.
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Affiliation(s)
- Maxime Courcelle
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
- CIRAD, UMR ASTRE, Montpellier, France
| | - Pierre-Henri Fabre
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
- Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, London, United Kingdom
- Institut Universitaire de France (IUF), Section Biologie-Médecine-Santé, Paris, France
| | - Emmanuel J P Douzery
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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15
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Kang M, Ahn B, Youk S, Jeon H, Soundarajan N, Cho ES, Park W, Park C. Individual and population diversity of 20 representative olfactory receptor genes in pigs. Sci Rep 2023; 13:18668. [PMID: 37907519 PMCID: PMC10618239 DOI: 10.1038/s41598-023-45784-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023] Open
Abstract
Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species.
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Affiliation(s)
- Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | | | - Eun-Seok Cho
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Woncheoul Park
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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16
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Carlson KB, Nguyen C, Wcisel DJ, Yoder JA, Dornburg A. Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution. Immunogenetics 2023; 75:465-478. [PMID: 37555888 DOI: 10.1007/s00251-023-01315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/28/2023] [Indexed: 08/10/2023]
Abstract
Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here, we investigate the diversification of vertebrate toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the RAG-mediated adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively, these results provide an unparalleled perspective of TLR diversity and offer a ready framework for testing gene annotations in non-model species.
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Affiliation(s)
- Kara B Carlson
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Genetics and Genomics Academy, North Carolina State University, Raleigh, NC, USA
| | - Cameron Nguyen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Genetics and Genomics Academy, North Carolina State University, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
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17
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Brovkina MV, Chapman MA, Holding ML, Clowney EJ. Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays. BMC Biol 2023; 21:179. [PMID: 37612705 PMCID: PMC10463633 DOI: 10.1186/s12915-023-01673-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND The radiation of mammals at the extinction of the dinosaurs produced a plethora of new forms-as diverse as bats, dolphins, and elephants-in only 10-20 million years. Behind the scenes, adaptation to new niches is accompanied by extensive innovation in large families of genes that allow animals to contact the environment, including chemosensors, xenobiotic enzymes, and immune and barrier proteins. Genes in these "outward-looking" families are allelically diverse among humans and exhibit tissue-specific and sometimes stochastic expression. RESULTS Here, we show that these tandem arrays of outward-looking genes occupy AT-biased isochores and comprise the "tissue-specific" gene class that lack CpG islands in their promoters. Models of mammalian genome evolution have not incorporated the sharply different functions and transcriptional patterns of genes in AT- versus GC-biased regions. To examine the relationship between gene family expansion, sequence content, and allelic diversity, we use population genetic data and comparative analysis. First, we find that AT bias can emerge during evolutionary expansion of gene families in cis. Second, human genes in AT-biased isochores or with GC-poor promoters experience relatively low rates of de novo point mutation today but are enriched for non-synonymous variants. Finally, we find that isochores containing gene clusters exhibit low rates of recombination. CONCLUSIONS Our analyses suggest that tolerance of non-synonymous variation and low recombination are two forces that have produced the depletion of GC bases in outward-facing gene arrays. In turn, high AT content exerts a profound effect on their chromatin organization and transcriptional regulation.
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Affiliation(s)
- Margarita V Brovkina
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Margaret A Chapman
- Neurosciences Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
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18
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Nevers Y, Glover NM, Dessimoz C, Lecompte O. Protein length distribution is remarkably uniform across the tree of life. Genome Biol 2023; 24:135. [PMID: 37291671 PMCID: PMC10251718 DOI: 10.1186/s13059-023-02973-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/16/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND In every living species, the function of a protein depends on its organization of structural domains, and the length of a protein is a direct reflection of this. Because every species evolved under different evolutionary pressures, the protein length distribution, much like other genomic features, is expected to vary across species but has so far been scarcely studied. RESULTS Here we evaluate this diversity by comparing protein length distribution across 2326 species (1688 bacteria, 153 archaea, and 485 eukaryotes). We find that proteins tend to be on average slightly longer in eukaryotes than in bacteria or archaea, but that the variation of length distribution across species is low, especially compared to the variation of other genomic features (genome size, number of proteins, gene length, GC content, isoelectric points of proteins). Moreover, most cases of atypical protein length distribution appear to be due to artifactual gene annotation, suggesting the actual variation of protein length distribution across species is even smaller. CONCLUSIONS These results open the way for developing a genome annotation quality metric based on protein length distribution to complement conventional quality measures. Overall, our findings show that protein length distribution between living species is more uniform than previously thought. Furthermore, we also provide evidence for a universal selection on protein length, yet its mechanism and fitness effect remain intriguing open questions.
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Affiliation(s)
- Yannis Nevers
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland.
| | - Natasha M Glover
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland
- Department of Computer Science, University College London, London, UK
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Odile Lecompte
- Department of Computer Science, Centre de Recherche en Biomédecine de Strasbourg, ICube, UMR 7357, University of Strasbourg, CNRS, Strasbourg, France
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19
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Martinez Q, Courcelle M, Douzery E, Fabre PH. When morphology does not fit the genomes: the case of rodent olfaction. Biol Lett 2023; 19:20230080. [PMID: 37042683 PMCID: PMC10092080 DOI: 10.1098/rsbl.2023.0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
Linking genes to phenotypes has been a major question in evolutionary biology for the last decades. In the genomic era, few studies attempted to link olfactory-related genes to different anatomical proxies. However, they found very inconsistent results. This study is the first to investigate a potential relation between olfactory turbinals and olfactory receptor (OR) genes. We demonstrated that despite the use of similar methodology in the acquisition of data, OR genes do not correlate with the relative and the absolute surface area of olfactory turbinals. These results challenged the interpretations of several studies based on different proxies related to olfaction and their potential relation to olfactory capabilities.
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Affiliation(s)
- Quentin Martinez
- Institut des Sciences de l'Évolution (ISEM, UMR 5554 CNRS-IRD-UM-EPHE), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France
- Staatliches Museum für Naturkunde Stuttgart DE-70191, Stuttgart, Germany
| | - Maxime Courcelle
- Institut des Sciences de l'Évolution (ISEM, UMR 5554 CNRS-IRD-UM-EPHE), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France
| | - Emmanuel Douzery
- Institut des Sciences de l'Évolution (ISEM, UMR 5554 CNRS-IRD-UM-EPHE), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Évolution (ISEM, UMR 5554 CNRS-IRD-UM-EPHE), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France
- Mammal Section, Department of Life Sciences, The Natural History Museum, London SW7 5DB, UK
- Institut Universitaire de France (IUF), Paris, France
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History, Central Park West, 79th St., New York, NY 10024-5192, USA
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20
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Li X, Wang X, Yang C, Lin L, Yuan H, Lei F, Huang Y. A de novo assembled genome of the Tibetan Partridge (Perdix hodgsoniae) and its high-altitude adaptation. Integr Zool 2023; 18:225-236. [PMID: 36049502 DOI: 10.1111/1749-4877.12673] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Tibetan Partridge (Perdix hodgsoniae) is an endemic species distributed in high-altitude areas of 3600-5600 m on the Qinghai-Tibet Plateau. To explore how the species is adapted to the high elevation environment, we assembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis. In total, 134.74 Gb short reads and 30.81 Gb long reads raw data were generated. The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb, with 91.94% complete BUSCOs. The 17 457 genes were annotated, and 11.35% of the genome was composed of repeat sequences. The phylogenetic tree showed that P. hodgsoniae was located at the basal position of the clade, including Golden Pheasant (Chrysolophus pictus), Common Pheasant (Phasianus colchicus), and Mikado Pheasant (Syrmaticus mikado). We found that 1014, 2595, and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P. hodgsoniae, detected using PAML, BUSTED, and aBSREL programs, respectively, of which 965 genes were common under positive selection with 3 different programs. Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected. Gene family evolution showed that 99 gene families experienced significant expansion events, while 6 gene families were under contraction. The total number of olfactory receptor genes was relatively low in P. hodgsoniae. Genomic data provide an important resource for a further study on the evolutionary history of P. hodgsoniae, which provides a new insight into its high-altitude adaptation mechanisms.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engeering, Xi'an University, Xi'an, China
| | - Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Fumin Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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21
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Label-free proteomics to identify keratins and keratin-associated proteins and their effects on the fleece traits of Inner Mongolia Cashmere Goats. CZECH JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.17221/93/2022-cjas] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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22
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Prostaglandin F 2α drives female pheromone signaling in cichlids, revealing a basis for evolutionary divergence in olfactory signaling. Proc Natl Acad Sci U S A 2023; 120:e2214418120. [PMID: 36584295 PMCID: PMC9910499 DOI: 10.1073/pnas.2214418120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pheromones play essential roles in reproduction in many species. Prostaglandin F2α (PGF2α) acts as a female reproductive hormone and as a sex pheromone in some species. An olfactory receptor (OR) for PGF2α was recently discovered in zebrafish, but this signaling pathway is evolutionarily labile. To understand the evolution of signals that attract males to fertile females, we used the African cichlid Astatotilapia burtoni and found that adult males strongly prefer fertile female odors. Injection of a prostaglandin synthesis inhibitor abolishes this attractivity of fertile females, indicating these hormones are necessary for pheromonal signaling. Unlike zebrafish, A. burtoni males are insensitive to PGF2α, but they do exhibit strong preference for females injected with PGF2α. This attractiveness is independent of the PGF2α hormonal receptor Ptgfr, indicating that this pheromone signaling derives from PGF2α metabolization into a yet-undiscovered pheromone. We further discovered that fish that are insensitive to PGF2α lack an ortholog for the OR Or114 that zebrafish use to detect PGF2α. These results indicate that PGF2α itself does not directly induce male preference in cichlids. Rather, it plays a vital role that primes females to become attractive via an alternative male OR.
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23
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Sato-Akuhara N, Trimmer C, Keller A, Niimura Y, Shirasu M, Mainland JD, Touhara K. Genetic variation in the human olfactory receptor OR5AN1 associates with the perception of musks. Chem Senses 2023; 48:bjac037. [PMID: 36625229 PMCID: PMC9874024 DOI: 10.1093/chemse/bjac037] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 01/11/2023] Open
Abstract
Humans have significant individual variations in odor perception, derived from their experience or sometimes from differences in the olfactory receptor (OR) gene repertoire. In several cases, the genetic variation of a single OR affects the perception of its cognate odor ligand. Musks are widely used for fragrance and are known to demonstrate specific anosmia. It, however, remains to be elucidated whether the OR polymorphism contributes to individual variations in musk odor perception. Previous studies reported that responses of the human musk receptor OR5AN1 to a variety of musks in vitro correlated well with perceptual sensitivity to those odors in humans and that the mouse ortholog, Olfr1440 (MOR215-1), plays a critical role in muscone perception. Here, we took advantage of genetic variation in OR5AN1 to examine how changes in receptor sensitivity are associated with human musk perception. We investigated the functional differences between OR5AN1 variants in an in vitro assay and measured both perceived intensity and detection threshold in human subjects with different OR5AN1 genotypes. Human subjects homozygous for the more sensitive L289F allele had a lower detection threshold for muscone and found macrocyclic musks to be more intense than subjects homozygous for the reference allele. These results demonstrate that the genetic variation in OR5AN1 contributes to perceptual differences for some musks. In addition, we found that the more functional variant of OR5A1, a receptor involved in β-ionone perception, is associated with the less functional variant of OR5AN1, suggesting that the perceived intensities of macrocyclic musks and β-ionone are inversely correlated.
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Affiliation(s)
- Narumi Sato-Akuhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Casey Trimmer
- Monell Chemical Senses Center, Philadelphia, PA 19104, United States
| | - Andreas Keller
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, United States
| | - Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, 1-1, Gakuen Kibanadai Nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Mika Shirasu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Joel D Mainland
- Monell Chemical Senses Center, Philadelphia, PA 19104, United States
- Department of Neuroscience, University of Pennsylvania School of Medicine, Philadelphia, PA, United States
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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24
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Han W, Wu Y, Zeng L, Zhao S. Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2539-2551. [PMID: 35696018 DOI: 10.1007/s11427-021-2081-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 06/15/2023]
Abstract
Olfactory receptors are poorly annotated for most genome-sequenced chordates. To address this deficiency, we developed a nhmmer-based olfactory receptor annotation tool Genome2OR ( https://github.com/ToHanwei/Genome2OR.git ), and used it to process 1,695 sequenced chordate genomes in the NCBI Assembly database as of January, 2021. In total, 765,248 olfactory receptor genes were annotated, with 404,426 functional genes and 360,822 pseudogenes, which represents a four-fold increase in the number of annotated olfactory receptors. Based on the annotation data, we built a database called Chordata Olfactory Receptor Database (CORD, https://cord.ihuman.shanghaitech.edu.cn ) for archiving, analysing and disseminating the data. Beyond the primary data, we offer derivative information, including pictures of species, cross references to public databases, structural models, sequence similarity networks and sequence profiles in the CORD. Furthermore, we did brief analyses on these receptors, including building a huge protein sequence similarity network covering all receptors in the database, and clustering them into 20 communities, classifying the 20 communities into three categories based on their presences/absences in ray-finned fish and/or lobe-finned fish. We infer that olfactory receptors should have unique activation and desensitization mechanisms by analysing their sequences and structural models. We believe the CORD can benefit the researchers and the general public who are interested in olfaction.
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Affiliation(s)
- Wei Han
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Liting Zeng
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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25
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Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics 2022; 16:56. [PMID: 36369063 PMCID: PMC9652883 DOI: 10.1186/s40246-022-00429-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA.
| | - Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel W Nebert
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, OH, 45267, USA
- Department of Pediatrics and Molecular Developmental Biology, Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey P Townsend
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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McGlone JJ, Archer C, Henderson M. Interpretive review: Semiochemicals in domestic pigs and dogs. Front Vet Sci 2022; 9:967980. [PMID: 36387395 PMCID: PMC9640746 DOI: 10.3389/fvets.2022.967980] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/05/2022] [Indexed: 01/14/2024] Open
Abstract
This interpretive review includes discussion of the available scientific literature with interpretations by the authors. The broad field of semiochemicals can be confusing to scientists and consumers. This review attempts to summarize the known scientific studies for pig and dog semiochemicals while at the same time attempting to refine our use of terminology. The specific objectives of this interpretive review are to summarize and interpret much of the key scientific literature (but not the lay literature) on semiochemicals in pigs and dogs to include (1) definitions of semiochemicals and related molecules including pheromones, (2) to briefly summarize olfactory organs, and (3) and to examine the scientific literature for semiochemical mechanisms and applications in dogs and pigs (two domesticated species with known olfactory acuity). Dogs and pigs have olfactory features that are similar in that they both lack certain olfactory organs (Grueneberg ganglion and Septal Organ) and they have a small vomeronasal organ (VNO) without some major receptors that are found in other species. The primary olfactory organs for both pigs and dogs are the main olfactory epithelium and perhaps the trigeminal nerve. Several examples of pheromones activating the brain via the MOE or Trigeminal nerve rather than the VNO challenge the concept that the VNO is the site of pheromone sensing. We believe it is not appropriate to label something a pheromone when evidence is not available to show that it is a pheromone. We offer definitions for the terms semiochemicals, pheromones, interomones and others and then determine if the evidence is sufficient to call certain semiochemicals a pheromone. Here we review mixed, largely negative, scientific reports of the efficacy of some products labeled as "pheromones" that are more appropriately called semiochemicals. Interomones can have a more powerful effect on dog behavior and physiology than semiochemicals marketed as pheromones. Because marketing of semiochemicals is far ahead of the science, bringing some logic and uniformity to the field will benefit animals and hopefully cause less consumer confusion. Semiochemicals have the potential to offer powerful solutions to behavioral problems using more naturally occurring molecules.
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Affiliation(s)
- John J. McGlone
- Laboratory of Animal Behavior, Physiology and Welfare, Texas Tech University, Lubbock, TX, United States
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Kim C, Lee KK, Kang MS, Shin DM, Oh JW, Lee CS, Han DW. Artificial olfactory sensor technology that mimics the olfactory mechanism: a comprehensive review. Biomater Res 2022; 26:40. [PMID: 35986395 PMCID: PMC9392354 DOI: 10.1186/s40824-022-00287-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/13/2022] [Indexed: 11/19/2022] Open
Abstract
Artificial olfactory sensors that recognize patterns transmitted by olfactory receptors are emerging as a technology for monitoring volatile organic compounds. Advances in statistical processing methods and data processing technology have made it possible to classify patterns in sensor arrays. Moreover, biomimetic olfactory recognition sensors in the form of pattern recognition have been developed. Deep learning and artificial intelligence technologies have enabled the classification of pattern data from more sensor arrays, and improved artificial olfactory sensor technology is being developed with the introduction of artificial neural networks. An example of an artificial olfactory sensor is the electronic nose. It is an array of various types of sensors, such as metal oxides, electrochemical sensors, surface acoustic waves, quartz crystal microbalances, organic dyes, colorimetric sensors, conductive polymers, and mass spectrometers. It can be tailored depending on the operating environment and the performance requirements of the artificial olfactory sensor. This review compiles artificial olfactory sensor technology based on olfactory mechanisms. We introduce the mechanisms of artificial olfactory sensors and examples used in food quality and stability assessment, environmental monitoring, and diagnostics. Although current artificial olfactory sensor technology has several limitations and there is limited commercialization owing to reliability and standardization issues, there is considerable potential for developing this technology. Artificial olfactory sensors are expected to be widely used in advanced pattern recognition and learning technologies, along with advanced sensor technology in the future.
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Berton MP, de Lemos MVA, Stafuzza NB, Simielli Fonseca LF, Silva DBDS, Peripolli E, Pereira ASC, Magalhães AFB, Albuquerque LG, Baldi F. Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle. Anim Genet 2022; 53:570-582. [PMID: 35811456 DOI: 10.1111/age.13242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 06/06/2022] [Accepted: 06/22/2022] [Indexed: 11/26/2022]
Abstract
This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p < 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.
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Affiliation(s)
- Mariana Piatto Berton
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | | | | | | | | | - Elisa Peripolli
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Angélica S C Pereira
- Departamento de Nutrição e Produção Animal, Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Pirassununga, Brazil
| | - Ana Fabricia Braga Magalhães
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Lucia G Albuquerque
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
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Zhu P, Liu S, Tian Y, Chen Y, Chen W, Wang P, Du L, Wu C. In Vivo Bioelectronic Nose Based on a Bioengineered Rat Realizes the Detection and Classification of Multiodorants. ACS Chem Neurosci 2022; 13:1727-1737. [PMID: 35642309 DOI: 10.1021/acschemneuro.2c00015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Inspired by the powerful capability of the biological olfactory system, we developed an in vivo bioelectronic nose based on a bioengineered rat by recording electrophysiological-responsive signals from the olfactory bulb with implanted multichannel microelectrodes. The bioengineered rat was prepared by overexpressing a selected olfactory receptor (OR3) on the rat olfactory epithelium, and multichannel electrophysiological signals were obtained from the mitral/tufted (M/T) cell population of the olfactory bulb. The classification of target multiodorants was realized by analyzing the redundant stimuli-responsive firing information. Ligand odorants induced significant firing changes with specific response patterns compared with nonligand odorants. The responsive curves were dependent on the concentration of target ligand odorants ranging from 10-6 to 10-3 M, and the detection limit was as low as 10-5 M. In addition, different ligand odorants were successfully discriminated via principal component analysis. This in vivo bioelectronic nose provides a novel approach for the detection of specific target odorants and has promising application potential in the field of rapid on-site odor discrimination.
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Affiliation(s)
- Ping Zhu
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Sciences, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, China
| | - Shuge Liu
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Sciences, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, China
| | - Yulan Tian
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Sciences, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, China
| | - Yating Chen
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Sciences, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, China
| | - Wei Chen
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Sciences, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, China
| | - Ping Wang
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, China
| | - Liping Du
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Sciences, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, China
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Chunsheng Wu
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Sciences, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, China
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30
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Zhou C, Liu Y, Zheng X, Shang K, Cheng M, Wang L, Yang N, Yue B. Characterization of olfactory receptor repertoires provides insights into the high-altitude adaptation of the yak based on the chromosome-level genome. Int J Biol Macromol 2022; 209:220-230. [PMID: 35378160 DOI: 10.1016/j.ijbiomac.2022.03.194] [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: 09/14/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/15/2022]
Abstract
Olfaction in vertebrates plays pivotal parts in many aspects, such as localizing prey or food, mating behavior, avoiding predators, and social communication. Yak (Bos grunniens) is the only Bos species that can thrive in high-altitude areas. In view of the critical role of olfactory receptors (ORs) in the specific recognition of diverse stimuli, investigating the evolutionary dynamics of ORs in the yak means a lot. In this study, we used the chromosome-level genome of the yak to identify the ORs genes and discussed the effects of high altitude on the yak's olfaction by comparing the yak with other low-altitude living Bos species (Bos frontalis (gayal), Bos gaurus (gaur), Bos indicus (zebu) and Bos taurus (cattle)). The yak had 400 OR genes, including 264 functional genes, 16 partial genes and 120 OR pseudo genes. There were 387 OR genes mapped to yak 31 chromosomes, and chromosomes 13 and 8 had the most OR genes and functional OR genes. Among these five Bos species, yak had the least number of OR gene subfamilies, OR genes and functional OR genes, while the total number of OR genes in gayal (n = 784) was almost twice as many as that of yak, indicating that the olfaction of yak may be less developed. In addition, the phylogenetic relationships of the functional Bos OR genes were illustrated, which comprised 79 families and 466 subfamilies distributed in two classes (Class I and Class II). There were 76 OR gene subfamilies shared by these five Bos species and 17 OR gene subfamilies were unique to the yak. The potential odor specificity of 44 yak OR genes was identified through the similarity to human OR protein sequences. Remarkably, yak lacks β-ionone and Isovaleric acid(IVA)-related ORs, which may be related to the decline of high-altitude herbaceous plant diversity and underdeveloped yak sweat glands. The conserved motifs of OR genes were highly conserved in Bos species. These results provided a solid foundation for further studies on the molecular mechanisms of the yak's adaptation to the high-altitude environment in olfaction.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Yi Liu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Xiaofeng Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Ke Shang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Meiling Cheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Lei Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, PR China; Collaborative Innovation Center for Ecological Animal Husbandry of Qinghai- Tibetan plateau, Southwest Minzu University.
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China.
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31
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Florini F, Visone JE, Deitsch KW. Shared Mechanisms for Mutually Exclusive Expression and Antigenic Variation by Protozoan Parasites. Front Cell Dev Biol 2022; 10:852239. [PMID: 35350381 PMCID: PMC8957917 DOI: 10.3389/fcell.2022.852239] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2022] [Indexed: 01/05/2023] Open
Abstract
Cellular decision-making at the level of gene expression is a key process in the development and evolution of every organism. Variations in gene expression can lead to phenotypic diversity and the development of subpopulations with adaptive advantages. A prime example is the mutually exclusive activation of a single gene from within a multicopy gene family. In mammals, this ranges from the activation of one of the two immunoglobulin (Ig) alleles to the choice in olfactory sensory neurons of a single odorant receptor (OR) gene from a family of more than 1,000. Similarly, in parasites like Trypanosoma brucei, Giardia lamblia or Plasmodium falciparum, the process of antigenic variation required to escape recognition by the host immune system involves the monoallelic expression of vsg, vsp or var genes, respectively. Despite the importance of this process, understanding how this choice is made remains an enigma. The development of powerful techniques such as single cell RNA-seq and Hi-C has provided new insights into the mechanisms these different systems employ to achieve monoallelic gene expression. Studies utilizing these techniques have shown how the complex interplay between nuclear architecture, physical interactions between chromosomes and different chromatin states lead to single allele expression. Additionally, in several instances it has been observed that high-level expression of a single gene is preceded by a transient state where multiple genes are expressed at a low level. In this review, we will describe and compare the different strategies that organisms have evolved to choose one gene from within a large family and how parasites employ this strategy to ensure survival within their hosts.
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Affiliation(s)
| | | | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States
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32
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Coppola DM. The sorption/chromatography hypothesis of olfactory discrimination: The rise, fall, and rebirth of a Phoenix. Bioessays 2022; 44:e2100263. [PMID: 34984707 DOI: 10.1002/bies.202100263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/09/2022]
Abstract
Herein, I discuss the enduring mystery of the receptor layout in the vertebrate olfactory system. Since the awarding of the 2004 Nobel Prize to Axel and Buck for their discovery of the gene family that encodes olfactory receptors, our field has enjoyed a golden era. Despite this Renaissance, an answer to one of the most fundamental questions for any sensory system-what is the anatomical logic of its receptor array?-eludes us, still, for olfaction! Indeed, the only widely debated hypothesis, finding its origins in the musing of another Nobel laureate Sir Edgar Adrian, has it that the vertebrate nose organizes its receptors according to the "sorptive" properties of their ligands. This idea, known as the "sorption" or "chromatography" hypothesis, enjoys considerable support despite being controversial. Here, I review the history of the hypothesis-its rises and falls-and discuss the latest data and future prospects for this perennial idea whose history I liken to the mythical Phoenix.
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Affiliation(s)
- David M Coppola
- Department of Biology, Randolph-Macon College, Ashland, Virginia, 23005, USA
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33
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Orrock JL, Abueg L, Gammie S, Munshi‐South J. Exome sequencing of deer mice on two California Channel Islands identifies potential adaptation to strongly contrasting ecological conditions. Ecol Evol 2021; 11:17191-17201. [PMID: 34938502 PMCID: PMC8668806 DOI: 10.1002/ece3.8357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding the forces that drive genotypic and phenotypic change in wild populations is a central goal of evolutionary biology. We examined exome variation in populations of deer mice from two of the California Channel Islands: Peromyscus maniculatus elusus from Santa Barbara Island and P. m. santacruzae from Santa Cruz Island exhibit significant differences in olfactory predator recognition, activity timing, aggressive behavior, morphology, prevalence of Sin Nombre virus, and population densities. We characterized variation in protein-coding regions using exome capture and sequencing of 25 mice from Santa Barbara Island and 22 mice from Santa Cruz Island. We identified and examined 386,256 SNPs using three complementary methods (BayeScan, pcadapt, and LFMM). We found strong differences in molecular variation between the two populations and 710 outlier SNPs in protein-coding genes that were detected by all three methods. We identified 35 candidate genes from this outlier set that were related to differences in phenotypes between island populations. Enrichment analyses demonstrated that patterns of molecular variation were associated with biological processes related to response to chemical stimuli and regulation of immune processes. Candidate genes associated with olfaction (Gfy, Tlr2, Vmn13r2, numerous olfactory receptor genes), circadian activity (Cry1), anxiety (Brca1), immunity (Cd28, Eif2ak4, Il12a, Syne1), aggression (Cyp19a, Lama2), and body size (Bc16, Syne1) exhibited non-synonymous mutations predicted to have moderate to large effects. Variation in olfaction-related genes, including a stop codon in the Santa Barbara Island population, suggests loss of predator-recognition traits at the molecular level, consistent with a lack of behavioral aversion to fox feces. These findings also suggest that divergent pathogen prevalence and population density may have influenced adaptive immunity and behavioral phenotypes, such as reduced aggression. Overall, our study indicates that ecological differences between islands are associated with signatures of selection in protein-coding genes underlying phenotypes that promote success in those environments.
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Affiliation(s)
- John L. Orrock
- Department of Integrative BiologyUniversity of WisconsinMadisonWisconsinUSA
| | - Linelle Abueg
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNew YorkUSA
| | - Stephen Gammie
- Department of Integrative BiologyUniversity of WisconsinMadisonWisconsinUSA
| | - Jason Munshi‐South
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNew YorkUSA
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Abbas G, Tang S, Noble J, Lane RP. Olfactory receptor coding sequences cause silencing of episomal constructs in multiple cell lines. Mol Cell Neurosci 2021; 117:103681. [PMID: 34742908 PMCID: PMC8669572 DOI: 10.1016/j.mcn.2021.103681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022] Open
Abstract
The mammalian olfactory system consists of sensory neurons with specialized odorant-binding capability accomplished by mutually exclusive odorant receptor (OR) expression. Mutually exclusive OR expression is a complex multi-step process regulated by a number of cis and trans factors, including pan-silencing of all OR genes preceding the robust and stable expression of the one OR selected in each sensory neuron. We transfected two olfactory-placode-derived cell lines modeling immature odorant sensory neurons, as well as the GD25 fibroblast cell line, with episomes containing CMV-driven GFP and TK-driven hygromycin reporter genes. We inserted various coding sequences, along with an IRES, immediately upstream of the GFP gene to produce bicistronic mRNAs driven from the local CMV promoter. We found that the presence of several OR coding sequences resulted in significantly diminished episomal expression of GFP in all three cell lines. These findings suggest that OR coding sequences have intrinsic self-silencing capability that might facilitate mutually exclusive OR expression in olfactory sensory neurons by making it less likely that multiple ORs acquire an above-threshold level of expression at once.
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Affiliation(s)
- Ghazia Abbas
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA
| | - Spencer Tang
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA
| | - Joyce Noble
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA
| | - Robert P Lane
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA.
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35
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Du H, Ong YS, Knittel M, Mawhorter R, Liu N, Gross G, Tojo R, Libeskind-Hadas R, Wu YC. Multiple Optimal Reconciliations Under the Duplication-Loss-Coalescence Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2144-2156. [PMID: 31199267 DOI: 10.1109/tcbb.2019.2922337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gene trees can differ from species trees due to a variety of biological phenomena, the most prevalent being gene duplication, horizontal gene transfer, gene loss, and coalescence. To explain topological incongruence between the two trees, researchers apply reconciliation methods, often relying on a maximum parsimony framework. However, while several studies have investigated the space of maximum parsimony reconciliations (MPRs) under the duplication-loss and duplication-transfer-loss models, the space of MPRs under the duplication-loss-coalescence (DLC) model remains poorly understood. To address this problem, we present new algorithms for computing the size of MPR space under the DLC model and sampling from this space uniformly at random. Our algorithms are efficient in practice, with runtime polynomial in the size of the species and gene tree when the number of genes that map to any given species is fixed, thus proving that the MPR problem is fixed-parameter tractable. We have applied our methods to a biological data set of 16 fungal species to provide the first key insights in the space of MPRs under the DLC model. Our results show that a plurality reconciliation, and underlying events, are likely to be representative of MPR space.
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36
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Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila. Genome Res 2021; 31:2069-2079. [PMID: 34675069 PMCID: PMC8559708 DOI: 10.1101/gr.275503.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/22/2021] [Indexed: 11/25/2022]
Abstract
Dosage compensation (DC) on the X Chromosome counteracts the deleterious effects of gene loss on the Y Chromosome. However, DC is not efficient if the X Chromosome also degenerates. This indeed occurs in Drosophila miranda, in which both the neo-Y and the neo-X are under accelerated pseudogenization. To examine the generality of this pattern, we investigated the evolution of two additional neo-sex chromosomes that emerged independently in D. albomicans and D. americana and reanalyzed neo-sex chromosome evolution in D. miranda. Comparative genomic and transcriptomic analyses revealed that the pseudogenization rate on the neo-X is also accelerated in D. albomicans and D. americana although to a lesser extent than in D. miranda. In males, neo-X-linked genes whose neo-Y-linked homologs are pseudogenized tended to be up-regulated more than those whose neo-Y-linked homologs remain functional. Moreover, genes under strong functional constraint and genes highly expressed in the testis tended to remain functional on the neo-X and neo-Y, respectively. Focusing on the D. miranda and D. albomicans neo-sex chromosomes that emerged independently from the same autosome, we further found that the same genes tend to become pseudogenized in parallel on the neo-Y. These genes include Idgf6 and JhI-26, which may be unnecessary or even harmful in males. Our results indicate that neo-sex chromosomes in Drosophila share a common evolutionary trajectory after their emergence, which may prevent sex chromosomes from being an evolutionary dead end.
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AlMatrouk A, Lemons K, Ogura T, Lin W. Modification of the Peripheral Olfactory System by Electronic Cigarettes. Compr Physiol 2021; 11:2621-2644. [PMID: 34661289 DOI: 10.1002/cphy.c210007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electronic cigarettes (e-cigs) are used by millions of adolescents and adults worldwide. Commercial e-liquids typically contain flavorants, propylene glycol, and vegetable glycerin with or without nicotine. These chemical constituents are detected and evaluated by chemosensory systems to guide and modulate vaping behavior and product choices of e-cig users. The flavorants in e-liquids are marketing tools. They evoke sensory percepts of appealing flavors through activation of chemical sensory systems to promote the initiation and sustained use of e-cigs. The vast majority of flavorants in e-liquids are volatile odorants, and as such, the olfactory system plays a dominant role in perceiving these molecules that enter the nasal cavity either orthonasally or retronasally during vaping. In addition to flavorants, e-cig aerosol contains a variety of by-products generated through heating the e-liquids, including odorous irritants, toxicants, and heavy metals. These harmful substances can directly and adversely impact the main olfactory epithelium (MOE). In this article, we first discuss the olfactory contribution to e-cig flavor perception. We then provide information on MOE cell types and their major functions in olfaction and epithelial maintenance. Olfactory detection of flavorants, nicotine, and odorous irritants and toxicants are also discussed. Finally, we discuss the cumulated data on modification of the MOE by flavorant exposure and toxicological impacts of formaldehyde, acrolein, and heavy metals. Together, the information presented in this overview may provide insight into how e-cig exposure may modify the olfactory system and adversely impact human health through the alteration of the chemosensory factor driving e-cig use behavior and product selections. © 2021 American Physiological Society. Compr Physiol 11:2621-2644, 2021.
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Affiliation(s)
- Abdullah AlMatrouk
- General Department of Criminal Evidence, Forensic Laboratories, Ministry of Interior, Farwaniyah, Kuwait.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Kayla Lemons
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Tatsuya Ogura
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Weihong Lin
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
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38
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Yohe LR, Leiser-Miller LB, Kaliszewska ZA, Donat P, Santana SE, Dávalos LM. Diversity in olfactory receptor repertoires is associated with dietary specialization in a genus of frugivorous bat. G3 (BETHESDA, MD.) 2021; 11:jkab260. [PMID: 34568918 PMCID: PMC8473985 DOI: 10.1093/g3journal/jkab260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/19/2021] [Indexed: 11/30/2022]
Abstract
Mammalian olfactory receptor genes (ORs) are a diverse family of genes encoding proteins that directly interact with environmental chemical cues. ORs evolve via gene duplication in a birth-death fashion, neofunctionalizing and pseudogenizing over time. Olfaction is a primary sense used for food detection in plant-visiting bats, but the relationship between dietary specialization and OR repertoire diversity is unclear. Within neotropical Leaf-nosed bats (Phyllostomidae), many lineages are plant specialists, and some have a distinct OR repertoire compared to insectivorous species. Yet, whether specialization on particular plant genera is associated with the evolution of specialized, less diverse OR repertoires has never been tested. Using targeted sequence capture, we sequenced the OR repertoires of three sympatric species of short-tailed fruit bats (Carollia), which vary in their degree of specialization on the fruits of Piper plants. We characterized orthologous vs duplicated receptors among Carollia species, and explored the diversity and redundancy of the receptor gene repertoire. At the species level, the most dedicated Piper specialist, Carollia castanea, had lower OR diversity compared to the two generalists (C. sowelli and C. perspicillata), but we discovered a few unique sets of ORs within C. castanea with high redundancy of similar gene duplicates. These unique receptors potentially enable C. castanea to detect Piper fruit odorants better than its two congeners. Carollia perspicillata, the species with the most generalist diet, had a higher diversity of intact receptors, suggesting the ability to detect a wider range of odorant molecules. Variation among ORs may be a factor in the coexistence of these sympatric species, facilitating the exploitation of different plant resources. Our study sheds light on how gene duplication and changes in OR diversity may play a role in dietary adaptations and underlie ecological interactions between bats and plants.
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Affiliation(s)
- Laurel R Yohe
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT 06511, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | | | | | - Paul Donat
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sharlene E Santana
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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Escoda L, Castresana J. The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species. Evol Appl 2021; 14:1898-1913. [PMID: 34295371 PMCID: PMC8288019 DOI: 10.1111/eva.13249] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/19/2021] [Accepted: 04/27/2021] [Indexed: 01/23/2023] Open
Abstract
The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. To understand these processes, the complete genome of the Pyrenean desman was sequenced and assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. In addition, a severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created one of the lowest genomic heterozygosity values recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals, revealing that functional diversity can be maintained up to a certain extent. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. In conclusion, the genomic landscape of each analysed Pyrenean desman turned out to be strikingly distinctive and was a clear reflection of its recent ancestry and current conservation conditions. These results may help characterize the genomic health of each individual, and can be crucial for the conservation and management of the species.
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Affiliation(s)
- Lídia Escoda
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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Driver RJ, Balakrishnan CN. Highly contiguous genomes improve the understanding of avian olfactory receptor repertoires. Integr Comp Biol 2021; 61:1281-1290. [PMID: 34180521 DOI: 10.1093/icb/icab150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/16/2021] [Accepted: 06/25/2021] [Indexed: 11/14/2022] Open
Abstract
Third generation (long read-based) sequencing technologies are reshaping our understanding of genome structure and function. One of the most persistent challenges in genome biology has been confidently reconstructing radiations of complex gene families. Olfactory receptors (ORs) represent just such a gene family with upwards of 1000s of receptors in some mammalian taxa. Whereas in birds olfaction was historically an overlooked sensory modality, new studies have revealed an important role for smell. Chromosome-level assemblies for birds allow a new opportunity to characterize patterns of OR diversity among major bird lineages. Previous studies of short read (second-generation) genome assemblies have associated OR gene family size with avian ecology, but such conclusions could be premature if new assembly methods reshape our understanding of avian OR evolution. Here we provide a fundamental characterization of OR repertoires in five recent genome assemblies, including the most recent assembly of golden-collared manakin (Manacus vitellinus). We find that short read-based assemblies systematically undercount the avian-specific gamma-c OR subfamily, a subfamily that comprises over 65% of avian OR diversity. Therefore, in contrast to previous studies we find a high diversity of gamma-c ORs across the avian tree of life. Building on these findings, ongoing sequencing efforts and improved genome assemblies will clarify the relationship between OR diversity and avian ecology.
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Arthington JD, Silveira ML, Caramalac LS, Fernandes HJ, Heldt JS, Ranches J. Effects of varying sources of Cu, Zn, and Mn on mineral status and preferential intake of salt-based supplements by beef cows and calves and rainfall-induced metal loss. Transl Anim Sci 2021; 5:txab046. [PMID: 34041445 PMCID: PMC8140367 DOI: 10.1093/tas/txab046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 11/12/2022] Open
Abstract
Three studies were completed to evaluate the effects of Cu, Zn, and Mn source on preferential intake, trace mineral status, and rainfall-induced metal loss of salt-based mineral supplements. Mineral supplements were formulated to contain 2,500, 5,500, and 4,000 mg/kg of Cu, Zn, and Mn, respectively. Supplements differed only by source of Cu, Zn, and Mn, which were hydroxychloride, organic, or sulfate sources. In Exp. 1, the three formulations were offered simultaneously for 18 wk to preweaned beef calves (four pastures; 17 calves per pasture) within separate containers inside covered cow-exclusion areas. Consumption averaged 21 ± 2.4 g/calf daily (sum of all three sources), with a greater (P < 0.001) percentage of the total intake coming from the hydroxychloride vs. organic or sulfate sources of Cu, Zn, and Mn. In Exp. 2, the same sulfate and hydroxychloride formulations were randomly assigned to pastures (n = 4 pastures per treatment) containing 18 to 20 cow–calf pairs/pasture. Treatments were offered for 20 wk within covered areas designed to assess cow and calf intake separately. At weaning, liver biopsies were collected from four cow–calf pairs/pasture (n = 16 cows and calves per treatment). Source of Cu, Zn, and Mn had no effect on voluntary mineral intake among calves (P = 0.44) and cows (P = 0.14). Calves consuming mineral containing hydroxychloride sources of Cu, Zn, and Mn tended (P = 0.06) to have greater average daily gain over the 20-wk period compared with calves consuming sulfate sources of the same elements (1.09 vs. 1.06 kg/d; SEM = 0.013). Mineral status of cows and calves was not affected (P ≥ 0.17) by source of Cu, Zn, and Mn. In Exp. 3, each of the mineral formulations from Exp. 1 was exposed to a 10.2-cm precipitation event delivered in three equal 3.4-cm applications within a week. To accomplish this, 750 g of mineral was placed into Buchner funnels (177 cm2) on 20- to 25-µm pore filter paper. Deionized water (pH adjusted to 5.6) was poured over the mineral. Total leaching losses of Cu, Zn, and Mn were less (P < 0.001) for formulations containing hydroxychloride vs. organic and sulfate sources. These results imply that, when offered a choice, calves preferentially consume mineral supplements formulated with hydroxychloride vs. sulfate or organic sources of Cu, Zn, and Mn. In addition, hydroxychloride sources of Cu, Zn, and Mn are less susceptible to rainfall-induced leaching losses compared with sulfate and organic sources.
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Affiliation(s)
- John D Arthington
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.,Range Cattle Research and Education Center, University of Florida, Ona, FL 33865, USA
| | - Maria L Silveira
- Range Cattle Research and Education Center, University of Florida, Ona, FL 33865, USA
| | - Luana S Caramalac
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.,State University of Mato Grosso do Sul, Aquidauana, MS 79804-970, Brazil
| | | | - Jeff S Heldt
- Micronutrients USA, LLC, Indianapolis, IN 46231, USA
| | - Juliana Ranches
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.,Range Cattle Research and Education Center, University of Florida, Ona, FL 33865, USA
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Liu H, Chen C, Lv M, Liu N, Hu Y, Zhang H, Enbody ED, Gao Z, Andersson L, Wang W. A chromosome-level assembly of blunt snout bream (Megalobrama amblycephala) reveals an expansion of olfactory receptor genes in freshwater fish. Mol Biol Evol 2021; 38:4238-4251. [PMID: 34003267 PMCID: PMC8476165 DOI: 10.1093/molbev/msab152] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The number of olfactory receptor genes (ORs), which are responsible for detecting diverse odor molecules varies extensively among mammals as a result of frequent gene gains and losses that contribute to olfactory specialization. However, how OR expansions/contractions in fish are influenced by habitat and feeding habit and which OR subfamilies are important in each ecological niche is unknown. Here, we report a major OR expansion in a freshwater herbivorous fish, Megalobrama amblycephala, using a highly contiguous, chromosome-level assembly. We evaluate the possible contribution of OR expansion to habitat and feeding specialization by comparing the OR repertoire in 28 phylogenetically and ecologically diverse teleosts. In total, we analyzed > 4,000 ORs including 3,253 intact, 122 truncated, and 913 pseudogenes. The number of intact ORs is highly variable ranging from 20 to 279. We estimate that the most recent common ancestor of Osteichthyes had 62 intact ORs, which declined in most lineages except the freshwater Otophysa clade that has a substantial expansion in subfamily β and ε ORs. Across teleosts, we found a strong association between duplications of β and ε ORs and freshwater habitat. Nearly, all ORs were expressed in the olfactory epithelium (OE) in three tested fish species. Specifically, all the expanded β and ε ORs were highly expressed in OE of M. amblycephala. Together, we provide molecular and functional evidence for how OR repertoires in fish have undergone gain and loss with respect to ecological factors and highlight the role of β and ε OR in freshwater adaptation.
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Affiliation(s)
- Han Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.,Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, 430070, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Maolin Lv
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ning Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Erik D Enbody
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE75237, Sweden
| | - Zexia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.,Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, 430070, China
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE75237, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Weimin Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
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43
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Concas MP, Cocca M, Francescatto M, Battistuzzi T, Spedicati B, Feresin A, Morgan A, Gasparini P, Girotto G. The Role of Knockout Olfactory Receptor Genes in Odor Discrimination. Genes (Basel) 2021; 12:631. [PMID: 33922566 PMCID: PMC8145969 DOI: 10.3390/genes12050631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022] Open
Abstract
To date, little is known about the role of olfactory receptor (OR) genes on smell performance. Thanks to the availability of whole-genome sequencing data of 802 samples, we identified 41 knockout (KO) OR genes (i.e., carriers of Loss of Function variants) and evaluated their effect on odor discrimination in 218 Italian individuals through recursive partitioning analysis. Furthermore, we checked the expression of these genes in human and mouse tissues using publicly available data and the presence of organ-related diseases in human KO (HKO) individuals for OR expressed in non-olfactory tissues (Fisher test). The recursive partitioning analysis showed that age and the high number (burden) of OR-KO genes impact the worsening of odor discrimination (p-value < 0.05). Human expression data showed that 33/41 OR genes are expressed in the olfactory system (OS) and 27 in other tissues. Sixty putative mouse homologs of the 41 humans ORs have been identified, 58 of which are expressed in the OS and 37 in other tissues. No association between OR-KO individuals and pathologies has been detected. In conclusion, our work highlights the role of the burden of OR-KO genes in worse odor discrimination.
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Affiliation(s)
- Maria Pina Concas
- Institute for Maternal and Child Health—IRCCS, Burlo Garofolo, 34127 Trieste, Italy; (M.P.C.); (M.C.); (P.G.); (G.G.)
| | - Massimiliano Cocca
- Institute for Maternal and Child Health—IRCCS, Burlo Garofolo, 34127 Trieste, Italy; (M.P.C.); (M.C.); (P.G.); (G.G.)
| | - Margherita Francescatto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.F.); (B.S.); (A.F.)
| | - Thomas Battistuzzi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.F.); (B.S.); (A.F.)
| | - Agnese Feresin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.F.); (B.S.); (A.F.)
| | - Anna Morgan
- Institute for Maternal and Child Health—IRCCS, Burlo Garofolo, 34127 Trieste, Italy; (M.P.C.); (M.C.); (P.G.); (G.G.)
| | - Paolo Gasparini
- Institute for Maternal and Child Health—IRCCS, Burlo Garofolo, 34127 Trieste, Italy; (M.P.C.); (M.C.); (P.G.); (G.G.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.F.); (B.S.); (A.F.)
| | - Giorgia Girotto
- Institute for Maternal and Child Health—IRCCS, Burlo Garofolo, 34127 Trieste, Italy; (M.P.C.); (M.C.); (P.G.); (G.G.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.F.); (B.S.); (A.F.)
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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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Ma L, Tao X, He X, Wang P, Ma L, Shi B, Yao X. Analysis of the heterogeneity of the BCR H-CDR3 repertoire in the bone marrow and spleen of 3-, 12-, and 20-month old mice. IMMUNITY & AGEING 2021; 18:17. [PMID: 33845848 PMCID: PMC8040230 DOI: 10.1186/s12979-021-00231-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 03/30/2021] [Indexed: 01/10/2023]
Abstract
The number of central and peripheral B cells and their responsiveness are decreased in aged mice. The diversity of mice central and peripheral B cell repertoires with increasing age has not been elucidated. In this study, we demonstrated that there were significant differences in the usage of some V, D, and J genes in the BCR H-CDR3 repertoire of bone marrow B cells, spleen B cells and spleen memory B cells in 3-, 12-, and 20-month-old mice. In the productive, pseudogene, and out-of-frame sequences, bone marrow B cells had significant differences in 5′J trimming with age; peripheral spleen B cells and memory B cells had significant differences in N1 insertion, N2 insertion, P5’D insertion, and 5’D trimming with age. The BCR H-CDR3 repertoire diversity of mice bone marrow B cells, spleen B cells and spleen memory B cells decreased with increasing age. The proportion of overlap in bone marrow and spleen B cells, but not spleen memory B cells, of mice at different ages was lower at 3 months than at 12 and 20 months. This study is the first to report the homogeneity and heterogeneity of the CDR3 repertoire of central and peripheral B cells change as mice age, to further investigation of the decline and response of B cell immunity in young/middle/old-aged mice.
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Affiliation(s)
- Lina Ma
- Department of Immunology, Center of ImmunoMolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, 563000, China
| | - Xinxin Tao
- Department of Immunology, Center of ImmunoMolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, 563000, China
| | - Xiaoyan He
- Department of Immunology, Center of ImmunoMolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, 563000, China
| | - Peng Wang
- Department of Immunology, Center of ImmunoMolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, 563000, China
| | - Long Ma
- Department of Immunology, Center of ImmunoMolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, 563000, China
| | - Bin Shi
- Department of Immunology, Center of ImmunoMolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, 563000, China
| | - Xinsheng Yao
- Department of Immunology, Center of ImmunoMolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, 563000, China.
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Abbas F, Vinberg F. Transduction and Adaptation Mechanisms in the Cilium or Microvilli of Photoreceptors and Olfactory Receptors From Insects to Humans. Front Cell Neurosci 2021; 15:662453. [PMID: 33867944 PMCID: PMC8046925 DOI: 10.3389/fncel.2021.662453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Sensing changes in the environment is crucial for survival. Animals from invertebrates to vertebrates use both visual and olfactory stimuli to direct survival behaviors including identification of food sources, finding mates, and predator avoidance. In primary sensory neurons there are signal transduction mechanisms that convert chemical or light signals into an electrical response through ligand binding or photoactivation of a receptor, that can be propagated to the olfactory and visual centers of the brain to create a perception of the odor and visual landscapes surrounding us. The fundamental principles of olfactory and phototransduction pathways within vertebrates are somewhat analogous. Signal transduction in both systems takes place in the ciliary sub-compartments of the sensory cells and relies upon the activation of G protein-coupled receptors (GPCRs) to close cyclic nucleotide-gated (CNG) cation channels in photoreceptors to produce a hyperpolarization of the cell, or in olfactory sensory neurons open CNG channels to produce a depolarization. However, while invertebrate phototransduction also involves GPCRs, invertebrate photoreceptors can be either ciliary and/or microvillar with hyperpolarizing and depolarizing responses to light, respectively. Moreover, olfactory transduction in invertebrates may be a mixture of metabotropic G protein and ionotropic signaling pathways. This review will highlight differences of the visual and olfactory transduction mechanisms between vertebrates and invertebrates, focusing on the implications to the gain of the transduction processes, and how they are modulated to allow detection of small changes in odor concentration and light intensity over a wide range of background stimulus levels.
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Affiliation(s)
- Fatima Abbas
- Vinberg Lab, Department of Ophthalmology and Visual Science, John A. Moran Center, University of Utah, Salt Lake City, UT, United States
| | - Frans Vinberg
- Vinberg Lab, Department of Ophthalmology and Visual Science, John A. Moran Center, University of Utah, Salt Lake City, UT, United States
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47
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Ali MA, Wang Y, Qin Z, Yuan X, Zhang Y, Zeng C. Odorant and Taste Receptors in Sperm Chemotaxis and Cryopreservation: Roles and Implications in Sperm Capacitation, Motility and Fertility. Genes (Basel) 2021; 12:genes12040488. [PMID: 33801624 PMCID: PMC8065900 DOI: 10.3390/genes12040488] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 11/24/2022] Open
Abstract
Sperm chemotaxis, which guide sperm toward oocyte, is tightly associated with sperm capacitation, motility, and fertility. However, the molecular mechanism of sperm chemotaxis is not known. Reproductive odorant and taste receptors, belong to G-protein-coupled receptors (GPCR) super-family, cause an increase in intracellular Ca2+ concentration which is pre-requisite for sperm capacitation and acrosomal reaction, and result in sperm hyperpolarization and increase motility through activation of Ca2+-dependent Cl¯ channels. Recently, odorant receptors (ORs) in olfactory transduction pathway were thought to be associated with post-thaw sperm motility, freeze tolerance or freezability and cryo-capacitation-like change during cryopreservation. Investigation of the roles of odorant and taste receptors (TRs) is important for our understanding of the freeze tolerance or freezability mechanism and improve the motility and fertility of post-thaw sperm. Here, we reviewed the roles, mode of action, impact of odorant and taste receptors on sperm chemotaxis and post-thaw sperm quality.
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Affiliation(s)
- Malik Ahsan Ali
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
- Department of Theriogenology, Riphah College of Veterinary Sciences, Lahore 54000, Punjab, Pakistan;
- Department of Theriogenology, Faculty of Veterinary Science, University of Agriculture, Faisalabad 38000, Punjab, Pakistan
| | - Yihan Wang
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
| | - Ziyue Qin
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
| | - Xiang Yuan
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
| | - Yan Zhang
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
| | - Changjun Zeng
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
- Correspondence: ; Tel./Fax: +86-28-86291010
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48
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Westbury MV, Le Duc D, Duchêne DA, Krishnan A, Prost S, Rutschmann S, Grau JH, Dalen L, Weyrich A, Norén K, Werdelin L, Dalerum F, Schöneberg T, Hofreiter M. Ecological Specialisation and Evolutionary Reticulation in Extant Hyaenidae. Mol Biol Evol 2021; 38:3884-3897. [PMID: 34426844 PMCID: PMC8382907 DOI: 10.1093/molbev/msab055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.
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Affiliation(s)
- M V Westbury
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.,Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Diana Le Duc
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, 04103, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - David A Duchêne
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark.,Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Arunkumar Krishnan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg, 60325, Germany. Frankfurt.,South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa
| | - Sereina Rutschmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Jose H Grau
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.,amedes Genetics, amedes Medizinische Dienstleistungen, Berlin, Germany
| | - Love Dalen
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm, 10405, Sweden
| | - Alexandra Weyrich
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, 10315, Germany
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, Stockholm, SE-10405, Sweden
| | - Fredrik Dalerum
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden.,Research Unit of Biodiversity (UO-CSIC-PA), Mieres Campus, University of Oviedo, Mieres, Asturias, 33600, Spain.,Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, South Africa
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Johannisallee 30, Leipzig, 04103, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
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49
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Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, Del Campo J, Cheves Hernandez S, Di Fiore A, Fontsere C, Hodgson JA, Janiak MC, Kuderna LFK, Lizano E, Martin MP, Niimura Y, Perry GH, Valverde CS, Tang J, Warren WC, de Magalhães JP, Kawamura S, Marquès-Bonet T, Krawetz R, Melin AD. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proc Natl Acad Sci U S A 2021; 118:e2010632118. [PMID: 33574059 PMCID: PMC7896301 DOI: 10.1073/pnas.2010632118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity.
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Affiliation(s)
- Joseph D Orkin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T38 6A8, Canada
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19146
| | - Daniela Tejada-Martinez
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
- Doctorado en Ciencias mención Ecología y Evolución, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, United Kingdom
| | - Marc de Manuel
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
| | - Javier Del Campo
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
| | | | - Anthony Di Fiore
- Department of Anthropology and Primate Molecular Ecology and Evolution Laboratory, University of Texas at Austin, Austin, TX 78712
- College of Biological and Environmental Sciences, Universidad San Francisco de Quito, 170901 Cumbayá, Ecuador
| | - Claudia Fontsere
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
| | - Jason A Hodgson
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T38 6A8, Canada
- School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, United Kingdom
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Maria Pia Martin
- Kids Saving the Rainforest Wildlife Rescue Center, 60601 Quepos, Costa Rica
| | - Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | | | - Jia Tang
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Wesley C Warren
- Division of Animal Sciences, School of Medicine, University of Missouri, Columbia, MO 65211
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, United Kingdom
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 277-8562 Chiba, Japan
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies, 08010 Barcelona, Spain
- Centro Nacional de Análisis Genómico-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Roman Krawetz
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T38 6A8, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T38 6A8, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T38 6A8, Canada
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50
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Valenta K, Schmitt MH, Ayasse M, Nevo O. The sensory ecology of fear: African elephants show aversion to olfactory predator signals. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Kim Valenta
- Department of Anthropology University of Florida Gainesville Florida USA
| | - Melissa H. Schmitt
- Department of Ecology Evolution and Marine Biology University of California Santa Barbara Santa Barbara California USA
- South African Environmental Observation Network, Ndlovu Node Phalaborwa South Africa
| | - Manfred Ayasse
- Ulm University, Institute of Evolutionary Ecology and Conservation Genomics Ulm Germany
| | - Omer Nevo
- Ulm University, Institute of Evolutionary Ecology and Conservation Genomics Ulm Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Friedrich Schiller University Jena, Institute of Biodiversity Jena Germany
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