Massive Loss of Olfactory Receptors But Not Trace Amine-Associated Receptors in the World’s Deepest-Living Fish (Pseudoliparis swirei)

Olfactory receptor repertoires show highly dynamic evolution associated with ecological adaptations in different species. The Mariana snailfish (Pseudoliparis swirei) living below a depth of 6000 m in the Mariana Trench evolved degraded vision and occupies a specific feeding habitat in a dark, low-food environment. However, whether such adaptations involve adaptive changes in the chemosensory receptor repertoire is not known. Here, we conducted a comparative analysis of the olfactory receptor (OR) and trace amine-associated receptor (TAAR) gene repertoires in nine teleosts with a focus on the evolutionary divergence between the Mariana snailfish and its shallow-sea relative, Tanaka’s snailfish (Liparis tanakae). We found many fewer functional OR genes and a significantly higher fraction of pseudogenes in the Mariana snailfish, but the numbers of functional TAAR genes in the two species were comparable. Phylogenetic analysis showed that the expansion patterns of the gene families were shared by the two species, but that Mariana snailfish underwent massive gene losses in its OR repertoire. Despite an overall decreased size in OR subfamilies and a reduced number of TAAR subfamilies in the Mariana snailfish, expansion of certain subfamilies was observed. Selective pressure analysis indicated greatly relaxed selective strength in ORs but a slightly enhanced selective strength in TAARs of Mariana snailfish. Overall, our study reveals simplified but specific OR and TAAR repertoires in the Mariana snailfish shaped by natural selection with respect to ecological adaptations in the hadal environment. This is the first study on the chemosensation evolution in vertebrates living in the hadal zone, which could provide new insights into evolutionary adaptation to the hadal environment.

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Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes

10.1101/2021.12.13.472396 ◽

2021 ◽

Author(s):

Maxime Policarpo ◽

Katherine E Bemis ◽

Patrick Laurenti ◽

Laurent Legendre ◽

Jean-Christophe Sandoz ◽

...

Keyword(s):

Olfactory Receptor ◽

Evolutionary Dynamics ◽

Olfactory Receptors ◽

Gene Families ◽

Olfactory Organ ◽

Functional Link ◽

Receptor Repertoire ◽

Mola Mola ◽

Main Gene ◽

Olfactory Receptor Genes

Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction 1,2. Anatomical diversity of the olfactory organ suggests that olfaction is differentially important among species 1,3,4. To explore this topic, we studied the evolutionary dynamics of the four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) 5 coding for olfactory receptors in 185 species of ray-finned fishes. The large variation in the number of functional genes, between 28 in the Ocean Sunfish Mola mola and 1317 in the Reedfish Erpetoichthys calabaricus, is the result of parallel expansions and contractions of the four main gene families. Several ancient and independent simplifications of the olfactory organ are associated with massive gene losses. In contrast, polypteriforms, which have a unique and complex olfactory organ, have almost twice as many olfactory receptor genes as any other ray-finned fish. These observations suggest a functional link between morphology of the olfactory organ and richness of the olfactory receptor repertoire. Further, our results demonstrate that the genomic underpinning of olfaction in ray-finned fishes is heterogeneous and presents a dynamic pattern of evolutionary expansions, simplifications and reacquisitions.

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InsectOR—Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes

PLoS ONE ◽

10.1371/journal.pone.0245324 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0245324

Author(s):

Snehal Dilip Karpe ◽

Vikas Tiwari ◽

Sowdhamini Ramanathan

Keyword(s):

Genome Annotation ◽

Olfactory Receptor ◽

Gene Prediction ◽

Olfactory Receptors ◽

Gene Families ◽

Link Type ◽

Preliminary Identification ◽

Olfactory Receptor Genes ◽

Or Gene ◽

Or Genes

Insect Olfactory Receptors (ORs) are diverse family of membrane protein receptors responsible for most of the insect olfactory perception and communication, and hence they are of utmost importance for developing repellents or pesticides. Accurate gene prediction of insect ORs from newly sequenced genomes is an important but challenging task. We have developed a dedicated webserver, ‘insectOR’, to predict and validate insect OR genes using multiple gene prediction algorithms, accompanied by relevant validations. It is possible to employ this server nearly automatically and perform rapid prediction of the OR gene loci from thousands of OR-protein-to-genome alignments, resolve gene boundaries for tandem OR genes and refine them further to provide more complete OR gene models. InsectOR outperformed the popular genome annotation pipelines (MAKER and NCBI eukaryotic genome annotation) in terms of overall sensitivity at base, exon and locus level, when tested on two distantly related insect genomes. It displayed more than 95% nucleotide level precision in both tests. Finally, given the same input data and parameters, InsectOR missed less than 2% gene loci, in contrast to 55% loci missed by MAKER for Drosophila melanogaster. The webserver is freely available on the web at http://caps.ncbs.res.in/insectOR/ and the basic package can be downloaded from https://github.com/sdk15/insectOR for local use. This tool will allow biologists to perform quick preliminary identification of insect olfactory receptor genes from newly sequenced genomes and also assist in their further detailed annotation. Its usage can also be extended to other divergent gene families.

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Primacy model and the evolution of the olfactory receptor repertoire

10.1101/255661 ◽

2018 ◽

Cited By ~ 2

Author(s):

Hamza Giaffar ◽

Dmitry Rinberg ◽

Alexei A. Koulakov

Keyword(s):

Olfactory Receptor ◽

Olfactory Receptors ◽

Dimensional Structure ◽

Sufficient Information ◽

High Affinity ◽

Receptor Repertoire ◽

Wide Range ◽

Evoked Activity ◽

Low Dimensional ◽

The Impact

For many animals, the neural activity in early olfactory circuits during a single sniff cycle contains sufficient information for fine odor discrimination. Whilst much is known about the transformations of neural representations in early olfactory circuits, exactly how odorant evoked activity in the main olfactory bulb shapes the perception of odors remains largely unknown. In olfaction, odorant identity is generally conserved over a wide range of conditions, including concentration. We present a theory of identity assignment in the olfactory system that accounts for this invariance with respect to stimulus intensity. We suggest that the identities of relatively few high affinity olfactory receptor types determine an odorant's perceived identity. This set of high-affinity receptors is defined as the primary set and the coding model based on their responses is called the primacy theory. In this study, we explore the impact that primacy coding may have on the evolution of the ensemble of olfactory receptors. A primacy coding mechanism predicts the arrangement of different receptor types in a low-dimensional structure that we call a primacy hull. We present several statistical analyses that can detect the presence of this structure, allowing the predictions of the primacy model to be tested experimentally.

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Olfactory receptor repertoire size in dinosaurs

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.0909 ◽

2019 ◽

Vol 286 (1904) ◽

pp. 20190909 ◽

Cited By ~ 4

Author(s):

Graham M. Hughes ◽

John A. Finarelli

Keyword(s):

Olfactory Receptor ◽

Ecological Niches ◽

Ancestral State ◽

Repertoire Size ◽

Receptor Repertoire ◽

Olfactory Acuity ◽

Sensory Evolution ◽

Evolutionary Trajectories ◽

Or Gene ◽

Or Genes

The olfactory bulb (OB) ratio is the size of the OB relative to the cerebral hemisphere, and is used to estimate the proportion of the forebrain devoted to smell. In birds, OB ratio correlates with the number of olfactory receptor (OR) genes and therefore has been used as a proxy for olfactory acuity. By coupling OB ratios with known OR gene repertoires in birds, we infer minimum repertoire sizes for extinct taxa, including non-avian dinosaurs, using phylogenetic modelling, ancestral state reconstruction and comparative genomics. We highlight a shift in the scaling of OB ratio to body size along the lineage leading to modern birds, demonstrating variable OR repertoires present in different dinosaur and crown-bird lineages, with varying factors potentially influencing sensory evolution in theropods. We investigate the ancestral sensory space available to extinct taxa, highlighting potential adaptations to ecological niches. Through combining morphological and genomic data, we show that, while genetic information for extinct taxa is forever lost, it is potentially feasible to investigate evolutionary trajectories in extinct genomes.

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Convergent degeneration of olfactory receptor gene repertoires in marine mammals

10.21203/rs.2.10030/v2 ◽

2019 ◽

Author(s):

Ake Liu ◽

Funan He ◽

Libing Shen ◽

Ruixiang Liu ◽

Zhijun Wang ◽

...

Keyword(s):

Olfactory Receptor ◽

Marine Mammals ◽

Purifying Selection ◽

Orthologous Gene ◽

Gene Families ◽

Average Gain ◽

Mammalian Gene ◽

Terrestrial Mammals ◽

Gain And Loss ◽

Or Genes

Abstract Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified and the factors that might underlie these variations are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had less OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous gene in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR genes compared with their related terrestrial lineages, which may be related to the weaker purifying selection. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

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Mosaic evolution of molecular pathways for sex pheromone communication in a butterfly

10.1101/2020.09.04.279224 ◽

2020 ◽

Author(s):

Caroline M. Nieberding ◽

Patrícia Beldade ◽

Véronique Baumlé ◽

Gilles San Martin ◽

Alok Arun ◽

...

Keyword(s):

Sex Pheromone ◽

Large Scale ◽

Olfactory Receptors ◽

Gene Families ◽

Pheromone Biosynthesis ◽

Specific Gene ◽

Evolutionary Divergence ◽

Molecular Pathways ◽

Pheromone Communication ◽

Bicyclus Anynana

AbstractUnraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved, ancestral traits, and newly evolved, derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~98 million years ago. In moths, females typically emit pheromones to attract male mates, but in butterflies pheromones and used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but have remained virtually unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics, to identify genes involved in different steps of sex pheromone communication in the butterfly Bicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly, B. anynana further appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulation of sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale analysis of the genetic pathways underlying sex pheromone communication in a butterfly.

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Convergent degeneration of olfactory receptor gene repertoires in marine mammals

10.21203/rs.2.10030/v4 ◽

2019 ◽

Author(s):

Ake Liu ◽

Funan He ◽

Libing Shen ◽

Ruixiang Liu ◽

Zhijun Wang ◽

...

Keyword(s):

Olfactory Receptor ◽

Marine Mammals ◽

Gene Families ◽

Future Research ◽

Average Gain ◽

Mammalian Gene ◽

Terrestrial Mammals ◽

Gain And Loss ◽

Or Genes ◽

Loss Rates

Abstract Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

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Convergent degeneration of olfactory receptor gene repertoires in marine mammals

10.21203/rs.2.10030/v3 ◽

2019 ◽

Author(s):

Ake Liu ◽

Funan He ◽

Libing Shen ◽

Ruixiang Liu ◽

Zhijun Wang ◽

...

Keyword(s):

Olfactory Receptor ◽

Marine Mammals ◽

Gene Families ◽

Future Research ◽

Average Gain ◽

Mammalian Gene ◽

Terrestrial Mammals ◽

Gain And Loss ◽

Or Genes ◽

Loss Rates

Abstract Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

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Convergent degeneration of olfactory receptor gene repertoires in marine mammals

BMC Genomics ◽

10.1186/s12864-019-6290-0 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 7

Author(s):

Ake Liu ◽

Funan He ◽

Libing Shen ◽

Ruixiang Liu ◽

Zhijun Wang ◽

...

Keyword(s):

Olfactory Receptor ◽

Marine Mammals ◽

Gene Families ◽

Future Research ◽

Average Gain ◽

Mammalian Gene ◽

Terrestrial Mammals ◽

Gain And Loss ◽

Or Genes ◽

Loss Rates

Abstract Background Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown. Results To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions Marine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

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Convergent degeneration of olfactory receptor gene repertories in marine mammals

10.21203/rs.2.10030/v1 ◽

2019 ◽

Author(s):

Ake Liu ◽

Funan He ◽

Libing Shen ◽

Jingqi Zhou

Keyword(s):

Olfactory Receptor ◽

Marine Mammals ◽

Purifying Selection ◽

Orthologous Gene ◽

Gene Families ◽

Average Gain ◽

Mammalian Gene ◽

Terrestrial Mammals ◽

Gain And Loss ◽

Or Genes

Abstract Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, it is still unclear whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals, and the factors that might underlie this variation are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs). There were significant differences in the numbers of both OR repertoires and OGGs among different species. We found that all marine mammals had less OR genes than their related terrestrial lineages, with the least OR genes in cetaceans; this result may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher, respectively, than those of mammalian gene families. Additionally, we failed to detect any one-to-one orthologous gene in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR genes compared with their related terrestrial lineages, which may result from the weaker purifying selection. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

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