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

PLoS ONE ◽  
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.

scholarly journals InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes

2020 ◽  
Author(s):  
Snehal D. Karpe ◽  
Vikas Tiwari ◽  
Sowdhamini Ramanathan
Keyword(s):  
Genome Annotation ◽  
Gene Prediction ◽  
Web Server ◽  
Olfactory Receptors ◽  
Rapid Prediction ◽  
Protein Receptors ◽  
Olfactory Receptor Genes ◽  
Or Gene ◽  
Or Genes ◽  
The Web

AbstractInsect 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. Hence, accurate gene prediction of insect ORs from newly sequenced genomes is an important but challenging task. We have developed a dedicated web-server, ‘insectOR’, to predict and validate insect OR genes using multiple gene prediction algorithms, accompanied by relevant validations. It is possible to employ this sever 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 web-server is freely available on the web at http://caps.ncbs.res.in/insectOR/. All major browsers are supported. Website is implemented in Python with Jinja2 for templating and bootstrap framework which uses HTML, CSS and JavaScript/Ajax. The core pipeline is written in Perl.

scholarly journals MHC-Linked Olfactory Receptor Loci Exhibit Polymorphism and Contribute to Extended HLA/OR-Haplotypes

2000 ◽  
Vol 10 (12) ◽  
pp. 1968-1978 ◽  
Author(s):  
Anke Ehlers ◽  
Stephan Beck ◽  
Simon A. Forbes ◽  
John Trowsdale ◽  
Armin Volz ◽  
...  
Keyword(s):  
Olfactory Receptor ◽  
Sequence Data ◽  
Allelic Variation ◽  
Mate Preferences ◽  
Coding Region ◽  
Link Type ◽  
Or Gene ◽  
Hla Haplotypes ◽  
A Minor ◽  
Or Genes

Clusters of olfactory receptor (OR) genes are found on most human chromosomes. They are one of the largest mammalian multigene families. Here, we report a systematic study of polymorphism of OR genes belonging to the largest fully sequenced OR cluster. The cluster contains 36 OR genes, of which two belong to the vomeronasal 1 (V1-OR) family. The cluster is divided into a major and a minor region at the telomeric end of the HLA complex on chromosome 6. These OR genes could be involved in MHC-related mate preferences. The polymorphism screen was carried out with 13 genes from the HLA-linked OR cluster and three genes from chromosomes 7, 17, and 19 as controls. Ten human cell lines, representing 18 different chromosome 6s, were analyzed. They were from various ethnic origins and exhibited different HLA haplotypes. All OR genes tested, including those not linked to the HLA complex, were polymorphic. These polymorphisms were dispersed along the coding region and resulted in up to seven alleles for a given OR gene. Three polymorphisms resulted either in stop codons (genes hs6M1-4P,hs6M1-17) or in a 16–bp deletion (gene hs6M1-19P), possibly leading to lack of ligand recognition by the respective receptors in the cell line donors. In total, 13 HLA-linked OR haplotypes could be defined. Therefore, allelic variation appears to be a general feature of human OR genes.[The sequence data reported in this paper have been submitted to EMBL under accession nos. AC006137, AC004178, AJ132194, AL022727, AL031983,AL035402, AL035542, Z98744, CAB55431, AL050339, AL035402, AL096770,AL133267, AL121944, Z98745, AL021808, and AL021807.]

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

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 910
Author(s):  
Haifeng Jiang ◽  
Kang Du ◽  
Xiaoni Gan ◽  
Liandong Yang ◽  
Shunping He
Keyword(s):  
Olfactory Receptor ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Evolutionary Divergence ◽  
Ecological Adaptations ◽  
Receptor Repertoire ◽  
Trace Amine ◽  
Feeding Habitat ◽  
Or Genes ◽  
Pressure Analysis

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.

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

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.

scholarly journals Organization and distribution of glomeruli in the bowhead whale olfactory bulb

2014 ◽  
Author(s):  
Takushi Kishida ◽  
J. G. M. Thewissen ◽  
Sharon Usip ◽  
John C George ◽  
Robert S Suydam
Keyword(s):  
Olfactory Bulb ◽  
Olfactory Receptor ◽  
Olfactory Receptors ◽  
Molecular Data ◽  
Dorsal Side ◽  
Bowhead Whale ◽  
Model Organisms ◽  
Marker Genes ◽  
Baleen Whales ◽  
Olfactory Receptor Genes

Although modern baleen whales still possess a functional olfactory systems that includes olfactory bulbs, cranial nerve I and olfactory receptor genes, their olfactory capabilities have been reduced profoundly. This is probably in response to their fully aquatic lifestyle. The glomeruli that occur in the olfactory bulb can be divided into two non-overlapping domains, a dorsal domain and a ventral domain. Recent molecular studies revealed that all modern whales have lost olfactory receptor genes and marker genes that are specific to the dorsal domain, and that a modern baleen whale possess only 60 olfactory receptor genes. Here we show that olfactory bulb of bowhead whales (Balaena mysticetus, Mysticeti) lacks glomeruli on the dorsal side, consistent with the molecular data. In addition, we estimate that there are more than 4,000 glomeruli in the bowhead whale olfactory bulb. Olfactory sensory neurons that express the same olfactory receptor in mice generally project to two specific glomeruli in an olfactory bulb, meaning that ratio of the number of olfactory receptors : the number of glomeruli is approximately 1:2. However, we show here that this ratio is not applicable to whales, indicating the limitation of mice as model organisms for understanding the initial coding of odor information among mammals.

scholarly journals A unified nomenclature for vertebrate olfactory receptors

2020 ◽  
Author(s):  
Tsviya Olender ◽  
Tamsin E.M. Jones ◽  
Elspeth Bruford ◽  
Doron Lancet
Keyword(s):  
Receptor Gene ◽  
Olfactory Receptors ◽  
Large Deletion ◽  
Ecological Niches ◽  
Gene Nomenclature ◽  
Nomenclature System ◽  
Or Gene ◽  
Species Specific ◽  
Or Genes ◽  
Genomic Cluster

Abstract Background Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. Results Here we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5 . Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~50% in dog and cow and to ~30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. Conclusions We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

scholarly journals Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons.

2019 ◽  
Author(s):  
If Barnes ◽  
Ximena Ibarra-Soria ◽  
Stephen Fitzgerald ◽  
Jose Gonzalez ◽  
Claire Davidson ◽  
...  
Keyword(s):  
Olfactory Receptor ◽  
Receptor Gene ◽  
Gene Repertoire ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Or Gene ◽  
Or Genes ◽  
Human And Mouse

Abstract Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with over 850 in human and nearly 1500 genes in mouse. The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.

scholarly journals Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons

2019 ◽  
Author(s):  
If H. A. Barnes ◽  
Ximena Ibarra-Soria ◽  
Stephen Fitzgerald ◽  
Jose M. Gonzalez ◽  
Claire Davidson ◽  
...  
Keyword(s):  
Olfactory Receptor ◽  
Receptor Gene ◽  
Gene Repertoire ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Or Gene ◽  
Or Genes ◽  
Human And Mouse

ABSTRACTOlfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with over 850 in human and nearly 1500 genes in mouse. The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.

scholarly journals Olfactory receptor repertoire size in dinosaurs

2019 ◽  
Vol 286 (1904) ◽  
pp. 20190909 ◽  
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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