Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR

Han, Wei; Wu, Yiran; Zeng, Liting; Zhao, Suwen

doi:10.1007/s11427-021-2081-6

Cited by 9 publications

(12 citation statements)

References 53 publications

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“…In other cases, orthologs may differ in their responses to the same stimuli. Nevertheless, detecting adaptation in olfactory receptors is tractable with well-parameterized models of molecular evolution and appropriate consideration of protein structure and function [ 204 ]. These receptors directly interact with environmental cues, with essential roles in the identification of stimuli that historically were directly related to fitness (e.g., finding food, mates, and predator avoidance).…”

Section: Sniffing Out the Genomic Basis Of Diverse Chemosensation Rec...mentioning

confidence: 99%

Placing human gene families into their evolutionary context

Dornburg

Mallik²,

Wang³

et al. 2022

Hum Genomics

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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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Section: Sniffing Out the Genomic Basis Of Diverse Chemosensation Rec...mentioning

confidence: 99%

Placing human gene families into their evolutionary context

Dornburg

Mallik²,

Wang³

et al. 2022

Hum Genomics

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“…Recently, baleen whales' olfactory capabilities have been investigated through morphological and genomic studies [24][25][26][27][28][29][30]. The skeletal components of the main olfactory organ, such as the cribriform plate and turbinals, have been observed in common minke whales (Balaenoptera acutorostrata) [24,25].…”

Section: Introductionmentioning

confidence: 99%

“…Gross and microscopic examinations have supported the presence of the main olfactory organ in bowhead whales (Balaena mysticetus) [27,28], and subsequent immunohistochemical staining has identified olfactory nerves in the nasal mucosa of this species [29]. Han et al [30] conducted a search for ORs in seven baleen whale species using publicly available whole genomes, annotating between 54 and 95 intact OR copies. The number of ORs identified in baleen whales is lower than in other mammals and corresponds to the reduced anatomical complexity of their main olfactory organ.…”

Section: Introductionmentioning

confidence: 99%

Localized Expression of Olfactory Receptor Genes in the Olfactory Organ of Common Minke Whales

Hirose,

Nakamura,

Nikaido

et al. 2024

IJMS

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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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“…Moreover, the interactions between iORs and odorant molecules have inspired the design of bionic electronic olfaction devices because of the extremely high sensitivity and accuracy of insect olfactory systems (Barbosa et al, 2018;Cheema et al, 2021;Yamada et al, 2021). Databases of human, mouse, and Drosophila olfactory receptors are widely available, such as ORDB (Crasto et al, 2002), DOR (Nagarathnam et al, 2014), Door (Mao et al, 2009), HORDE (Olender et al, 2013), ODORactor (Liu et al, 2011), and Genome2OR (Han et al, 2022). However, there is still no specific database for the structure and function of iORs.…”

Section: Introductionmentioning

confidence: 99%

“…, 2011), and Genome2OR (Han et al. , 2022). However, there is still no specific database for the structure and function of iORs.…”

Section: Introductionmentioning

confidence: 99%

iORbase: A database for the prediction of the structures and functions of insect olfactory receptors

Zhang

Tian-min

et al. 2023

Insect Science

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Insect olfactory receptors (iORs) with atypical 7‐transmembrane domains, unlike Chordata olfactory receptors, are not in the GPCR protein family. iORs selectively bind to volatile ligands in the environment and affect essential insect behaviors. In this study, we constructed a new platform (iORbase, https://www.iorbase.com) for the structural and functional analysis of iORs based on a combined algorithm for gene annotation and protein structure prediction. Moreover, it provides the option to calculate the binding affinities and binding residues between iORs and pheromone molecules by virtual screening of docking. Furthermore, iORbase supports the automatic structural and functional prediction of user‐submitted iORs or pheromones. iORbase contains the well‐analyzed results of approximately 6 000 iORs and their 3D protein structures identified from 59 insect species and 2 077 insect pheromones from the literature, as well as approximately 12 million pairs of simulated interactions between functional iORs and pheromones. We also built 4 online modules, iORPDB, iInteraction, iModelTM, and iOdorTool to easily retrieve and visualize the 3D structures and interactions. iORbase can help greatly improve the experimental efficiency and success rate, identify new insecticide targets, or develop electronic nose technology. This study will shed light on the olfactory recognition mechanism and evolutionary characteristics from the perspectives of omics and macroevolution.

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Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR

Cited by 9 publications

References 53 publications

Placing human gene families into their evolutionary context

Placing human gene families into their evolutionary context

Localized Expression of Olfactory Receptor Genes in the Olfactory Organ of Common Minke Whales

iORbase: A database for the prediction of the structures and functions of insect olfactory receptors

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