![]() The genomic location of each extracted OR sequence was compiled in the Supplementary File S1. Despite the high number of available actinopterygian genomes, we selected the 25 that best represented the most basal subclasses of ray-finned fishes and had available high-quality genome assemblies’ level. In order to explore the diversity of ORs throughout the major fish lineages, we performed a representative genome sampling from jawless (Cyclostomata, N = 5), cartilaginous (Chondrichthyes, N = 10) and bony (Sarcopterygii: N = 3 and Actinopterygii: N = 25) fishes. ![]() Those were developed based on reduced Data collection Such broader sampling strategy enlightened our understanding of the fish ORs evolution and enabled us to propose a more complete, detailed and standardized classification system (Alioto and Ngai, 2005 Niimura, 2009 Olender et al., 2020), while still accommodating the previous nomenclatures whenever possible. Our study considers a high-scale search of the entire OR repertoire throughout 43 representative genomes of jawless, cartilaginous, and bony fishes. For the naming of each OR family identified in the present study, we maintained, whenever it was possible, the classification proposed by Alioto and Ngai (2005) A new and integrative fish OR classification system – towards a universal OR nomenclature Intact OR sequences were used for a general phylogenetic reconstruction and the proposal of a new, in-depth, and integrative OR classification system (Fig. We retrieved 5143 intact OR sequences, 277 putative OR pseudogenes, and 79 truncated sequences that resulted from the abrupt end of the contig/scaffold (Supplementary File S1). OR family nomenclature, distribution and expansion/contraction patterns Liliana Silva: Conceptualization, Methodology, Writing – Original draft Tito Mendes: Conceptualization, Methodology, Writing – Original draft Luana Ramos: Writing – Review & Editing Guojie Zhang: Writing – Review & Editing Agostinho Antunes: Writing – Review & Editing Funding acquisition Supervision. Finally, we identified 25 distinct OR families, allowing us to propose an updated universal nomenclature for the fish ORs. Additionally, we verified that the OR repertoire of moderns actinopterygians has not increased as expected following a whole genome duplication, likely due to regulatory mechanisms compensating the gene load excess. While the early vertebrates performed gas exchange through gills, we hypothesize that the emergence of new breathing structures (swim bladder and paired lungs) in early osteichthyans may be associated to expansions in the ORs gene families sensitive to airborne molecules. Here, we conducted an exhaustive gene screening upon 43 high-quality fish genomes exhibiting varied gene repertoires (2 to 583 genes). However, OR repertoires remain poorly studied in fish lineages, precluding finely retracing their origin, evolution and diversification, especially in the most basal groups. ORs are a subgroup of G-protein coupled receptors that exhibit highly complex subgenomes in vertebrates. Olfactory receptors (ORs) play a key role in the prime sensorial perception, being highly relevant for intra/interspecific interactions.
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