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Research article - Peer-reviewed, 2021

A Chromosome-Level Assembly of Blunt Snout Bream (Megalobrama amblycephala) Genome Reveals an Expansion of Olfactory Receptor Genes in Freshwater Fish

Liu, Han; Chen, Chunhai; Lv, Maolin; Liu, Ning; Hu, Yafei; Zhang, Hailin; Enbody, Erik D.; Gao, Zexia; Andersson, Leif; Wang, Weimin

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 beta and epsilon ORs. Across teleosts, we found a strong association between duplications of beta and epsilon ORs and freshwater habitat. Nearly, all ORs were expressed in the olfactory epithelium (OE) in three tested fish species. Specifically, all the expanded beta and epsilon 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 beta and epsilon OR in freshwater adaptation.

Keywords

Cyprinid fish; comparative genomics; olfactory receptor; evolutionary dynamics; ecological adaptation

Published in

Molecular Biology and Evolution
2021, volume: 38, number: 10, pages: 4238-4251
Publisher: OXFORD UNIV PRESS

Authors' information

Liu, Han
Huazhong Agricultural University
Chen, Chunhai
Beijing Genomics Institute (BGI)
Lv, Maolin
Huazhong Agricultural University
Liu, Ning
Huazhong Agricultural University
Hu, Yafei
Beijing Genomics Institute (BGI)
Zhang, Hailin
Beijing Genomics Institute (BGI)
Enbody, Erik D.
Uppsala University
Gao, Zexia
Huazhong Agricultural University
Andersson, Leif
Uppsala University
Andersson, Leif
Texas A&M University
Wang, Weimin
Huazhong Agricultural University
Andersson, Leif
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Genetics
Evolutionary Biology

Publication Identifiers

DOI: https://doi.org/10.1093/molbev/msab152

URI (permanent link to this page)

https://res.slu.se/id/publ/114390