Annotation of the Nuclear Receptors in an Estuarine Fish species, Fundulus heteroclitus

Abstract

The nuclear receptors (NRs) are ligand-dependent transcription factors that respond to various internal as well as external cues such as nutrients, pheromones, and steroid hormones that play crucial roles in regulation and maintenance of homeostasis and orchestrating the physiological and stress responses of an organism. We annotated the Fundulus heteroclitus (mummichog; Atlantic killifish) nuclear receptors. Mummichog are a non-migratory, estuarine fish with a limited home range often used in environmental research as a field model for studying ecological and evolutionary responses to variable environmental conditions such as salinity, oxygen, temperature, pH, and toxic compounds because of their hardiness. F. heteroclitus have at least 74 NRs spanning all seven gene subfamilies. F. heteroclitus is unique in that no RXRα member was found within the genome. Interestingly, some of the NRs are highly conserved between species, while others show a higher degree of divergence such as PXR, SF1, and ARα. Fundulus like other fish species show expansion of the RAR (NR1B), Rev-erb (NR1D), ROR (NR1F), COUPTF (NR2F), ERR (NR3B), RXR (NR2B), and to a lesser extent the NGF (NR4A), and NR3C steroid receptors (GR/AR). Of particular interest is the co-expansion of opposing NRs, Reverb-ROR, and RAR/RXR-COUPTF.

Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography

“…These SNPs were most strongly associated with primary productivity variation in the RDA. The third SNP in an exonic region correspond to candidate gene NR2F6 (also known as CoupTFII), which is related to the regulation of adipogenesis, glucose, homeostasis and energy metabolism [63][64][65], and was correlated with the salinity gradient in the RDA. Although the correlations between candidate SNPs and the environmental variables were generally low (r 2 < 0.5), the correlations were still significant (Fisher's p-value < 0.05), and considerable variation in allele frequencies of these candidate SNPs were observed across the seascape (Additional file 1: Fig.…”

Tributyltin disrupts fin development in Fundulus heteroclitus from both PCB-sensitive and resistant populations: Investigations of potential interactions between AHR and PPARγ

“…Killifish, along with other fish species characterized to date, express a single form of PPARγ. Killifish express at least one form of RXRα and multiple forms of both RXRβ and RXRγ (Karchner and Hahn, unpublished analysis of XP_012719647; (Baldwin et al, 2017). Rosiglitazone and TBT induce adiposity in zebrafish larvae (Ouadah-Boussouf and Babin, 2016;Tingaud-Sequeira et al, 2011).…”

Non-Mammalian Nuclear Receptors: From Evolution to Human Disease

“…The Baldwin et al article [ 14 ] describes the phylogenetic analysis and annotation of nuclear receptor genes in Fundulus heteroclitus (mummichog; Atlantic killifish). This species is an important field model for environmental research due to its ability to respond to and withstand variable environmental conditions.…”