Contents lists available at ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene Research paper Pck-ing up steam: Widening the salmonid gluconeogenic gene duplication trail L. Marandel a,1 , D.J. Kostyniuk b,1 , C. Best b , J.L.I. Forbes b , J. Liu a , S. Panserat a , J.A. Mennigen b, ⁎ a INRA, Université de Pau et Pays d'Adour, UMR 1419, Nutrition, Metabolism and Aquaculture, Saint Pée-sur-Nivelle F-64310, France b Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada ARTICLE INFO Keywords: Rainbow trout Teleost Phosphoenolpyruvate carboxykinase Duplicated genes Gluconeogenesis glucose intolerance ABSTRACT Rainbow trout have, as salmonid fish species, undergone sequential genome duplication events in their evolu- tionary history. In addition to a teleost-specific whole genome duplication approximately 320–350 million years ago, rainbow trout and salmonids in general underwent an additional salmonid lineage-specific genome du- plication event approximately 80 million years ago. Through the recent sequencing of salmonid genome se- quences, including the rainbow trout, the identification and study of duplicated genes has become available. A particular focus of interest has been the evolution and regulation of rainbow trout gluconeogenic genes, as recent molecular and gene expression evidence points to a possible contribution of previously uncharacterized glu- coneogenic gene paralogues to the rainbow trout long-studied glucose intolerant phenotype. Since the pub- lication of the initial rainbow trout genome draft, resequencing and annotation have further improved genome coverage. Taking advantage of these recent improvements, we here identify a salmonid-specific genome du- plication of ancestral mitochondrial phosphoenolpyruvate carboxykinase 2 isoenzyme, we termed pck2a and pck2b. Cytosolic phosphoenolpyruvate carboxykinase (Pck1) and, more recently mitochondrial Pck2, are con- sidered to be the rate-limiting enzymes in de novo gluconeogenesis. Following in silico confirmation of salmonid pck2a and pck2b evolutionary history, we simultaneously profiled cytosolic pck1 and mitochondrial pck2a and pck2b expression in rainbow trout liver under several experimental conditions known to regulate hepatic glu- coneogenesis. Cytosolic pck1 abundance was increased by nutritional (diets with a high protein to carbohydrate ratio compared to diets with a low carbohydrate to protein ratio) and glucoregulatory endocrine factors (glu- cagon and cortisol), revealing that the well-described transcriptional regulation of pck1 in mammals is present in rainbow trout. Conversely, and in contrast to mammals, we here describe endocrine regulation of pck2a (de- crease in abundance in response to glucagon infusion), and nutritional, social-status-dependent and hypoxia- dependent regulation of pck2b. Specifically, pck2b transcript abundance increased in trout fed a diet with a low protein to carbohydrate ratio compared to a diet with a high protein to carbohydrate ratio, in dominant fish compared to subordinate fish as well as hypoxia. This specific and differential expression of rainbow trout pck2 ohnologues is indicative of functional diversification, and possible functional consequences are discussed in light of the recently highlighted gluconeogenic roles of mitochondrial pck2 in mammalian models. 1. Introduction Over the last decade, whole genome sequencing of model and non- model species has increased dramatically, especially in teleost fishes and salmonid species in particular (Berthelot et al., 2014; Chen et al., 2014; Hu and Chen, 2015; Lien et al., 2016). The availability of these genome sequences has opened up novel avenues to better understand species diversification at the genome and gene expression level. Indeed, in animal evolution, several whole genome duplications (GD) have occurred, two before or around the vertebrate radiation (termed VGD1 and VGD2 for vertebrate genome duplication events 1 and 2, respec- tively), one at the radiation of teleost fishes (termed TGD for teleost- specific genome duplication), and finally one at the radiation of sal- monids (called SaGD for salmonid-specific genome duplication), which https://doi.org/10.1016/j.gene.2019.02.079 Received 3 December 2018; Received in revised form 3 February 2019; Accepted 21 February 2019 Abbreviations: pck1, phosphoenolpyruvate carboxykinase 1 (cytosolic); pck2, phosphoenolpyruvate carboxykinase 2 (mitochondrial); SaGD, salmonid specific genome duplication; GD, genome duplication; PEP, phosphoenolpyruvate; GTP, guanosine triphosphate ⁎ Corresponding author. E-mail address: jan.mennigen@uottawa.ca (J.A. Mennigen). 1 These authors contributed equally to the present work. Gene 698 (2019) 129–140 Available online 05 March 2019 0378-1119/ © 2019 Elsevier B.V. All rights reserved. T