An integrated transcriptomic and comparative genomic analysis of differential gene expression in Arctic charr (Salvelinus alpinus) following seawater exposure

Abstract

High-throughput RNA sequencing was used to compare expression profiles in two Arctic charr (Salvelinus alpinus) families post-seawater exposure to identify genes and biological processes involved in hypoosmoregulation and regulation of salinity tolerance. To further understand the genetic architecture of hypo-osmoregulation, the genomic organization of differentially expressed (DE) genes was also analysed. Using a de novo gill transcriptome assembly we found over 2300 contigs to be DE. Major transporters from the seawater mitochondrion-rich cell (MRC) complex were up-regulated in seawater. Expression ratios for 257 differentially expressed contigs were highly correlated between families, suggesting they are strictly regulated. Based on expression profiles and known molecular pathways we inferred that seawater exposure induced changes in methylation states and elevated peroxynitrite formation in gill. We hypothesized that concomitance between DE immune genes and the transition to a hypo-osmoregulatory state could be related to Cl -sequestration by antimicrobial defence mechanisms. Gene ontology analysis revealed that cell division genes were up-regulated, which could reflect the proliferation of ATP1α1b-type seawater MRCs. Comparative genomics analyses suggest that hypo-osmoregulation is influenced by the relative proximities among a contingent of genes on Arctic charr linkage groups AC-4 and AC-12 that exhibit homologous affinities with a region on stickleback chromosome Ga-I. This supports the hypothesis that relative gene location along a chromosome is a property of the genetic architecture of hypoosmoregulation. Evidence of non-random structure between hypoosmoregulation candidate genes was found on AC-1/11 and AC-28, suggesting that interchromosomal rearrangements played a role in the evolution of hypo-osmoregulation in Arctic charr.KEY WORDS: RNA-Seq, Gene expression, Osmoregulation, Salinity tolerance, Salmonidae, Salvelinus alpinus INTRODUCTIONMigration between freshwater and seawater habitats is an important stage in the ontogeny of anadromous salmonids (Hoar, 1988). Freshwater and seawater impose adverse and contrasting types of osmoregulatory stress, such that maintenance of internal ion homeostasis is paramount for survival. The transition from freshwater to seawater requires osmoregulatory mechanisms to switch from a state of ion absorption (i.e. hyper-osmoregulation) to one of ion excretion (i.e. hypo-osmoregulation). Gill tissue epithelial RESEARCH ARTICLEDepartment of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1. cells play an integral role in this process (Evans et al., 2005;Marshall and Grosell, 2006).Mitochondrion-rich cells (MRCs) form a complex with accessory cells and pavement cells in the epithelial layer of gill tissue (Evans et al., 2005;Marshall and Grosell, 2006). In seawater, this complex facilitates excretion of excess Cl -and Na + from blood to seawater. Cl -excretion is achieved via the collective function of three interdependent membrane-bound ion...

Genetic basis for variation in salinity tolerance between stickleback ecotypes

“…) and under high osmotic stress in the Arctic charr (Norman et al . ), sockeye salmon (Evans et al . ) and longjaw mudsucker (Evans & Somero ).…”

Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats

“…Recent studies have provided evidence for salinityinduced plasticity in gills of euryhaline fish (Evans & Somero 2008;McCairns & Bernatchez 2010;Whitehead et al 2012;Lam et al 2014;Norman et al 2014;Taugbøl et al 2014;Velotta et al 2014Velotta et al , 2015Kavembe et al 2015;Zhang et al 2015). However, there are relatively few studies comparing the extent of gene expression plasticity between related marine and freshwater forms (although see McCairns & Bernatchez (2010), Whitehead et al (2011), Velotta et al (2014Velotta et al ( , 2015 and Kozak et al (2014)).…”

Gene Expression in the Three-Spined Stickleback (Gasterosteus aculeatus) of Marine and Freshwater Ecotypes

“…Diadromous fish are especially suitable for this type of research, since they can live in both marine and fresh water and have physiological mechanisms for adaptation to water of differing salinity. In addition, global changes in gene expression in the marine and freshwater forms of such species as Plecoglossus altivelis ayu [ 8 ], Japanese river acne Anguilla japonica [ 9 ], European acne A. anguilla [ 10 ], tilapia Oreochromis mossambicus [ 11 , 12 ], Fundulus heteroclotus [ 13 ], common laurel Dicentrarchus labrax [ 14 ], sockeye Oncorhynchus nerka [ 15 ], arctic char Salvelinus alpinus [ 16 ] are studied by the RNA-seq method. In most cases, the RNA-seq method is used to evaluate subsequent changes in gene expression after changes in the external environment with gills as the target tissue.…”