Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon)

Abstract

Background: Comparative genomic studies suggest that the modern day assemblage of ray-finned fishes have descended from an ancestral grouping of fishes that possessed 12-13 linkage groups. All jawed vertebrates are postulated to have experienced two whole genome duplications (WGD) in their ancestry (2R duplication). Salmonids have experienced one additional WGD (4R duplication event) compared to most extant teleosts which underwent a further 3R WGD compared to other vertebrates. We describe the organization of the 4R chromosomal segments of the proto-rayfinned fish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenies with two model species of 3R ray-finned fishes.

Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes

“…On these occasions, synteny maps of stickleback with Atlantic salmon and rainbow trout (48) were used in the same manner to make predictions about gene positions in those species. Known homologous linkage group affinities among Arctic charr, Atlantic salmon, and rainbow trout (9,10,63) were then used to make predictions about the position of differentially expressed genes on the Arctic charr linkage map.…”

Identification of an additional two-cysteine containing type I interferon in rainbow trout Oncorhynchus mykiss provides evidence of a major gene duplication event within this gene family in teleosts

“…Accumulating data from phylogenetic analysis of gene families and genomes support the evolutionary model that a fourth round of genome duplication has taken place in salmonids (Danzmann et al 2008;Hoegg et al 2004). In this study, we describe a novel member of the 2C containing IFN family (termed IFN5) in rainbow trout Oncorhynchus mykiss, which identifies a fourth subgroup of salmonid IFNs.…”

Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

“…We added additional markers to the linkage groups using information from Guyomard et al (2012) and Danzmann et al (2008). The sequences of the rainbow trout markers were obtained when possible from the National Center for Biotechnology Information (NCBI) or the Dana-Farber Cancer Institute (DFCI) databases.…”

“…Due to the low coverage of markers used in the present study, and their targeted selection from the opposite ends of chromosomes and also central regions, some of the markers were identified as unlinked within some of the larger chromosomes surveyed. When this occurred they were assigned to their designated chromosomes using the map distances reported in Danzmann et al (2008) for the construction of GridQTL map files. Chromosomewide significance was determined with 1000 permutations of the trait data against the genotypes (Churchill and Doerge 1994).…”