Allele-specific expression variation at different ploidy levels in Squalius alburnoides

Abstract

Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides . Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides .

The importance and prevalence of allopolyploidy in Aotearoa New Zealand

“…The persistence of allopolyploidy across Eukarya (Yoo et al 2013;Cox et al 2014;Sehrish et al 2014;Session et al 2016;Matos et al 2019) suggests that successful adaptation to all of these challenges may grant the allopolyploid advantages previously unavailable to its parent lineages. Their doubled and hybrid genomes can facilitate intergenomic heterosis (hybrid vigour); a phenotypic consequence where hybrid species demonstrate increased biological fitness when compared with either parental line (Baranwal et al 2012;Fujimoto et al 2018).…”