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Background   Squalius alburnoides  is an Iberian cyprinid fish resulting from an interspecific hybridisation between  Squalius pyrenaicus  females (P genome) and males of an unknown  Anaecypris hispanica- like species (A genome).  S. alburnoides  is an allopolyploid hybridogenetic complex, which makes it a likely candidate for ploidy mosaicism occurrence, and is also an interesting model to address questions about gene expression regulation and genomic interactions. Indeed, it was previously suggested that in  S. alburnoides  triploids (PAA composition) silencing of one of the three alleles (mainly of the P allele) occurs. However, not a whole haplome is inactivated but a more or less random inactivation of alleles varying between individuals and even between organs of the same fish was seen.  In this work we intended to correlate expression differences between individuals and/or between organs to the occurrence of mosaicism, evaluating if mosaics could explain previous observations and its impact on the assessment of gene expression patterns.    Results  To achieve our goal, we developed flow cytometry and cell sorting protocols for this system generating more homogenous cellular and transcriptional samples. With this set-up we detected 10% ploidy mosaicism within the  S. alburnoides  complex, and determined the allelic expression profiles of ubiquitously expressed genes ( rpl8 ;  gapdh  and  β-actin ) in cells from liver and kidney of mosaic and non-mosaic individuals coming from different rivers over a wide geographic range.    Conclusions  Ploidy mosaicism occurs sporadically within the  S. alburnoides  complex, but in a frequency significantly higher than reported for other organisms. Moreover, we could exclude the influence of this phenomenon on the detection of variable allelic expression profiles of ubiquitously expressed genes ( rpl8 ;  gapdh  and  β-actin ) in cells from liver and kidney of triploid individuals. Finally, we determined that the expression patterns previously detected only in a narrow geographic range is not a local restricted phenomenon but is pervasive in rivers where  S. pyrenaicus  is sympatric with  S. alburnoides .  We discuss mechanisms that could lead to the formation of mosaic  S. alburnoides  and hypothesise about a relaxation of the mechanisms that impose a tight control over mitosis and ploidy control in mixoploids.

Ploidy mosaicism and allele-specific gene expression differences in the allopolyploid Squalius alburnoides