Gene copy silencing and DNA methylation in natural and artificially produced allopolyploid fish

Abstract

Allelic silencing is an important mechanism for coping with gene dosage changes in polyploid organisms that is well known in allopolyploid plants. Only recently, it was shown in the allotriploid fish Squalius alburnoides that this process also occurs in vertebrates. However, it is still unknown whether this silencing mechanism is common to other allopolyploid fish, and which mechanisms might be responsible for allelic silencing. We addressed these questions in a comparative study between Squalius alburnoides and another allopolyploid complex, the Amazon molly (Poecilia formosa). We examined the allelic expression patterns for three target genes in four somatic tissues of natural allo-anorthoploids and laboratory-produced trigenomic hybrids of S. alburnoides and P. formosa. Also, for both complexes, we evaluated the correlation between total DNA methylation level and the ploidy status and genomic composition of the individuals. We found that allelic silencing also occurs in other allopolyploid organisms besides the single one that was previously known. We found and discuss disparities within and between the two considered complexes concerning the pattern of allele-specific expression and DNA methylation levels. Disparities might be due to intrinsic characteristics of each genome involved in the hybridization process. Our findings also support the idea that long-term evolutionary processes have an effect on the allele expression patterns and possibly also on DNA methylation levels.

Adaptation and convergence in circadian‐related genes in Iberian freshwater fish

“…Samples of S. pyrenaicus were also stored at -80ºC from previous projects. This work includes two sampling sites: Almargem (37°09′ 50.7" N; 7° 37′ 13.2" W) [63] and Tagus (39° 43′ 48.2" N; 7° 45′ 38.1" W) [64].…”

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

“…In triploid S. alburnoides (liv-PAA and juv-PAA) we found, besides the biallelic expression, monoallelic expression of P but also P allelic silencing. P homoeolog silencing in triploid S. alburnoides has already been reported previously 16,17,21,36 , but monoallelic P expression has not been observed so far in Squalius genus. This new finding of expression from only one allele in the context of allotriploidy in this fish, agrees with a previous report of the same pattern in another successful allopolyploid complex, the allopolyploid Poecilia formosa 36 .…”

“…However, P. formosa is a clonal hybrid organism, resultant from a single time successful hybridization event at least 100.000 years old 34,35 . This makes P. formosa much different from the reproductive complex of S. alburnoides , which results from a continuum of intricated networks of genetic exchanges, de novo hybridizations and ploidy levels shifts 36 . The old “frozen” hybrid genomic context of P. formosa may have evolved mechanism that counteract HEB.…”

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

“…exhibited correlation between levels of promoter methylation and levels of expression, suggesting functional interactions of promoter methylation and growth in triploid sea cucumbers ( Han et al, 2021a ). DNA methylation is believed to regulate gene expression in polyploid organisms (for a review, see Osborn et al, 2003 ), and such regulation by DNA methylation was a part of the regulatory mechanism for allelic silencing in allopolyploid fish ( Matos et al, 2016 ). In a study with tilapia, Konstantinidis et al (2021) showed tissue-specific differential methylation of genes involved in somatic growth, such as growth factors and their receptors, with hypomethylation in the muscle tissues.…”