Abstract
Genome fractionation (also known as diploidization) frequently occurs following paleopolyploidization events. Biased fractionation between subgenomes has been found in some paleo-allopolyploids, while this phenomenon is absent in paleo-autopolyploids. Pear (Pyrus bretschneideri Rehd.) experienced a recent whole-genome duplication (WGD, ~30 million years ago); however, the evolutionary fate of the two subgenomes derived from this WGD event is not clear. In this study, we identified the two paleo-subgenomes in pear using peach (Prunus persica) as an outgroup and investigated differences in the gene loss rate, evolutionary rate, gene expression level, and DNA methylation level between these two subgenomes. Fractionation bias was not found between the two pear subgenomes, which evolved at similar evolutionary rates. The DNA methylation level of the two subgenomes showed little bias, and we found no expression dominance between the subgenomes. However, we found that singleton genes and homeologous genes within each subgenome showed divergent evolutionary patterns of selective constraints, expression and epigenetic modification. These results provide insights into subgenome evolution following paleopolyploidization in pear.
Highlights
The evolution of plant genomes has been influenced by frequent occurrences of ancient whole-genome duplication (WGD; known as paleopolyploidization), which provide abundant genetic material for survival, phenotypic diversification and radiation of plants[1,2,3,4,5,6]
Peach, and strawberry genomes There are 42,341, 26,873, and 32,831 genes annotated in pear[27], peach (Prunus persica)[39] and woodland strawberry (Fragaria vesca)[40], respectively
Syntenic blocks derived from ancient WGDs were removed based on the ancient Ks peak
Summary
The evolution of plant genomes has been influenced by frequent occurrences of ancient whole-genome duplication (WGD; known as paleopolyploidization), which provide abundant genetic material for survival, phenotypic diversification and radiation of plants[1,2,3,4,5,6]. Extensive genome fractionation ( known as diploidization) occurs following WGD, reverting the polyploids to stable diploid status[6,8,9]. Subgenome dominance is absent in paleoautopolyploids such as poplar (Populus trichocarpa)[14] and even some paleo-allopolyploids, such as soybean (Glycine max)[15] and cucurbits (Cucurbita maxima and Cucurbita moschata)[16]. The phenomenon of biased fractionation between two paleo-subgenomes was first uncovered in maize[12]. Investigation of diverse maize inbred lines found that differential fractionation among individuals is rare[17]
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