Unbiased subgenome evolution following a recent whole-genome duplication in pear (Pyrus bretschneideri Rehd.)

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.

Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus bretschneideri)

“…The fruit samples were collected on 26th May (45 DAF), 27th June (75 DAF), 28th July (105 DAF) and 6th Sep (145 DAF) in 2017. Previously published RNA-seq data was used to analyze the expression patterns of 'Dangshan suli' BAHD [61,62]. All the samples were ground in liquid nitrogen and stored at − 80°C.…”

“…The RNA-seq data of 15 'Dangshansuli' samples were used to analyze the expression patterns of 'Dangshansuli' BAHD, including Fruit_S1, Fruit_S2, Fruit_S3, Fruit_S4 (obtained from the NCBI biproject PRJNA563942), Root (data not shown), Stem, Leaf, Bud, Petal, Sepal, Ovary, Mature pollen, Hydrated pollen, Pollen tube and Stop growth pollen [61,62]. Then, the gene expression heatmap was drawn using TB-Tools [66].…”

Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus☓ bretschneideri)

“…All the BAHD members of strawberry, peach and European pear experienced purifying selection. Similar results Hydrated pollen, Pollen tube and Stop growth pollen [64,65]. Then, the gene expression heatmap was drawn using TB-Tools [69].…”

The importance and prevalence of allopolyploidy in Aotearoa New Zealand

“…The evolutionary history of pears is also unclear, with some studies supporting an allopolyploid origin (Evans et al 2008), while others support the autopolyploidy hypothesis . The latter study drew their conclusions from the observed unbiased subgenome evolution in the pear genome; a common trend among paleo-autopolyploids, but one that has also been observed in some paleo-allopolyploid lineages (Sun et al 2017;Li et al 2019).…”