Unbiased subgenome evolution following a recent whole-genome duplication in pear (

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.
Following a trail of duplicated pear DNA Genomic sleuthing reveals insights into an ancestral chromosomal duplication event from the early evolution of the pear tree. Such ‘whole-genome duplication’ is common among plants, and can arise from the combination of genetic material of plants from either the same (autopolyploid) or different (allopolyploid) species. The pear is known to have undergone a duplication event 30 million years ago, and Shaoling Zhang and colleagues at Nanjing Agricultural University in China set out to assess the nature of this genome expansion. After analysis of pear genome data and comparison against other fruit plant species, the researchers determined that the pear is an autopolyploid, and that genes found in just one ‘subgenome’ have subsequently evolved expression profiles that differ noticeably from those genes that are present as multiple homologues amongst the duplicated chromosomes.