Modes of Gene Duplication and Gene Family Expansion and Evolution in Chinese White Pear

Pear is a member of the Rosaceae family and is also an important temperate fruit species. At present, the genome of Chinese white pear (Pyrus bretschneideri) has been fully sequenced. Based on the genome-wide analysis, two genome-wide duplication (WGD) events have been observed in pear genome. Also, single-gene duplication was found to be prevalent in pear genome. Recurrent gene duplication and genome duplication drive the expansion and evolution of gene family in pear. In this study, we detected 38,593 duplicated genes in the  whole pear genome. All duplicated genes were further assigned to five different origins. 19,352 were duplicated and retained from genome-wide duplications, while 3,364, 2,655, 217 and 1,188 respectively from tandem, proximal, retrotransposed (RNA-based transposed), and DNA-based transposed duplications. Non-synonymous (Ka) and synonymous substitution (Ks) rates were estimated to reveal the evolutionary patterns underlying different types of duplication. Then we classified all the pear genes into families and identified the origins of duplicated genes for the large gene families in pear. The results showed that different patterns of gene duplication contributed differentially to the expansion of specific gene families. Furthermore, transcriptome data were used to measure the level of duplicated gene expression divergence. The results suggested that the evolutionary fates and biased retention of duplicated genes might be driven by multiple mechanisms, such as dosage balance, neofunctionalization, and subfunctionalization. The results of this work will be useful for better understanding the complexity of gene duplications, expansion of gene families, and gene expression divergence in pear genome.