Whole-Genome Duplications in Pear and Apple

Abstract

Whole-genome duplications (WGDs) are widespread in angiosperms, and are proposed to have contributed to angiosperm diversification. Pear (Pyrus) and apple (Malus) belong to the large and diverse Maleae tribe, and their genome sequences have extensive syntenic blocks covering much of the chromosomes, thus providing strong support for WGDs. Comparative analyses further indicate that at least a single WGD is shared by both pear and apple, and it has likely occurred following pear/apple lineage split from that of strawberry (Fragaria). Furthermore, phylogenomic analysis of thousands of nuclear genes, from public genome datasets and from over 120 transcriptomic datasets, has uncovered strong evidence of presence of thousands of gene duplicates for a WGD in the ancestor of pear, apple, and of other fleshy-fruit-producing genera of the subtribe Malinae, following divergence of dry-fruit-bearing lineages of Maleae. Moreover, over 1000 gene duplicates from the Malinae WGD have been mapped to syntenic blocks in the apple genome, thus supporting the hypothesis that syntenic blocks found in apple (and pear) have been generated by the Malinae WGD, dated in late Eocene ({\textasciitilde}38--42 million years ago). Further, nearly two-thirds of gene duplicates, initially retained following the Malinae WGD, have been lost in the apple genome, with relatively rapid losses in early Oligocene. Finally, the Malinae-WGD-generated duplicates are enriched in GO categories for transcriptional regulation, including members of the MADS-box gene family, possibly contributing to the evolution of fleshy fruits in Malinae. There is also supporting evidence for this finding provided by functional analysis of several apple MADS-box genes.