Rosaceae phylogenomics/phylotranscriptomics provide insights into whole genome duplication and implication on character evolution Lin Zhang1,2,3, Hao Li2,4, Chien-Hsun Huang2,5 Taikui Zhang2, Guojin Zhang2, Diego F Morales-Briones6, Fude Shang3,7, Hong Ma2* 1 College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; 2 Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 3 Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China; 4 Bryology Laboratory, School of Life Sciences, East China Normal University Shanghai, China; 5 Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; 6 Princess Therese von Bayern chair of Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Menzinger Str. 67, Munich 80638, Germany; 7 College of Life Science, Henan Agricultural University, Zhengzhou 450002, China. * Corresponding authors: Hong Ma (hxm16@psu.edu). Abstract Rosaceae are a moderately large family of ~3,000 species, with several fleshy fruits, such as apple, pear, quince, peach, plum, cherry, apricot, strawberry, raspberry, and blackberry. Many Rosaceae species also produce dry fruits, including achenes (achenetum) and follicles (follicetum). Phylogenomics/phylotranscriptomics of many thousands of nuclear gene families have uncovered numerous gene duplications. Gene tree – species tree reconciliation has detected gene duplication clusters, providing support for whole genome duplications (WGDs). Additional analyses revealed that gene duplicates from a WGD in early Maleae history exhibit progressive losses during the evolutionary history of the lineages affected by the WGD. Ancestral character reconstruction suggests that there were several transitions from dry to fleshy fruits during Rosaceae evolution with distinct patterns of morphological changes. Moreover, gene duplicates from WGDs might have contributed morphological innovations associated with the origin of some fleshy fruits. These results and more recent analyses related to these aspects of Rosaceae evolution will be presented and the possible impact of WGD on gene function and character evolution will be discussed.