title: Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication.
abstract: Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Yezi
authors.initials: Y
authors.lastname: Xiang
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Chien-Hsun
authors.initials: CH
authors.lastname: Huang
authors.affiliation: Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Hu
authors.affiliation: The Smithsonian Institution, Washington, DC.
authors.forename: Jun
authors.initials: J
authors.lastname: Wen
authors.affiliation: Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China.
authors.forename: Shisheng
authors.initials: S
authors.lastname: Li
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
authors.forename: Tingshuang
authors.initials: T
authors.lastname: Yi
authors.affiliation: Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China.
authors.forename: Hongyi
authors.initials: H
authors.lastname: Chen
authors.affiliation: Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Xiang
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
mesh_terms: D005075:Biological Evolution; D062126:Databases, Chemical; D019143:Evolution, Molecular; D005638:Fruit / Q000235:genetics; D020440:Gene Duplication; D018745:Genome, Plant; D023281:Genomics; D027845:Malus / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D027824:Rosaceae / Q000235:genetics*; D012639:Seeds / Q000235:genetics; D059467:Transcriptome
chemical_list: D010940:Plant Proteins
keywords: Rosaceae; coalescence; fruit evolution; genome duplication; molecular clock; nuclear phylogeny