TY - JOUR
T1 - Evolution of rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication
AU - Xiang, Yezi
AU - Huang, Chien Hsun
AU - Hu, Yi
AU - Wen, Jun
AU - Li, Shisheng
AU - Yi, Tingshuang
AU - Chen, Hongyi
AU - Xiang, Jun
AU - Ma, Hong
N1 - Funding Information:
We thank the Arnold Arboretum at Harvard University, the Beijing Botanical Garden, the Wuhan Botanical Garden, the Shanghai Botanical Garden, the UC Berkeley Botanical Garden, the University of Bonn Botanical Garden, the United States Botanical Garden and the United States National Arboretum, and Drs Holly Forbes, Kun Sun, Xun Gong, Stefan Lura, William McLaufflin, Zheng Meng, Weimin Ni, Yi Ren, Kyle Wallick, Fusheng Yang, Jinqing Wu, Shoujun Zhang, Yuanping Fang, Yingchun Wang, Zhiping Song, Wenju Zhang, Yaqiong Wang, Fenqin Zhang, Liye Zhang, Ning Zhang, Liqing Zhao, and Ms Liming Cai, for help with plant materials, and Drs Ji Qi, Maoteng Li, Longjiang Yu, Fu Xiang, Chenjiang You, Caifei Zhang, Ren Ren, Xinping Qi, and Mian Liu for technical assistance and discussion. This work was supported by funds from grants from the National Natural Science Foundation of China (91531301 and 31670209), from State Key Laboratory of Genetic Engineering at Fudan University, and the National Top Talent Undergraduate Training Program for outstanding undergraduates and the Wangdao Program for undergraduate research at Fudan.
Funding Information:
A Well Resolved Rosaceae Phylogeny Supported by Multiple Analyses
Publisher Copyright:
© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
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U2 - 10.1093/molbev/msw242
DO - 10.1093/molbev/msw242
M3 - Article
C2 - 27856652
AN - SCOPUS:85016806218
SN - 0737-4038
VL - 34
SP - 262
EP - 281
JO - Molecular biology and evolution
JF - Molecular biology and evolution
IS - 2
ER -