Frontiers in Genetics (Sep 2019)
Polyploidy Index and Its Implications for the Evolution of Polyploids
- Jinpeng Wang,
- Jinpeng Wang,
- Jinpeng Wang,
- Jinpeng Wang,
- Jun Qin,
- Pengchuan Sun,
- Pengchuan Sun,
- Xuelian Ma,
- Jigao Yu,
- Jigao Yu,
- Yuxian Li,
- Yuxian Li,
- Sangrong Sun,
- Sangrong Sun,
- Tianyu Lei,
- Tianyu Lei,
- Fanbo Meng,
- Fanbo Meng,
- Chendan Wei,
- Chendan Wei,
- Xinyu Li,
- Xinyu Li,
- He Guo,
- He Guo,
- Xiaojian Liu,
- Ruiyan Xia,
- Li Wang,
- Li Wang,
- Weina Ge,
- Weina Ge,
- Xiaoming Song,
- Xiaoming Song,
- Lan Zhang,
- Lan Zhang,
- Di Guo,
- Di Guo,
- Jinyu Wang,
- Shoutong Bao,
- Shan Jiang,
- Yishan Feng,
- Xueping Li,
- Andrew H. Paterson,
- Xiyin Wang,
- Xiyin Wang
Affiliations
- Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Jinpeng Wang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Jinpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China
- Jinpeng Wang
- University of Chinese Academy of Sciences, Beijing, China
- Jun Qin
- Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Pengchuan Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Pengchuan Sun
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Xuelian Ma
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Jigao Yu
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Yuxian Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Yuxian Li
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Sangrong Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Sangrong Sun
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Tianyu Lei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Tianyu Lei
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Fanbo Meng
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Chendan Wei
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Xinyu Li
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- He Guo
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Xiaojian Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Ruiyan Xia
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Li Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Li Wang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Weina Ge
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Weina Ge
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Xiaoming Song
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Lan Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Lan Zhang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Di Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Di Guo
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- Jinyu Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Shoutong Bao
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Shan Jiang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Yishan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Xueping Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
- Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Xiyin Wang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- DOI
- https://doi.org/10.3389/fgene.2019.00807
- Journal volume & issue
-
Vol. 10
Abstract
Polyploidy has contributed to the divergence and domestication of plants; however, estimation of the relative roles that different types of polyploidy have played during evolution has been difficult. Unbalanced and balanced gene removal was previously related to allopolyploidies and autopolyploidies, respectively. Here, to infer the types of polyploidies and evaluate their evolutionary effects, we devised a statistic, the Polyploidy-index or P-index, to characterize the degree of divergence between subgenomes of a polyploidy, to find whether there has been a balanced or unbalanced gene removal from the homoeologous regions. Based on a P-index threshold of 0.3 that distinguishes between known or previously inferred allo- or autopolyploidies, we found that 87.5% of 24 angiosperm paleo-polyploidies were likely produced by allopolyploidizations, responsible for establishment of major tribes such as Poaceae and Fabaceae, and large groups such as monocots and eudicots. These findings suggest that >99.7% of plant genomes likely derived directly from allopolyploidies, with autopolyploidies responsible for the establishment of only a few small genera, including Glycine, Malus, and Populus, each containing tens of species. Overall, these findings show that polyploids with high divergence between subgenomes (presumably allopolyploids) established the major plant groups, possibly through secondary contact between previously isolated populations and hybrid vigor associated with their re-joining.
Keywords
