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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00807

Polyploidy index and its implications for the evolution of polyploids

 Jinpeng Wang1, 2, 3, 4,  Pengchuan sun2, 5, Tianyu Lei5, 6, Fanbo Meng5, 6, Chendan Wei5, Xinyu Li7, 8, He Guo7, 8,  Xiaojian Liu7, 8, Ruiyan Xia7,  Li Wang7, 8, 9,  Weina Ge7, 8, 9,  Xiaoming Song7, 8, 9, Lan Zhang7, 8, 9,  Di Guo7, 8, 9, Jinyu Wang7, Shoutong Bao7, Shan Jiang7, Yishan Feng7, Xueping Li7,  Andrew H. Paterson10 and  Xiyin Wang11*
  • 1North China University of Science and Technology , School of Life Sciences ,, China
  • 2North China University of Science and Technology, Center for Genomics and Computational Biology, China
  • 3State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, China
  • 4University of Chinese Academy of Sciencesnor, China
  • 5School of Life Sciences, North China University of Science and Technology, China
  • 6Center for Genomics and Computational Biology, North China University of Science and Technology, China
  • 7School of Life Sciences, North China University of Science and Technology, China
  • 8Genomics and Computational Biology Research Center, North China University of Science and Technology, China
  • 9Genomics and Computational Biology Research Center, North China University of Science and Technology, China
  • 10Plant Genome Mapping Laboratory, University of Georgia, United States
  • 11School of Life Sciences, North China University of Science and Technology, China

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 auto-polyploidies, 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: Polyploidy, angiosperm, P-Index, Genomics, bioinformatics

Received: 31 May 2019; Accepted: 02 Aug 2019.

Copyright: © 2019 Wang, sun, Lei, Meng, Wei, Li, Guo, Liu, Xia, Wang, Ge, Song, Zhang, Guo, Wang, Bao, Jiang, Feng, Li, H. Paterson and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Xiyin Wang, North China University of Science and Technology, School of Life Sciences, Tangshan, China, wang.xiyin@gmail.com