Polyploidy Index and Its Implications for the Evolution of Polyploids
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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-09-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00807/full |
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| author | 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 |
| author_facet | 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 |
| author_sort | Jinpeng Wang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T04:03:58Z |
| format | Article |
| id | doaj.art-052d394a065b464b9e246127961da199 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T04:03:58Z |
| publishDate | 2019-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-052d394a065b464b9e246127961da1992022-12-22T03:03:22ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-09-011010.3389/fgene.2019.00807475779Polyploidy Index and Its Implications for the Evolution of PolyploidsJinpeng Wang0Jinpeng Wang1Jinpeng Wang2Jinpeng Wang3Jun Qin4Pengchuan Sun5Pengchuan Sun6Xuelian Ma7Jigao Yu8Jigao Yu9Yuxian Li10Yuxian Li11Sangrong Sun12Sangrong Sun13Tianyu Lei14Tianyu Lei15Fanbo Meng16Fanbo Meng17Chendan Wei18Chendan Wei19Xinyu Li20Xinyu Li21He Guo22He Guo23Xiaojian Liu24Ruiyan Xia25Li Wang26Li Wang27Weina Ge28Weina Ge29Xiaoming Song30Xiaoming Song31Lan Zhang32Lan Zhang33Di Guo34Di Guo35Jinyu Wang36Shoutong Bao37Shan Jiang38Yishan Feng39Xueping Li40Andrew H. Paterson41Xiyin Wang42Xiyin Wang43School of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaPlant Genome Mapping Laboratory, University of Georgia, Athens, GA, United StatesSchool of Life Sciences, North China University of Science and Technology, Tangshan, ChinaCenter for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, ChinaPolyploidy 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.https://www.frontiersin.org/article/10.3389/fgene.2019.00807/fullpolyploidyangiospermP-indexgenomicsbioinformatics |
| spellingShingle | 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 Polyploidy Index and Its Implications for the Evolution of Polyploids Frontiers in Genetics polyploidy angiosperm P-index genomics bioinformatics |
| title | Polyploidy Index and Its Implications for the Evolution of Polyploids |
| title_full | Polyploidy Index and Its Implications for the Evolution of Polyploids |
| title_fullStr | Polyploidy Index and Its Implications for the Evolution of Polyploids |
| title_full_unstemmed | Polyploidy Index and Its Implications for the Evolution of Polyploids |
| title_short | Polyploidy Index and Its Implications for the Evolution of Polyploids |
| title_sort | polyploidy index and its implications for the evolution of polyploids |
| topic | polyploidy angiosperm P-index genomics bioinformatics |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00807/full |
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