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Cao Y, Xu X, Jiang L. Integrative analysis of the RNA interference toolbox in two Salicaceae willow species, and their roles in stress response in poplar (Populus trichocarpa Torr. & Gray). Int J Biol Macromol 2020; 162:1127-1139. [DOI: 10.1016/j.ijbiomac.2020.06.235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/31/2020] [Accepted: 06/24/2020] [Indexed: 10/24/2022]
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Liu Y, Wang J, Ge W, Wang Z, Li Y, Yang N, Sun S, Zhang L, Wang X. Two Highly Similar Poplar Paleo-subgenomes Suggest an Autotetraploid Ancestor of Salicaceae Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:571. [PMID: 28446920 PMCID: PMC5388744 DOI: 10.3389/fpls.2017.00571] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/29/2017] [Indexed: 05/12/2023]
Abstract
As a model plant to study perennial trees in the Salicaceae family, the poplar (Populus trichocarpa) genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar's genome structure and gene family evolution. Here, by adopting the relatively simpler grape (Vitis vinifera) genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation. We uncovered homologous blocks in the grape and poplar genomes and also between them. Moreover, we characterized the genes missing and found that poplar had two considerably similar subgenomes (≤0.05 difference in gene deletion) produced by the Salicaceae-common tetraploidization, suggesting its autotetraploid nature. Taken together, this work provides a timely and valuable dataset of orthologous and paralogous genes for further study of the genome structure and functional evolution of poplar and other Salicaceae plants.
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Affiliation(s)
- Yinzhe Liu
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Jinpeng Wang
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Weina Ge
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Zhenyi Wang
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Yuxian Li
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Nanshan Yang
- School of Life Science, North China University of Science and TechnologyTangshan, China
| | - Sangrong Sun
- School of Life Science, North China University of Science and TechnologyTangshan, China
| | - Liwei Zhang
- School of Life Science, North China University of Science and TechnologyTangshan, China
| | - Xiyin Wang
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
- *Correspondence: Xiyin Wang,
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