Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology
A phylogenetic tree can be used to illustrate the evolutionary relationship between a group of genes, especially duplicated genes, which are sources of genetic innovation and are often a hotspot of research. However, duplicated genes may have complex phylogenetic topologies due to changes in their e...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00239/full |
| _version_ | 1818453609817309184 |
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| author | Fanbo Meng Yuxin Pan Jinpeng Wang Jigao Yu Chao Liu Zhikang Zhang Chendan Wei He Guo Xiyin Wang Xiyin Wang |
| author_facet | Fanbo Meng Yuxin Pan Jinpeng Wang Jigao Yu Chao Liu Zhikang Zhang Chendan Wei He Guo Xiyin Wang Xiyin Wang |
| author_sort | Fanbo Meng |
| collection | DOAJ |
| description | A phylogenetic tree can be used to illustrate the evolutionary relationship between a group of genes, especially duplicated genes, which are sources of genetic innovation and are often a hotspot of research. However, duplicated genes may have complex phylogenetic topologies due to changes in their evolutionary rates. Here, by constructing phylogenetic trees using different methods, we evaluated the phylogenetic relationships of duplicated genes produced by polyploidization in cotton. We found that at least 83.2% of phylogenetic trees did not conform the expected topology. Moreover, cotton homologous gene copy number has little effect on the topology of duplicated genes. Compared with their cacao orthologs, elevated evolutionary rates of cotton genes are responsible for distorted tree topology. Furthermore, as to both branch and site models, we inferred that positive natural selection during the divergence of fiber-development-related MYB genes was likely, and found that the reconstructed tree topology may often overestimate natural selection, as compared to the inference with the expected trees. Therefore, we emphasize the importance of borrowing precious information from gene collinearity in tree construction and evaluation, and have evidence to alert the citation of thousands of previous reports of adaptivity and functional innovation of duplicated genes. |
| first_indexed | 2024-12-14T21:41:43Z |
| format | Article |
| id | doaj.art-2686611d24ee41c4bfbc39cca732e119 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T21:41:43Z |
| publishDate | 2020-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-2686611d24ee41c4bfbc39cca732e1192022-12-21T22:46:26ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-04-011110.3389/fgene.2020.00239519231Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree TopologyFanbo Meng0Yuxin Pan1Jinpeng Wang2Jigao Yu3Chao Liu4Zhikang Zhang5Chendan Wei6He Guo7Xiyin Wang8Xiyin Wang9School 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, 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, ChinaInstitute for Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, ChinaA phylogenetic tree can be used to illustrate the evolutionary relationship between a group of genes, especially duplicated genes, which are sources of genetic innovation and are often a hotspot of research. However, duplicated genes may have complex phylogenetic topologies due to changes in their evolutionary rates. Here, by constructing phylogenetic trees using different methods, we evaluated the phylogenetic relationships of duplicated genes produced by polyploidization in cotton. We found that at least 83.2% of phylogenetic trees did not conform the expected topology. Moreover, cotton homologous gene copy number has little effect on the topology of duplicated genes. Compared with their cacao orthologs, elevated evolutionary rates of cotton genes are responsible for distorted tree topology. Furthermore, as to both branch and site models, we inferred that positive natural selection during the divergence of fiber-development-related MYB genes was likely, and found that the reconstructed tree topology may often overestimate natural selection, as compared to the inference with the expected trees. Therefore, we emphasize the importance of borrowing precious information from gene collinearity in tree construction and evaluation, and have evidence to alert the citation of thousands of previous reports of adaptivity and functional innovation of duplicated genes.https://www.frontiersin.org/article/10.3389/fgene.2020.00239/fullcottongene collinearityduplicated genesorthologsphylogenyevolutionary rate |
| spellingShingle | Fanbo Meng Yuxin Pan Jinpeng Wang Jigao Yu Chao Liu Zhikang Zhang Chendan Wei He Guo Xiyin Wang Xiyin Wang Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology Frontiers in Genetics cotton gene collinearity duplicated genes orthologs phylogeny evolutionary rate |
| title | Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology |
| title_full | Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology |
| title_fullStr | Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology |
| title_full_unstemmed | Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology |
| title_short | Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology |
| title_sort | cotton duplicated genes produced by polyploidy show significantly elevated and unbalanced evolutionary rates overwhelmingly perturbing gene tree topology |
| topic | cotton gene collinearity duplicated genes orthologs phylogeny evolutionary rate |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00239/full |
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