Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow
Abstract Background Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-022-03684-9 |
| _version_ | 1811243791133179904 |
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| author | Jianyu Wang Lan Zhang Jiaqi Wang Yanan Hao Qimeng Xiao Jia Teng Shaoqi Shen Yan Zhang Yishan Feng Shoutong Bao Yu Li Zimo Yan Chendan Wei Li Wang Jinpeng Wang |
| author_facet | Jianyu Wang Lan Zhang Jiaqi Wang Yanan Hao Qimeng Xiao Jia Teng Shaoqi Shen Yan Zhang Yishan Feng Shoutong Bao Yu Li Zimo Yan Chendan Wei Li Wang Jinpeng Wang |
| author_sort | Jianyu Wang |
| collection | DOAJ |
| description | Abstract Background Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remains poorly understood. Results Here, through genomic synteny analyses, we identified duplicate genes generated by the Salicaceae common tetraploidization (SCT) in the poplar and willow genomes. We estimated that at least 0.58% and 0.25% of poplar and willow duplicates were affected by whole-gene conversion after the poplar-willow divergence, with more (5.73% and 2.66%) affected by partial-gene conversion. Moreover, we found that the converted duplicated genes were unevenly distributed on each chromosome in the two genomes, and the well-preserved homoeologous chromosome regions may facilitate the conversion of duplicates. Notably, we found that conversion maintained the similarity of duplicates, likely contributing to the conservation of certain sequences, but is essentially accelerated the rate of evolution and increased species divergence. In addition, we found that converted duplicates tended to have more similar expression patterns than nonconverted duplicates. We found that genes associated with multigene families were preferentially converted. We also found that the genes encoding conserved structural domains associated with specific traits exhibited a high frequency of conversion. Conclusions Extensive conversion between duplicate genes generated from the SCT contributes to the diversification of the family Salicaceae and has had long-lasting effects on those genes with important biological functions. |
| first_indexed | 2024-04-12T14:14:42Z |
| format | Article |
| id | doaj.art-df49cc6b917545758b94a4af90c5515f |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-12T14:14:42Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-df49cc6b917545758b94a4af90c5515f2022-12-22T03:29:47ZengBMCBMC Plant Biology1471-22292022-06-0122111510.1186/s12870-022-03684-9Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willowJianyu Wang0Lan Zhang1Jiaqi Wang2Yanan Hao3Qimeng Xiao4Jia Teng5Shaoqi Shen6Yan Zhang7Yishan Feng8Shoutong Bao9Yu Li10Zimo Yan11Chendan Wei12Li Wang13Jinpeng Wang14School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologySchool of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and TechnologyAbstract Background Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remains poorly understood. Results Here, through genomic synteny analyses, we identified duplicate genes generated by the Salicaceae common tetraploidization (SCT) in the poplar and willow genomes. We estimated that at least 0.58% and 0.25% of poplar and willow duplicates were affected by whole-gene conversion after the poplar-willow divergence, with more (5.73% and 2.66%) affected by partial-gene conversion. Moreover, we found that the converted duplicated genes were unevenly distributed on each chromosome in the two genomes, and the well-preserved homoeologous chromosome regions may facilitate the conversion of duplicates. Notably, we found that conversion maintained the similarity of duplicates, likely contributing to the conservation of certain sequences, but is essentially accelerated the rate of evolution and increased species divergence. In addition, we found that converted duplicates tended to have more similar expression patterns than nonconverted duplicates. We found that genes associated with multigene families were preferentially converted. We also found that the genes encoding conserved structural domains associated with specific traits exhibited a high frequency of conversion. Conclusions Extensive conversion between duplicate genes generated from the SCT contributes to the diversification of the family Salicaceae and has had long-lasting effects on those genes with important biological functions.https://doi.org/10.1186/s12870-022-03684-9PoplarWillowPolyploidizationDuplicated genesGene conversion |
| spellingShingle | Jianyu Wang Lan Zhang Jiaqi Wang Yanan Hao Qimeng Xiao Jia Teng Shaoqi Shen Yan Zhang Yishan Feng Shoutong Bao Yu Li Zimo Yan Chendan Wei Li Wang Jinpeng Wang Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow BMC Plant Biology Poplar Willow Polyploidization Duplicated genes Gene conversion |
| title | Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow |
| title_full | Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow |
| title_fullStr | Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow |
| title_full_unstemmed | Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow |
| title_short | Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow |
| title_sort | conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow |
| topic | Poplar Willow Polyploidization Duplicated genes Gene conversion |
| url | https://doi.org/10.1186/s12870-022-03684-9 |
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