Genomes shed light on the evolution of Begonia, a mega‐diverse genus
- Author
- Lingfei Li, Xiaoli Chen, Dongming Fang, Shanshan Dong, Xing Guo, Na Li, Lucia Campos‐Dominguez, Wenguang Wang, Yang Liu, Xiaoan Lang, Yang Peng, Daike Tian, Daniel C. Thomas, Weixue Mu, Min Liu, Chenyu Wu, Ting Yang, Suzhou Zhang, Leilei Yang, Jianfen Yang, Zhong‐Jian Liu, Liangsheng Zhang, Xingtan Zhang, Fei Chen, Yuannian Jiao, Yalong Guo, Mark Hughes, Wei Wang, Xiaofei Liu, Chunmei Zhong, Airong Li, Sunil Kumar Sahu, Huanming Yang, Ernest Wu, Joel Sharbrough, Michael Lisby, Xin Liu, Xun Xu, Douglas E. Soltis, Yves Van de Peer (UGent) , Catherine Kidner, Shouzhou Zhang and Huan Liu
- Organization
- Project
- Abstract
- Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with ~2,000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana, and B. peltatifolia), and whole genome shot-gun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22,059 - 23,444 protein-coding genes. Synteny analysis revealed a lineage specific whole-genome duplication (WGD) that occurred just before the diversification of the Begonia. Functional enrichment of gene families retained after WGD highlight the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade-adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.
- Keywords
- Begonia, evolution, genomes, introgression, shade adaptation, whole-genome duplication, SEQUENCE, PHYLOGENIES, IMPROVEMENT, POLYPLOIDY, PLANTS
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8734098
- MLA
- Li, Lingfei, et al. “Genomes Shed Light on the Evolution of Begonia, a Mega‐diverse Genus.” NEW PHYTOLOGIST, vol. 234, no. 1, 2022, pp. 295–310, doi:10.1111/nph.17949.
- APA
- Li, L., Chen, X., Fang, D., Dong, S., Guo, X., Li, N., … Liu, H. (2022). Genomes shed light on the evolution of Begonia, a mega‐diverse genus. NEW PHYTOLOGIST, 234(1), 295–310. https://doi.org/10.1111/nph.17949
- Chicago author-date
- Li, Lingfei, Xiaoli Chen, Dongming Fang, Shanshan Dong, Xing Guo, Na Li, Lucia Campos‐Dominguez, et al. 2022. “Genomes Shed Light on the Evolution of Begonia, a Mega‐diverse Genus.” NEW PHYTOLOGIST 234 (1): 295–310. https://doi.org/10.1111/nph.17949.
- Chicago author-date (all authors)
- Li, Lingfei, Xiaoli Chen, Dongming Fang, Shanshan Dong, Xing Guo, Na Li, Lucia Campos‐Dominguez, Wenguang Wang, Yang Liu, Xiaoan Lang, Yang Peng, Daike Tian, Daniel C. Thomas, Weixue Mu, Min Liu, Chenyu Wu, Ting Yang, Suzhou Zhang, Leilei Yang, Jianfen Yang, Zhong‐Jian Liu, Liangsheng Zhang, Xingtan Zhang, Fei Chen, Yuannian Jiao, Yalong Guo, Mark Hughes, Wei Wang, Xiaofei Liu, Chunmei Zhong, Airong Li, Sunil Kumar Sahu, Huanming Yang, Ernest Wu, Joel Sharbrough, Michael Lisby, Xin Liu, Xun Xu, Douglas E. Soltis, Yves Van de Peer, Catherine Kidner, Shouzhou Zhang, and Huan Liu. 2022. “Genomes Shed Light on the Evolution of Begonia, a Mega‐diverse Genus.” NEW PHYTOLOGIST 234 (1): 295–310. doi:10.1111/nph.17949.
- Vancouver
- 1.Li L, Chen X, Fang D, Dong S, Guo X, Li N, et al. Genomes shed light on the evolution of Begonia, a mega‐diverse genus. NEW PHYTOLOGIST. 2022;234(1):295–310.
- IEEE
- [1]L. Li et al., “Genomes shed light on the evolution of Begonia, a mega‐diverse genus,” NEW PHYTOLOGIST, vol. 234, no. 1, pp. 295–310, 2022.
@article{8734098,
abstract = {{Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with ~2,000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana, and B. peltatifolia), and whole genome shot-gun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22,059 - 23,444 protein-coding genes. Synteny analysis revealed a lineage specific whole-genome duplication (WGD) that occurred just before the diversification of the Begonia. Functional enrichment of gene families retained after WGD highlight the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade-adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.}},
author = {{Li, Lingfei and Chen, Xiaoli and Fang, Dongming and Dong, Shanshan and Guo, Xing and Li, Na and Campos‐Dominguez, Lucia and Wang, Wenguang and Liu, Yang and Lang, Xiaoan and Peng, Yang and Tian, Daike and Thomas, Daniel C. and Mu, Weixue and Liu, Min and Wu, Chenyu and Yang, Ting and Zhang, Suzhou and Yang, Leilei and Yang, Jianfen and Liu, Zhong‐Jian and Zhang, Liangsheng and Zhang, Xingtan and Chen, Fei and Jiao, Yuannian and Guo, Yalong and Hughes, Mark and Wang, Wei and Liu, Xiaofei and Zhong, Chunmei and Li, Airong and Sahu, Sunil Kumar and Yang, Huanming and Wu, Ernest and Sharbrough, Joel and Lisby, Michael and Liu, Xin and Xu, Xun and Soltis, Douglas E. and Van de Peer, Yves and Kidner, Catherine and Zhang, Shouzhou and Liu, Huan}},
issn = {{0028-646X}},
journal = {{NEW PHYTOLOGIST}},
keywords = {{Begonia,evolution,genomes,introgression,shade adaptation,whole-genome duplication,SEQUENCE,PHYLOGENIES,IMPROVEMENT,POLYPLOIDY,PLANTS}},
language = {{eng}},
number = {{1}},
pages = {{295--310}},
title = {{Genomes shed light on the evolution of Begonia, a mega‐diverse genus}},
url = {{http://doi.org/10.1111/nph.17949}},
volume = {{234}},
year = {{2022}},
}
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