Genomes shed light on the evolution of Begonia, a mega-diverse genus

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Genomes shed light on the evolution of Begonia, a mega-diverse genus. / Li, Lingfei; Chen, Xiaoli; Fang, Dongming; Dong, Shanshan; Guo, Xing; Li, Na; Campos-Dominguez, Lucia; Wang, Wenguang; Liu, Yang; Lang, Xiaoan; Peng, Yang; Tian, Daike; Thomas, Daniel C.; Mu, Weixue; Liu, Min; Wu, Chenyu; Yang, Ting; Zhang, Suzhou; Yang, Leilei; Yang, Jianfen; Liu, Zhong-Jian; Zhang, Liangsheng; Zhang, Xingtan; Chen, Fei; Jiao, Yuannian; Guo, Yalong; Hughes, Mark; Wang, Wei; Liu, Xiaofei; Zhong, Chunmei; Li, Airong; Sahu, Sunil Kumar; Yang, Huanming; Wu, Ernest; Sharbrough, Joel; Lisby, Michael; Liu, Xin; Xu, Xun; Soltis, Douglas E.; Van de Peer, Yves; Kidner, Catherine; Zhang, Shouzhou; Liu, Huan.

In: New Phytologist, Vol. 234, No. 1, 2022, p. 295-310.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Li, L, Chen, X, Fang, D, Dong, S, Guo, X, Li, N, Campos-Dominguez, L, Wang, W, Liu, Y, Lang, X, Peng, Y, Tian, D, Thomas, DC, Mu, W, Liu, M, Wu, C, Yang, T, Zhang, S, Yang, L, Yang, J, Liu, Z-J, Zhang, L, Zhang, X, Chen, F, Jiao, Y, Guo, Y, Hughes, M, Wang, W, Liu, X, Zhong, C, Li, A, Sahu, SK, Yang, H, Wu, E, Sharbrough, J, Lisby, M, Liu, X, Xu, X, Soltis, DE, Van de Peer, Y, Kidner, C, Zhang, S & Liu, H 2022, 'Genomes shed light on the evolution of Begonia, a mega-diverse genus', New Phytologist, vol. 234, no. 1, pp. 295-310. https://doi.org/10.1111/nph.17949

APA

Li, L., Chen, X., Fang, D., Dong, S., Guo, X., Li, N., Campos-Dominguez, L., Wang, W., Liu, Y., Lang, X., Peng, Y., Tian, D., Thomas, D. C., Mu, W., Liu, M., Wu, C., Yang, T., Zhang, S., Yang, L., ... 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

Vancouver

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. https://doi.org/10.1111/nph.17949

Author

Li, Lingfei ; Chen, Xiaoli ; Fang, Dongming ; Dong, Shanshan ; Guo, Xing ; Li, Na ; Campos-Dominguez, Lucia ; Wang, Wenguang ; Liu, Yang ; Lang, Xiaoan ; Peng, Yang ; Tian, Daike ; Thomas, Daniel C. ; Mu, Weixue ; Liu, Min ; Wu, Chenyu ; Yang, Ting ; Zhang, Suzhou ; Yang, Leilei ; Yang, Jianfen ; Liu, Zhong-Jian ; Zhang, Liangsheng ; Zhang, Xingtan ; Chen, Fei ; Jiao, Yuannian ; Guo, Yalong ; Hughes, Mark ; Wang, Wei ; Liu, Xiaofei ; Zhong, Chunmei ; Li, Airong ; Sahu, Sunil Kumar ; Yang, Huanming ; Wu, Ernest ; Sharbrough, Joel ; Lisby, Michael ; Liu, Xin ; Xu, Xun ; Soltis, Douglas E. ; Van de Peer, Yves ; Kidner, Catherine ; Zhang, Shouzhou ; Liu, Huan. / Genomes shed light on the evolution of Begonia, a mega-diverse genus. In: New Phytologist. 2022 ; Vol. 234, No. 1. pp. 295-310.

Bibtex

@article{6b2d9f52d4b04a8aa3c9df19a06a0982,
title = "Genomes shed light on the evolution of Begonia, a mega-diverse genus",
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 c. 2000 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 shotgun 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 Begonia. Functional enrichment of gene families retained after WGD highlights 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",
author = "Lingfei Li and Xiaoli Chen and Dongming Fang and Shanshan Dong and Xing Guo and Na Li and Lucia Campos-Dominguez and Wenguang Wang and Yang Liu and Xiaoan Lang and Yang Peng and Daike Tian and Thomas, {Daniel C.} and Weixue Mu and Min Liu and Chenyu Wu and Ting Yang and Suzhou Zhang and Leilei Yang and Jianfen Yang and Zhong-Jian Liu and Liangsheng Zhang and Xingtan Zhang and Fei Chen and Yuannian Jiao and Yalong Guo and Mark Hughes and Wei Wang and Xiaofei Liu and Chunmei Zhong and Airong Li and Sahu, {Sunil Kumar} and Huanming Yang and Ernest Wu and Joel Sharbrough and Michael Lisby and Xin Liu and Xun Xu and Soltis, {Douglas E.} and {Van de Peer}, Yves and Catherine Kidner and Shouzhou Zhang and Huan Liu",
note = "Publisher Copyright: {\textcopyright} 2022 The Authors. New Phytologist {\textcopyright} 2022 New Phytologist Foundation",
year = "2022",
doi = "10.1111/nph.17949",
language = "English",
volume = "234",
pages = "295--310",
journal = "New Phytologist",
issn = "0028-646X",
publisher = "Academic Press",
number = "1",

}

RIS

TY - JOUR

T1 - Genomes shed light on the evolution of Begonia, a mega-diverse genus

AU - Li, Lingfei

AU - Chen, Xiaoli

AU - Fang, Dongming

AU - Dong, Shanshan

AU - Guo, Xing

AU - Li, Na

AU - Campos-Dominguez, Lucia

AU - Wang, Wenguang

AU - Liu, Yang

AU - Lang, Xiaoan

AU - Peng, Yang

AU - Tian, Daike

AU - Thomas, Daniel C.

AU - Mu, Weixue

AU - Liu, Min

AU - Wu, Chenyu

AU - Yang, Ting

AU - Zhang, Suzhou

AU - Yang, Leilei

AU - Yang, Jianfen

AU - Liu, Zhong-Jian

AU - Zhang, Liangsheng

AU - Zhang, Xingtan

AU - Chen, Fei

AU - Jiao, Yuannian

AU - Guo, Yalong

AU - Hughes, Mark

AU - Wang, Wei

AU - Liu, Xiaofei

AU - Zhong, Chunmei

AU - Li, Airong

AU - Sahu, Sunil Kumar

AU - Yang, Huanming

AU - Wu, Ernest

AU - Sharbrough, Joel

AU - Lisby, Michael

AU - Liu, Xin

AU - Xu, Xun

AU - Soltis, Douglas E.

AU - Van de Peer, Yves

AU - Kidner, Catherine

AU - Zhang, Shouzhou

AU - Liu, Huan

N1 - Publisher Copyright: © 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation

PY - 2022

Y1 - 2022

N2 - 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 c. 2000 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 shotgun 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 Begonia. Functional enrichment of gene families retained after WGD highlights 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.

AB - 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 c. 2000 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 shotgun 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 Begonia. Functional enrichment of gene families retained after WGD highlights 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.

KW - Begonia

KW - evolution

KW - genomes

KW - introgression

KW - shade adaptation

KW - whole-genome duplication

U2 - 10.1111/nph.17949

DO - 10.1111/nph.17949

M3 - Journal article

C2 - 34997964

AN - SCOPUS:85124533435

VL - 234

SP - 295

EP - 310

JO - New Phytologist

JF - New Phytologist

SN - 0028-646X

IS - 1

ER -

ID: 298734102