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