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| Genomes shed light on the evolution of Begonia, a mega-diverse genus | |
Li, Lingfei; Chen, Xiaoli1; Fang, Dongming1; Dong, Shanshan; Guo, Xing1; Li, Na; Campos-Dominguez, Lucia; Wang, Wenguang4; Liu, Yang1; Lang, Xiaoan5; Peng, Yang; Tian, Daike6; Thomas, Daniel C.; Mu, Weixue1; Liu, Min1; Wu, Chenyu1; Yang, Ting1; Zhang, Suzhou; Yang, Leilei; Yang, Jianfen; Liu, Zhong-Jian; Zhang, Liangsheng8; Zhang, Xingtan8; Chen, Fei9; Jiao, Yuannian10,11 ; Guo, Yalong10,11; Hughes, Mark2; Wang, Wei10,11; Liu, Xiaofei12; Zhong, Chunmei13; Li, Airong14; Sahu, Sunil Kumar1; Yang, Huanming1; Wu, Ernest15; Sharbrough, Joel16; Lisby, Michael17; Liu, Xin1,18; Xu, Xun1,19; Soltis, Douglas E.; Van de Peer, Yves9,21,22,23; Kidner, Catherine2,3; Zhang, Shouzhou; Liu, Huan1,17
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| 2022 | |
| Source Publication | NEW PHYTOLOGIST
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| ISSN | 0028-646X |
| Volume | 234Issue:1Pages:295-310 |
| 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. |
| Keyword | Begonia evolution genomes introgression shade adaptation whole-genome duplication |
| Subject Area | Plant Sciences |
| DOI | 10.1111/nph.17949 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | SEQUENCE ; PHYLOGENIES ; IMPROVEMENT ; POLYPLOIDY ; PLANTS |
| WOS Research Area | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS ID | WOS:000752964900001 |
| Publisher | WILEY |
| Subtype | Article |
| Publication Place | HOBOKEN |
| EISSN | 1469-8137 |
| Funding Organization | National Key R&D Program of China [2019YFC1711000] ; Shenzhen Municipal Government of China [JCYJ20170817145512476] ; Shenzhen Urban Administration [201917] ; Fairy Lake Botanical Garden [FLSF-2021-01] ; Public Welfare Forestry Industry Project of State Forestry Administration of China [201504322] ; National Natural Science Foundation of China [31601784] ; European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [833522] ; Ghent University [BOF.MET.2021.0005.01] |
| Corresponding Author Email | shouzhouz@szbg.ac.cn ; liuhuan@genomics.cn |
| OA | hybrid, Green Published |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/28583 |
| Collection | 系统与进化植物学国家重点实验室 |
| Affiliation | 1.Shenzhen & Chinese Acad Sci, Key Lab Southern Subtrop Plant Divers, Fairy Lake Bot Garden, Shenzhen 518004, Peoples R China 2.BGI Shenzhen, State Key Lab Agr Genom, Shenzhen 518083, Peoples R China 3.Univ Edinburgh, Inst Mol Plant Sci, Daniel Rutherford Bldg Max Born Crescent, Edinburgh EH9 3BF, Midlothian, Scotland 4.Royal Bot Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, Midlothian, Scotland 5.Chinese Acad Sci, Xishuangbanna Trop Bot Garden, Mengla 666303, Yunnan, Peoples R China 6.Nanning Bot Garden, Nanning 530021, Peoples R China 7.Chinese Acad Sci, Shanghai Chenshan Bot Garden, Shanghai Chenshan Plant Sci Res Ctr, Shanghai 201602, Peoples R China 8.Thomas, Daniel C.] Singapore Bot Gardens, Singapore 259569, Singapore 9.Fujian Agr & Forestry Univ, Key Lab Natl Forestry & Grassland Adm Orchid Cons, Fuzhou 350002, Peoples R China 10.Nanjing Agr Univ, Acad Adv Interdisciplinary Studies, Coll Hort, Nanjing 210095, Peoples R China 11.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 12.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 13.Guangdong Acad Agr Sci, Environm Hort Res Inst, Guangzhou 510640, Peoples R China 14.South China Agr Univ, Coll Forestry & Landscape Architecture, Key Lab Energy Plants Resource & Utilizat, Minist Agr, Guangzhou 510642, Peoples R China 15.Chinese Acad Sci, Kunming Inst Bot, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China 16.Univ British Columbia, Dept Biol, Vancouver, BC V6T 1Z4, Canada 17.New Mexico Inst Min & Technol, Biol Dept, Socorro, NM 87801 USA 18.Univ Copenhagen, Dept Biol, DK-2100 Copenhagen, Denmark 19.BGI Shenzhen, BGI Fuyang, Fuyang 236009, Peoples R China 20.BGI Shenzhen, Guangdong Prov Key Lab Genome Read & Write, Shenzhen 518083, Peoples R China 21.Soltis, Douglas E.] Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA 22.Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium 23.Ctr Plant Syst Biol VIB, B-9052 Ghent, Belgium 24.Univ Pretoria, Ctr Microbial Ecol & Genom CMEG, Dept Biochem Genet & Microbiol, ZA-0028 Hatfield, South Africa |
| Recommended Citation GB/T 7714 | Li, Lingfei,Chen, Xiaoli,Fang, Dongming,et al. Genomes shed light on the evolution of Begonia, a mega-diverse genus[J]. NEW PHYTOLOGIST,2022,234(1):295-310. |
| APA | Li, Lingfei.,Chen, Xiaoli.,Fang, Dongming.,Dong, Shanshan.,Guo, Xing.,...&Liu, Huan.(2022).Genomes shed light on the evolution of Begonia, a mega-diverse genus.NEW PHYTOLOGIST,234(1),295-310. |
| MLA | Li, Lingfei,et al."Genomes shed light on the evolution of Begonia, a mega-diverse genus".NEW PHYTOLOGIST 234.1(2022):295-310. |
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| Li-2022-Genomes shed（3399KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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