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Xia XM, Du HL, Hu XD, Wu JJ, Yang FS, Li CL, Huang SX, Wang Q, Liang C, Wang XQ. Genomic insights into adaptive evolution of the species-rich cosmopolitan plant genus Rhododendron. Cell Rep 2024; 43:114745. [PMID: 39298317 DOI: 10.1016/j.celrep.2024.114745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 07/17/2024] [Accepted: 08/28/2024] [Indexed: 09/21/2024] Open
Abstract
The species-rich cosmopolitan genus Rhododendron offers a good system for exploring the genomic mechanisms underlying adaptation to diverse habitats. Here, we report high-quality chromosomal-level genome assemblies of nine species, representing all five subgenera, different altitudinal distributions, and all flower color types of this genus. Further comprehensive genomic analyses indicate diverse adaptive strategies employed by Rhododendron, particularly adaptation to alpine and subalpine habitats by expansion/contraction of gene families involved in pathogen defense and oxidative phosphorylation, genomic convergent evolution, and gene copy-number variation. The convergent adaptation to high altitudes is further shown by population genomic analysis of R. nivale from the Himalaya-Hengduan Mountains. Moreover, we identify the genes involved in the biosynthesis of anthocyanins and carotenoids, which play a crucial role in shaping flower color diversity and environmental adaptation. Our study is significant for comprehending plant adaptive evolution and the uneven distribution of species diversity across different geographical regions.
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Affiliation(s)
- Xiao-Mei Xia
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Hui-Long Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Xiao-Di Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jing-Jie Wu
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Fu-Sheng Yang
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Cong-Li Li
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Si-Xin Huang
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Qiang Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Chengzhi Liang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Landis JB, Guercio AM, Brown KE, Fiscus CJ, Morrell PL, Koenig D. Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley. Science 2024; 385:eadl0038. [PMID: 38991084 DOI: 10.1126/science.adl0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 05/21/2024] [Indexed: 07/13/2024]
Abstract
Direct observation is central to our understanding of adaptation, but evolution is rarely documented in a large, multicellular organism for more than a few generations. In this study, we observed evolution across a century-scale competition experiment, barley composite cross II (CCII). CCII was founded in 1929 in Davis, California, with thousands of genotypes, but we found that natural selection has massively reduced genetic diversity, leading to a single lineage constituting most of the population by generation 50. Selection favored alleles originating from climates similar to that of Davis and targeted loci contributing to reproductive development, including the barley diversification loci Vrs1, HvCEN, Ppd-H1, and Vrn-H2. Our findings point to selection as the predominant force shaping genomic variation in one of the world's oldest biological experiments.
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Affiliation(s)
- Jacob B Landis
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Angelica M Guercio
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Keely E Brown
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Christopher J Fiscus
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Kelly JK. Rapid adaptation of Viola arvensis to pollinator declines. THE NEW PHYTOLOGIST 2024; 242:331-332. [PMID: 38258430 DOI: 10.1111/nph.19547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
This article is a Commentary on Acoca‐Pidolle et al. (2023), 242: 717–726.
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Affiliation(s)
- John K Kelly
- The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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