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Fu Z, Zhan Q, Lenoir J, Wang S, Qian H, Yang J, Sun W, Mbuni YM, Ngumbau VM, Hu G, Yan X, Wang Q, Chen SC, Zhou Y. Climate change drives plant diversity attrition at the summit of Mount Kenya. THE NEW PHYTOLOGIST 2024. [PMID: 39690499 DOI: 10.1111/nph.20344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 11/25/2024] [Indexed: 12/19/2024]
Affiliation(s)
- Zhihao Fu
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Qinghua Zhan
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Jonathan Lenoir
- UMR CNRS 7058, Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN), Université de Picardie Jules Verne, Amiens, 1 Rue des Louvels, 80000, France
| | - Shengwei Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Hong Qian
- Research and Collections Center, Illinois State Museum, Springfield, 62703, IL, USA
| | - Jiongming Yang
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Wenxuan Sun
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | | | | | - Guangwan Hu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan, 430200, Hubei, China
| | - Xue Yan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Qingfeng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Si-Chong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Millennium Seed Bank, Royal Botanic Gardens Kew, Wakehurst, RH17 6TN, UK
| | - Yadong Zhou
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
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Lyu ZY, Yang GM, Zhou XL, Wang SQ, Zhang R, Shen SK. Deciphering the complex organelle genomes of two Rhododendron species and insights into adaptive evolution patterns in high-altitude. BMC PLANT BIOLOGY 2024; 24:1054. [PMID: 39511517 PMCID: PMC11545642 DOI: 10.1186/s12870-024-05761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 10/29/2024] [Indexed: 11/15/2024]
Abstract
BACKGROUND The genomes within organelles are crucial for physiological functions such as respiration and photosynthesis and may also contribute to environmental adaptation. However, the limited availability of genetic resources, particularly mitochondrial genomes, poses significant challenges for in-depth investigations. RESULTS Here, we explored various assembly methodologies and successfully reconstructed the complex organelle genomes of two Rhododendron species: Rhododendron nivale subsp. boreale and Rhododendron vialii. The mitogenomes of these species exhibit various conformations, as evidenced by long-reads mapping. Notably, only the mitogenome of R. vialii can be depicted as a singular circular molecule. The plastomes of both species conform to the typical quadripartite structure but exhibit elongated inverted repeat (IR) regions. Compared to the high similarity between plastomes, the mitogenomes display more obvious differences in structure, repeat sequences, and codon usage. Based on the analysis of 58 organelle genomes from angiosperms inhabiting various altitudes, we inferred the genetic adaptations associated with high-altitude environments. Phylogenetic analysis revealed partial inconsistencies between plastome- and mitogenome-derived phylogenies. Additionally, evolutionary lineage was determined to exert a greater influence on codon usage than altitude. Importantly, genes such as atp4, atp9, mttB, and clpP exhibited signs of positive selection in several high-altitude species, suggesting a potential link to alpine adaptation. CONCLUSIONS We tested the effectiveness of different organelle assembly methods for dealing with complex genomes, while also providing and validating high-quality organelle genomes of two Rhododendron species. Additionally, we hypothesized potential strategies for high-altitude adaptation of organelles. These findings offer a reference for the assembly of complex organelle genomes, while also providing new insights and valuable resources for understanding their adaptive evolution patterns.
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Affiliation(s)
- Zhen-Yu Lyu
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650504, China
| | - Gao-Ming Yang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650504, China
| | - Xiong-Li Zhou
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650504, China
| | - Si-Qi Wang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650504, China
| | - Rui Zhang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650504, China
| | - Shi-Kang Shen
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650504, China.
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Li KJ, Liu XF, Yang L, Shen SK. Alpine Rhododendron population contractions lead to spatial distribution mismatch with their pollinators under climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171832. [PMID: 38521263 DOI: 10.1016/j.scitotenv.2024.171832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
The effect of global climate change on plant-pollinator interaction is not limited to changes in phenology and richness within communities but also includes the spatial mismatch caused by the inconsistency of geographical distribution changes. Subsequently, the pollinator interaction network may be remodeled or even disrupted. In this study, we simulated the suitable habitat niche of 15 Rhododendron species and their eight pollinator species as well as their overlapping versus geographical mismatch under the current and three future climate change scenarios in 2090s, using MaxEnt. Results showed that the suitable habitat of all Rhododendron species would decrease in 2090s. In particular, 10, 8, and 13 Rhododendron-pollinator assemblages would have a reduced spatial match region under the climate change scenarios, mainly due to the contraction of the suitable habitat of Rhododendron species. The results provide novel insights into the response of plant-pollinator interactions to global warming, useful to prioritize conservation actions of alpine plant ecosystems.
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Affiliation(s)
- Kun-Ji Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China
| | - Xiao-Fei Liu
- Institute of international river and eco-security Yunnan University, Kunming 650504, Yunnan, China
| | - Liu Yang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China
| | - Shi-Kang Shen
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China.
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Lyu ZY, Zhou XL, Wang SQ, Yang GM, Sun WG, Zhang JY, Zhang R, Shen SK. The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation. Gigascience 2024; 13:giae052. [PMID: 39110622 PMCID: PMC11304948 DOI: 10.1093/gigascience/giae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/26/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Rhododendron nivale subsp. boreale Philipson et M. N. Philipson is an alpine woody species with ornamental qualities that serve as the predominant species in mountainous scrub habitats found at an altitude of ∼4,200 m. As a high-altitude woody polyploid, this species may serve as a model to understand how plants adapt to alpine environments. Despite its ecological significance, the lack of genomic resources has hindered a comprehensive understanding of its evolutionary and adaptive characteristics in high-altitude mountainous environments. FINDINGS We sequenced and assembled the genome of R. nivale subsp. boreale, an assembly of the first subgenus Rhododendron and the first high-altitude woody flowering tetraploid, contributing an important genomic resource for alpine woody flora. The assembly included 52 pseudochromosomes (scaffold N50 = 42.93 Mb; BUSCO = 98.8%; QV = 45.51; S-AQI = 98.69), which belonged to 4 haplotypes, harboring 127,810 predicted protein-coding genes. Conjoint k-mer analysis, collinearity assessment, and phylogenetic investigation corroborated autotetraploid identity. Comparative genomic analysis revealed that R. nivale subsp. boreale originated as a neopolyploid of R. nivale and underwent 2 rounds of ancient polyploidy events. Transcriptional expression analysis showed that differences in expression between alleles were common and randomly distributed in the genome. We identified extended gene families and signatures of positive selection that are involved not only in adaptation to the mountaintop ecosystem (response to stress and developmental regulation) but also in autotetraploid reproduction (meiotic stabilization). Additionally, the expression levels of the (group VII ethylene response factor transcription factors) ERF VIIs were significantly higher than the mean global gene expression. We suspect that these changes have enabled the success of this species at high altitudes. CONCLUSIONS We assembled the first high-altitude autopolyploid genome and achieved chromosome-level assembly within the subgenus Rhododendron. In addition, a high-altitude adaptation strategy of R. nivale subsp. boreale was reasonably speculated. This study provides valuable data for the exploration of alpine mountaintop adaptations and the correlation between extreme environments and species polyploidization.
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Affiliation(s)
- Zhen-Yu Lyu
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Xiong-Li Zhou
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Si-Qi Wang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Gao-Ming Yang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Wen-Guang Sun
- School of Life Sciences, Yunnan Normal University, Kunming 650500 Yunnan, China
| | - Jie-Yu Zhang
- School of Life Sciences, Yunnan Normal University, Kunming 650500 Yunnan, China
| | - Rui Zhang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Shi-Kang Shen
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
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