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Zhao R, He Q, Chu X, He A, Zhang Y, Zhu Z. Regional environmental differences significantly affect the genetic structure and genetic differentiation of Carpinus tientaiensis Cheng, an endemic and extremely endangered species from China. FRONTIERS IN PLANT SCIENCE 2024; 15:1277173. [PMID: 38405582 PMCID: PMC10885731 DOI: 10.3389/fpls.2024.1277173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/10/2024] [Indexed: 02/27/2024]
Abstract
Differences in topography and environment greatly affect the genetic structure and genetic differentiation of species, and endemic or endangered species with limited geographic ranges seem to be more sensitive to changes in climate and other environmental factors. The complex topography of eastern China is likely to affect genetic differentiation of plants there. Carpinus tientaiensis Cheng is a native and endangered plants from China, and exploring its genetic diversity has profound significance for protection and the collection of germplasm resources. Based on AFLP markers, this study found that C. tientaiensis has low genetic diversity, which mainly came from within populations, while Shangshantou and Tiantai Mountain populations have relatively high genetic diversity. The Nei genetic distance was closely related to geographical distance, and temperature and precipitation notablely affected the genetic variation and genetic differentiation of C. tientaiensis. Based on cpDNA, this study indicated that C. tientaiensis exhibits a moderate level of genetic diversity, and which mainly came from among populations, while Tiantai Mountain population have the highest genetic diversity. It demonstrated that there was genetic differentiation between populations, which can be divided into two independent geographical groups, but there was no significant phylogeographic structure between them. The MaxEnt model showed that climate change significantly affects its distribution, and the suitable distribution areas in Zhejiang were primarily divided into two regions, eastern Zhejiang and southern Zhejiang, and there was niche differentiation in its suitable distribution areas. Therefore, this study speculated that the climate and the terrain of mountains and hills in East China jointly shape the genetic structure of C. tientaiensis, which gived rise to an obvious north-south differentiation trend of these species, and the populations located in the hilly areas of eastern Zhejiang and the mountainous areas of southern Zhejiang formed two genetic branches respectively.
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Affiliation(s)
- Runan Zhao
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Qianqian He
- Research Center for Urban and Rural Living Environment, Zhijiang College of Zhejiang University of Technology, Shaoxing, China
| | - Xiaojie Chu
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Anguo He
- Administration of Zhejiang Dapanshan National Nature Reserve, Pan’an, China
| | - Yuanlan Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Zunling Zhu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Jinpu Research Institute, Nanjing Forestry University, Nanjing, China
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Jiang ZY, Yang AA, Zhang HG, Wang WB, Zhang RH. Population structure and genetic diversity of Tamarix chinensis as revealed with microsatellite markers in two estuarine flats. PeerJ 2023; 11:e15882. [PMID: 37719128 PMCID: PMC10501381 DOI: 10.7717/peerj.15882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/20/2023] [Indexed: 09/19/2023] Open
Abstract
Background Tamarix chinensis Lour. is a 3-6-meter-tall small tree with high salt- and alkali- tolerance and aggressive invasiveness, mainly distributed in the eastern part of China in warm-temperate and subtropical climate zones, yet there is little information available regarding genetic diversity and population structure. Methods A total of 204 individuals of nine T. chinensis populations were investigated for genetic diversity and population structure using a set of 12 highly polymorphic microsatellite markers. Results The total number of alleles detected was 162, the average number of effective allele was 4.607, the average polymorphism information content (PIC) value of the 12 loci was 0.685, and the mean observed heterozygosity (Ho) and the mean expected heterozygosity (He) was 0.653 and 0.711, respectively. Analysis of molecular variance (AMOVA) showed a 5.32% genetic variation among T. chinensis populations. Despite a low population differentiation, Bayesian clustering analysis, discriminant analysis of principal components (DAPC) and the unweighted pair group method with arithmetic mean (UPGMA) clearly identified three genetic clusters correlated to the populations' geographic origin: the northern populations including those from Yellow River Delta, the Fangshan (FS) population from Beijing, the Changyi (CY) population from Bohai Bay, the Huanjiabu (HHJ) population from Hangzhou Bay, and the remaining two populations from Hangzhou Bay. There was a significant relationship between the genetic distance and geographical distance of the paired populations. Gene flow (Nm) was 4.254 estimated from FST. Conclusion T. chinensis possessed high genetic diversity comparable to tree species, and although the population differentiation is shallow, our results classified the sampled populations according to sampling localities, suggesting the different origins of the study populations.
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Affiliation(s)
- Zhao-Yu Jiang
- Linyi University, College of Life Science, Linyi City, Shandong Province, China
| | - Ao-Ao Yang
- Linyi University, College of Life Science, Linyi City, Shandong Province, China
| | - Hai-Guang Zhang
- Linyi University, College of Life Science, Linyi City, Shandong Province, China
| | - Wen-Bo Wang
- Linyi University, College of Life Science, Linyi City, Shandong Province, China
| | - Ru-Hua Zhang
- Linyi University, College of Life Science, Linyi City, Shandong Province, China
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Li Q, Liu X, Sun X, Zhao M, Liu L, Wang N, Gao Q, Fan P, Du N, Wang H, Wang R. Effects of drought hardening on the carbohydrate dynamics of Quercus acutissima seedlings under successional drought. FRONTIERS IN PLANT SCIENCE 2023; 14:1184584. [PMID: 37692418 PMCID: PMC10485557 DOI: 10.3389/fpls.2023.1184584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023]
Abstract
Introduction As precipitation patterns are predicted to become increasingly erratic, the functional maintenance of warm-temperate forests constitutes a key challenge for forest managers. In this study, 2-year-old Quercus acutissima seedlings were selected to elucidate the mechanisms whereby they respond to soil water fluctuations and the drought hardening effects on plant carbohydrate dynamics. Methods Seedlings were trained under different soil water conditions for 2 months: drought (D), well-watered (W), 1-month drought and then 1-month well-watered (D-W), and 1-month well-watered and then 1-month drought (W-D). The functional traits involved in water- and carbon-use strategies were explored at the end of the hardening period. Compared with seedlings in group W, seedlings in groups D, D-W, and W-D had increased potential for carbon uptake (i.e., light saturated point, maximum ribulose-1,5-bisphosphate (RuBP) saturated rate, and electron transport rate) and water uptake (i.e., fine root-to-coarse root ratio) and downregulated growth and mitochondrial respiration to decrease carbon consumption. After water fluctuation hardening, we performed a successional dry-down experiment for 1 month to detect carbohydrate dynamics and explore the acclimation caused by prior hardening. Results and discussion Our results revealed that there were more soluble sugars allocated in the leaves and more starch allocated in the stems and roots of seedlings hardened in the D, W-D, and D-W treatments than that of seedlings hardened in the W treatment. No significant changes in total non-structural carbohydrates were found. In addition, we found near-zero (seedlings trained by D and D-W treatments) or negative (seedlings trained by W-D treatment) growth of structural biomass at the end of the dry-down experiment, which was significantly lower than that of W-hardened seedlings. This suggests that there was a shift in allocation patterns between carbon storage and growth under recurrent soil drought, which can be strengthened by drought memory. We conclude that Q. acutissima seedlings adjusted water- and carbon-use strategies in response to water fluctuations, whereas stress memory can enhance their overall performance in reoccurring drought. Therefore, taking advantage of stress memory is a promising management strategy in forest nurseries, and drought-trained seedlings might be more suitable for afforestation practices in sites characterized by fluctuating soil water content, considering the ongoing global climatic changes.
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Affiliation(s)
- Qiang Li
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
- School of Tropical Medicine, Hainan Medical University, Haikou, China
| | - Xiao Liu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
- Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, China
- Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, China
| | - Xinke Sun
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
| | - Mingming Zhao
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
| | - Lele Liu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
- Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, China
- Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, China
| | - Ning Wang
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
- Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, China
- Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, China
| | - Qun Gao
- Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, China
| | - Peixian Fan
- Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, China
| | - Ning Du
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
- Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, China
- Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, China
| | - Hui Wang
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
- Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, China
- Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, China
| | - Renqing Wang
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
- Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, China
- Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, China
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Liu D, Xie X, Tong B, Zhou C, Qu K, Guo H, Zhao Z, El-Kassaby YA, Li W, Li W. A high -quality genome assembly and annotation of Quercus acutissima Carruth. FRONTIERS IN PLANT SCIENCE 2022; 13:1068802. [PMID: 36507419 PMCID: PMC9729791 DOI: 10.3389/fpls.2022.1068802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered as an excellent tree for soil and water conservation. METHODS Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble Q. acutissima genome. RESULTS We generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome. Ab initio, homology-based and RNA sequence-based gene prediction identified 29,889 protein-coding genes, of which 82.6% could be functionally annotated. Phylogenetic analysis showed that Q. acutissima and Q. variabilis were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication. CONCLUSION The assembled and annotated high-quality Q. acutissima genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.
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Affiliation(s)
- Dan Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Xiaoman Xie
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Chengcheng Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai Qu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Haili Guo
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Zhiheng Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Wei Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wenqing Li
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
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Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How. Int J Mol Sci 2022; 23:ijms23179980. [PMID: 36077370 PMCID: PMC9456323 DOI: 10.3390/ijms23179980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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Guo B, Hao X, Han L, Zhai Y, Zhou S, Chen S, Ren D, An X. Unraveling the genetic diversity and structure of Quercus liaotungensis population through analysis of microsatellite markers. PeerJ 2021; 9:e10922. [PMID: 33954024 PMCID: PMC8052960 DOI: 10.7717/peerj.10922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/19/2021] [Indexed: 11/21/2022] Open
Abstract
Background Quercus liaotungensis Koidz. is an ecologically and economically important tree species widely distributed in Northern China. However, the effective assessment, utilization, and protection of Q. liaotungensis resources remain unexplored. Methods In total, 120 samples obtained from 12 Q. liaotungensis populations of Northern China were investigated for genetic diversity and structure using 19 simple sequence repeat (SSR) primer pairs. Results The total number of alleles detected was 293, the average number of effective allele (Ne) was 6.084, the genetic differentiation coefficient (Fst) was 0.033, and the mean observed heterozygosity (Ho) and expected heterozygosity (He) were 0.690 and 0.801, respectively. Moreover, analysis of molecular variance (AMOVA) showed a 5.5% genetic variation among 12 Q. liaotungensis populations, indicating that a high level of genetic diversity and a low degree of genetic differentiation among Q. liaotungensis populations. STRUCTURE and cluster analysis divided the 12 Q. liaotungensis populations into the following three subpopulations: Bashang Plateau subpopulation (SH), Liaodong Peninsula subpopulation (NC), and Loess Plateau subpopulation (other 10 populations). The cluster analysis based on 19 climatic factors was consistent with the genetic structure. A positive correlation was found between genetic distance and geographical distance (r = 0.638, p = 0.028) by the Mantel test, and two boundaries were found among the 12 Q. liaotungensis populations by the Barrier analysis, indicating that Q. liaotungensis populations existed isolated by geographical distance and physical barrier. Conclusion This study suggests that geographical isolation, physical barrier, climatic types, and natural hybridization promote the formation of genetic structures, which can contribute to future protection and genetic improvement of Q. liaotungensis.
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Affiliation(s)
- Bin Guo
- Beijing Forestry University, Beijing, China.,Shanxi Academy of Forestry and Grassland Sciences, Taiyuan, China
| | - Xiangchun Hao
- Shanxi Academy of Forestry and Grassland Sciences, Taiyuan, China
| | - Lijun Han
- Shanxi Academy of Forestry and Grassland Sciences, Taiyuan, China
| | - Yu Zhai
- Shanxi Academy of Forestry and Grassland Sciences, Taiyuan, China
| | - Shuai Zhou
- Shanxi Academy of Forestry and Grassland Sciences, Taiyuan, China
| | - Si Chen
- Shanxi Academy of Forestry and Grassland Sciences, Taiyuan, China
| | - Da Ren
- Shanxi Academy of Forestry and Grassland Sciences, Taiyuan, China
| | - Xinmin An
- Beijing Forestry University, Beijing, China
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Chen XD, Yang J, Guo YF, Zhao YM, Zhou T, Zhang X, Ju MM, Li ZH, Zhao GF. Spatial Genetic Structure and Demographic History of the Dominant Forest Oak Quercus fabri Hance in Subtropical China. FRONTIERS IN PLANT SCIENCE 2021; 11:583284. [PMID: 33613578 PMCID: PMC7889815 DOI: 10.3389/fpls.2020.583284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Oak trees (Quercus L.) are important models for estimating abiotic impacts on the population structure and demography of long life span tree species. In this study, we generated genetic data for 17 nuclear microsatellite loci in 29 natural populations of Quercus fabri to estimate the population genetic structure. We also integrated approximate Bayesian computation (ABC) and ecological niche analysis to infer the population differentiation processes and demographic history of this oak species. The genetic analyses indicated two genetic clusters across the 29 populations collected, where most approximately corresponded to the intraspecific differentiation among populations from western and eastern China, whereas admixed populations were mainly found in central mountains of China. The best model obtained from hierarchical ABC simulations suggested that the initial intraspecific divergence of Q. fabri potentially occurred during the late Pliocene (ca. 3.99 Ma) to form the two genetic clusters, and the admixed population group might have been generated by genetic admixture of the two differentiated groups at ca. 53.76 ka. Ecological analyses demonstrated clear differentiation among the Q. fabri population structures, and association estimations also indicated significant correlations between geography and climate with the genetic variation in this oak species. Our results suggest abiotic influences, including past climatic changes and ecological factors, might have affected the genetic differentiation and demographic history of Q. fabri in subtropical China.
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Affiliation(s)
- Xiao-Dan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yu-Fan Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yue-Mei Zhao
- School of Biological Sciences, Guizhou Education University, Guiyang, China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Miao-Miao Ju
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
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Kremer A, Hipp AL. Oaks: an evolutionary success story. THE NEW PHYTOLOGIST 2020; 226:987-1011. [PMID: 31630400 PMCID: PMC7166131 DOI: 10.1111/nph.16274] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 09/13/2019] [Indexed: 05/10/2023]
Abstract
The genus Quercus is among the most widespread and species-rich tree genera in the northern hemisphere. The extraordinary species diversity in America and Asia together with the continuous continental distribution of a limited number of European species raise questions about how macro- and microevolutionary processes made the genus Quercus an evolutionary success. Synthesizing conclusions reached during the past three decades by complementary approaches in phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology and quantitative genetics, this review aims to illuminate evolutionary processes leading to the radiation and expansion of oaks. From opposing scales of time and geography, we converge on four overarching explanations of evolutionary success in oaks: accumulation of large reservoirs of diversity within populations and species; ability for rapid migration contributing to ecological priority effects on lineage diversification; high rates of evolutionary divergence within clades combined with convergent solutions to ecological problems across clades; and propensity for hybridization, contributing to adaptive introgression and facilitating migration. Finally, we explore potential future research avenues, emphasizing the integration of microevolutionary and macroevolutionary perspectives.
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Affiliation(s)
- Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, 69 Route
d'Arcachon, 33612 Cestas, France
| | - Andrew L. Hipp
- The Morton Arboretum, Lisle IL 60532-1293, USA
- The Field Museum, Chicago IL 60605, USA
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Zhang RS, Yang J, Hu HL, Xia RX, Li YP, Su JF, Li Q, Liu YQ, Qin L. A high level of chloroplast genome sequence variability in the Sawtooth Oak Quercus acutissima. Int J Biol Macromol 2020; 152:340-348. [PMID: 32109476 DOI: 10.1016/j.ijbiomac.2020.02.201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/18/2022]
Abstract
The Sawtooth Oak, Quercus acutissima Carruth., is an economically and ecologically important tree species in the family Fagaceae with a wide distribution in China. Here, we examined its intraspecific chloroplast (cp) genome variability using available and a newly sequenced genome. The new cp genome comes from a Q. acutissima individual collected from Shenyang (Northeast China; "Q. acutissima Shenyang" in the following), and then is compared with two recently published cp genomes from Tongchuan (Northwest China) and Nanjing (East China). The cp genome of Q. acutissima Shenyang exhibits a slightly larger genome size than the other two individuals, although each encodes 86 protein-coding genes, 40 tRNA genes and eight rRNA genes. We also found the length difference for the IR/SC boundary region among the three cp genomes. Sequence comparison revealed a high intraspecific genetic divergence: the three cp genomes differ by 332 sequence patterns including 77 single nucleotide polymorphisms, and 255 indels (each gap considered) scattering across 67 regions. Phylogenetic analyses based on the cp genome recovered the split between the subgenus Cerris and the subgenus Quercus, but revealed that three Q. acutissima individuals did not cluster together, indicating that even complete cp genome data fail to reproduce species boundaries in Asian members of section Cerris. Our results show that more complete plastomes covering remote ranges needs to be sequenced to provide a solid backbone for future population-scale in-depth studies and phylogenetic analysis of section Cerris.
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Affiliation(s)
- Ru-Song Zhang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jian Yang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Hua-Lei Hu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Run-Xi Xia
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Yu-Ping Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jun-Fang Su
- Center for Experimental Teaching, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Qun Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
| | - Yan-Qun Liu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
| | - Li Qin
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
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Effects of Stand Age on Biomass Allocation and Allometry of Quercus Acutissima in the Central Loess Plateau of China. FORESTS 2019. [DOI: 10.3390/f10010041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We studied the effects of stand age on allocation and equation fitting of aboveground and below-ground biomass in four Quercus acutissima stands (14, 31, 46, and 63 years old) in the Central Loess Plateau of China. The stem wood, stem bark, branch, foliage, and belowground biomass of each of the 20 destructive harvesting trees were quantified. The mean total biomass of each tree was 28.8, 106.8, 380.6, and 603.4 kg/tree in the 14-, 31-, 46-, and 63-year-old stands, respectively. Aboveground biomass accounted for 72.25%, 73.05%, 76.14%, and 80.37% of the total tree biomass in the 14-, 31-, 46-, and 63-year-old stands, respectively, and stem wood was the major component of tree biomass. The proportion of stem (with bark) biomass to total tree biomass increased with stand age while the proportions of branch, foliage, and belowground biomass to total tree biomass decreased with stand age. The ratio of belowground biomass to aboveground biomass decreased from 0.39 in the 14-year-old stand to 0.37, 0.31, and 0.24 in the 31-, 46-, and 63-year-old stands, respectively. Age-specific biomass equations in each stand were developed for stem wood, stem bark, aboveground, and total tree. The inclusion of tree height as a second variable improved the total tree biomass equation fitting for middle-aged (31-year-old and 46-year-old) stands but not young (14 years old) and mature (63 years old) stands. Moreover, biomass conversion and expansion factors (BCEFs) varied with stand age, showing a decreasing trend with increasing stand age. These results indicate that stand age alters the biomass allocation of Q. acutissima and results in age-specific allometric biomass equations and BCEFs. Therefore, to obtain accurate estimates of Q. acutissima forest biomass and carbon stocks, age-specific changes need to be considered.
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Genetic Diversity and Structure of Natural Quercus variabilis Population in China as Revealed by Microsatellites Markers. FORESTS 2017. [DOI: 10.3390/f8120495] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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The Relationship between Sap Flow Density and Environmental Factors in the Yangtze River Delta Region of China. FORESTS 2017. [DOI: 10.3390/f8030074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zhang X, Li Y, Liu C, Xia T, Zhang Q, Fang Y. Phylogeography of the temperate tree species Quercus acutissima in China: Inferences from chloroplast DNA variations. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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