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Marinček P, Léveillé-Bourret É, Heiduk F, Leong J, Bailleul SM, Volf M, Wagner ND. Challenge accepted: Evolutionary lineages versus taxonomic classification of North American shrub willows (Salix). AMERICAN JOURNAL OF BOTANY 2024:e16361. [PMID: 38924532 DOI: 10.1002/ajb2.16361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 06/28/2024]
Abstract
PREMISE The huge diversity of Salix subgenus Chamaetia/Vetrix clade in North America and the lack of phylogenetic resolution within this clade has presented a difficult but fascinating challenge for taxonomists to resolve. Here we tested the existing taxonomic classification with molecular tools. METHODS In this study, 132 samples representing 46 species from 22 described sections of shrub willows from the United States and Canada were analyzed and combined with 67 samples from Eurasia. The ploidy levels of the samples were determined using flow cytometry and nQuire. Sequences were produced using a RAD sequencing approach and subsequently analyzed with ipyrad, then used for phylogenetic reconstructions (RAxML, SplitsTree), dating analyses (BEAST, SNAPPER), and character evolution analyses of 14 selected morphological traits (Mesquite). RESULTS The RAD sequencing approach allowed the production of a well-resolved phylogeny of shrub willows. The resulting tree showed an exclusively North American (NA) clade in sister position to a Eurasian clade, which included some North American endemics. The NA clade began to diversify in the Miocene. Polyploid species appeared in each observed clade. Character evolution analyses revealed that adaptive traits such as habit and adaxial nectaries evolved multiple times independently. CONCLUSIONS The diversity in shrub willows was shaped by an evolutionary radiation in North America. Most species were monophyletic, but the existing sectional classification could not be supported by molecular data. Nevertheless, monophyletic lineages share several morphological characters, which might be useful in the revision of the taxonomic classification of shrub willows.
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Affiliation(s)
- Pia Marinček
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Untere Karspüle 2, D-37073, Göttingen, Germany
| | - Étienne Léveillé-Bourret
- Institut de recherche en biologie végétale (IRBV), Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, QC, Canada
| | - Ferris Heiduk
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Untere Karspüle 2, D-37073, Göttingen, Germany
| | - Jing Leong
- Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Stéphane M Bailleul
- Division recherche et développement scientifique, Jardin botanique de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, QC, Canada
| | - Martin Volf
- Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Natascha D Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Untere Karspüle 2, D-37073, Göttingen, Germany
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Yang Q, Li J, Wang Y, Wang Z, Pei Z, Street NR, Bhalerao RP, Yu Z, Gao Y, Ni J, Jiao Y, Sun M, Yang X, Chen Y, Liu P, Wang J, Liu Y, Li G. Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species. THE NEW PHYTOLOGIST 2024; 242:2702-2718. [PMID: 38515244 DOI: 10.1111/nph.19711] [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: 10/18/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024]
Abstract
Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.
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Affiliation(s)
- Qinsong Yang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Jinjin Li
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Yan Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zefu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Ziqi Pei
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, 90754, Sweden
- SciLifeLab, Umeå University, Umeå, 90754, Sweden
| | - Rishikesh P Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187, Umeå, Sweden
| | - Zhaowei Yu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Junbei Ni
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yang Jiao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Minghui Sun
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Xiong Yang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Yixin Chen
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Puyuan Liu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Jiaxi Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Yong Liu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Guolei Li
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
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Morales-Saldaña S, Hipp AL, Valencia-Ávalos S, Hahn M, González-Elizondo MS, Gernandt DS, Pham KK, Oyama K, González-Rodríguez A. Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae). ANNALS OF BOTANY 2024; 133:1007-1024. [PMID: 38428030 PMCID: PMC11089265 DOI: 10.1093/aob/mcae030] [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: 11/07/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND AND AIMS Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.
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Affiliation(s)
- Saddan Morales-Saldaña
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL 60532-1293, USA
- The Field Museum, Chicago, IL 60605, USA
| | - Susana Valencia-Ávalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | | | | | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex‐Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
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Cai Y, Anderson E, Xue W, Wong S, Cui L, Cheng X, Wang O, Mao Q, Liu SJ, Davis JT, Magalang PR, Schmidt D, Kasuga T, Garbelotto M, Drmanac R, Kua CS, Cannon C, Maloof JN, Peters BA. Assembly and analysis of the genome of Notholithocarpus densiflorus. G3 (BETHESDA, MD.) 2024; 14:jkae043. [PMID: 38427916 PMCID: PMC11075539 DOI: 10.1093/g3journal/jkae043] [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: 12/04/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes, and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to "sudden oak death" (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread deaths of tanoaks. In this study, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced and de novo assembled a draft reference genome of N. densiflorus using cobarcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore long reads to 30× coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published to date, with a contig N50 of ∼1.2 Mb, a scaffold N50 of ∼2.1 Mb, and a complete gene score of 95.5% through BUSCO analysis. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome, enabling the discovery of almost 25 million single nucleotide polymorphisms and ∼4.4 million small insertions and deletions. Finally, using cobarcoded data, we were able to generate a complete haplotype coverage of all 11 genomes.
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Affiliation(s)
- Ying Cai
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Ellis Anderson
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Wen Xue
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Sylvia Wong
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Luman Cui
- Department of Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaofang Cheng
- Department of Research, MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Ou Wang
- Department of Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Mao
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Sophie Jia Liu
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - John T Davis
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Paulo R Magalang
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Douglas Schmidt
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service, Davis, CA 95616, USA
| | - Matteo Garbelotto
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Radoje Drmanac
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Chai-Shian Kua
- Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA
| | - Charles Cannon
- Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Brock A Peters
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
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Kougioumoutzis K, Constantinou I, Panitsa M. Rising Temperatures, Falling Leaves: Predicting the Fate of Cyprus's Endemic Oak under Climate and Land Use Change. PLANTS (BASEL, SWITZERLAND) 2024; 13:1109. [PMID: 38674518 PMCID: PMC11053427 DOI: 10.3390/plants13081109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
Endemic island species face heightened extinction risk from climate-driven shifts, yet standard models often underestimate threat levels for those like Quercus alnifolia, an iconic Cypriot oak with pre-adaptations to aridity. Through species distribution modelling, we investigated the potential shifts in its distribution under future climate and land-use change scenarios. Our approach uniquely combines dispersal constraints, detailed soil characteristics, hydrological factors, and anticipated soil erosion data, offering a comprehensive assessment of environmental suitability. We quantified the species' sensitivity, exposure, and vulnerability to projected changes, conducting a preliminary IUCN extinction risk assessment according to Criteria A and B. Our projections uniformly predict range reductions, with a median decrease of 67.8% by the 2070s under the most extreme scenarios. Additionally, our research indicates Quercus alnifolia's resilience to diverse erosion conditions and preference for relatively dry climates within a specific annual temperature range. The preliminary IUCN risk assessment designates Quercus alnifolia as Critically Endangered in the future, highlighting the need for focused conservation efforts. Climate and land-use changes are critical threats to the species' survival, emphasising the importance of comprehensive modelling techniques and the urgent requirement for dedicated conservation measures to safeguard this iconic species.
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Affiliation(s)
| | | | - Maria Panitsa
- Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (K.K.); (I.C.)
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Cao RB, Chen R, Liao KX, Li H, Xu GB, Jiang XL. Karyotype and LTR-RTs analysis provide insights into oak genomic evolution. BMC Genomics 2024; 25:328. [PMID: 38566015 PMCID: PMC10988972 DOI: 10.1186/s12864-024-10177-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests. RESULTS Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes. CONCLUSION Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.
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Affiliation(s)
- Rui-Bin Cao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Ran Chen
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Ke-Xin Liao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - He Li
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Gang-Biao Xu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Xiao-Long Jiang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China.
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Luo CS, Li TT, Jiang XL, Song Y, Fan TT, Shen XB, Yi R, Ao XP, Xu GB, Deng M. High-quality haplotype-resolved genome assembly for ring-cup oak (Quercus glauca) provides insight into oaks demographic dynamics. Mol Ecol Resour 2024; 24:e13914. [PMID: 38108568 DOI: 10.1111/1755-0998.13914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
Quercus section Cyclobalanopsis represents a dominant woody lineage in East Asian evergreen broadleaved forests. Regardless of its ecological and economic importance, little is known about the genomes of species in this unique oak lineage. Quercus glauca is one of the most widespread tree species in the section Cyclobalanopsis. In this study, a high-quality haplotype-resolved reference genome was assembled for Q. glauca from PacBio HiFi and Hi-C reads. The genome size, contig N50, and scaffold N50 measured 902.88, 7.60, and 69.28 Mb, respectively, for haplotype1, and 913.28, 7.20, and 71.53 Mb, respectively, for haplotype2. A total of 37,457 and 38,311 protein-coding genes were predicted in haplotype1 and haplotype2, respectively. Homologous chromosomes in the Q. glauca genome had excellent gene pair collinearity. The number of R-genes in Q. glauca was similar to most East Asian oaks but less than oak species from Europe and America. Abundant structural variation in the Q. glauca genome could contribute to environmental stress tolerance in Q. glauca. Sections Cyclobalanopsis and Cerris diverged in the Oligocene, in agreement with fossil records for section Cyclobalanopsis, which document its presence in East Asia since the early Miocene. The demographic dynamics of closely related oak species were largely similar. The high-quality reference genome provided here for the most widespread species in section Cyclobalanopsis will serve as an essential genomic resource for evolutionary studies of key oak lineages while also supporting studies of interspecific introgression, local adaptation, and speciation in oaks.
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Affiliation(s)
- Chang-Sha Luo
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Tian-Tian Li
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Xiao-Long Jiang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ying Song
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ting-Ting Fan
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Xiang-Bao Shen
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Rong Yi
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Xiao-Ping Ao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Gang-Biao Xu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Min Deng
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming, Yunnan, China
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8
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Fkiri S, Mohamed B, Khouja M, Stiti B, Ben Salem R, Nasr Z, Ben Slimane L, Nagaz K, Ghayth R, Khaldi A. Effect of geographical origin on the chemical characteristics of Q. canariensis acorns: profiling fatty acids, tocopherols, and phenolic composition. Nat Prod Res 2024:1-7. [PMID: 38557271 DOI: 10.1080/14786419.2024.2335355] [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: 12/05/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
The impact of geographical origin on the chemical composition of acorns from Quercus species has significant attention. This study aimed to explore the phenolic composition of methanolic extracts, tocopherol content, and fatty acid composition of acorn oils from six different populations of Q. canariensis acorns. The obtained results revealed that acorn oil from BniMtir exhibited high levels of α-tocopherol (58 mg/kg). The fatty acids identified across all samples were Z-vaccenic + oleic acids (38.44-58.58%). In addition, the data highlighted the presence of quinic (32.514-60.216 µg/g DW) and gallic acids (1.674-10.849 µg/g DW), as well as catechin (+) (0.096-12.647 µg/g DW) in all populations. These variations in chemical composition from different regions are likely linked to their geographical origin. In conclusion, this study's finding should significance for the industry, offering valuable insights into the potential production of bioactive compounds from Q. canariensis acorns, which could have various applications.
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Affiliation(s)
- Sondes Fkiri
- National Institute for Researches on Rural Engineering, Water and Forests, INRGREF, Ariana, Tunisia
| | - Bagues Mohamed
- Laboratory of Drylands and Oases Cropping, Arid Regions Institute of Medenine, University of Gabes, Medenine, Tunisia
| | - Mariem Khouja
- Laboratory of Nanobiotechnology and Valorization of Medicinal Phytoresources, Department of Biology, National Institute of Applied Science and Technology, University of Carthage, Tunis Cedex, Tunisia
| | - Boutheina Stiti
- National Institute for Researches on Rural Engineering, Water and Forests, INRGREF, Ariana, Tunisia
| | - Ridha Ben Salem
- Laboratory of Organic Chemistry LR17ES08, Sciences Faculty of Sfax, University of Sfax, Sfax, Tunisia
| | - Zouhair Nasr
- National Institute for Researches on Rural Engineering, Water and Forests, INRGREF, Ariana, Tunisia
| | | | - Kamel Nagaz
- Laboratory of Drylands and Oases Cropping, Arid Regions Institute of Medenine, University of Gabes, Medenine, Tunisia
| | - Rigane Ghayth
- Laboratory of Organic Chemistry LR17ES08, Sciences Faculty of Sfax, University of Sfax, Sfax, Tunisia
- Chemistry-Physics Department, Sciences and Technology Faculty, University of Kairouan, Sidi Bouzid, Tunisia
| | - Abdelhamid Khaldi
- National Institute for Researches on Rural Engineering, Water and Forests, INRGREF, Ariana, Tunisia
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Koontz AC, Schumacher EK, Spence ES, Hoban SM. Ex situ conservation of two rare oak species using microsatellite and SNP markers. Evol Appl 2024; 17:e13650. [PMID: 38524684 PMCID: PMC10960078 DOI: 10.1111/eva.13650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 03/26/2024] Open
Abstract
Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
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Affiliation(s)
| | | | - Emma S. Spence
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
- Cornell UniversityDepartment of Public and Ecosystem HealthIthacaNew YorkUSA
| | - Sean M. Hoban
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
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10
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Wang LL, Li Y, Zheng SS, Kozlowski G, Xu J, Song YG. Complete Chloroplast Genomes of Four Oaks from the Section Cyclobalanopsis Improve the Phylogenetic Analysis and Understanding of Evolutionary Processes in the Genus Quercus. Genes (Basel) 2024; 15:230. [PMID: 38397219 PMCID: PMC10888318 DOI: 10.3390/genes15020230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ-trnG-GCC, rbcL-accD, and rpl32-trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.
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Affiliation(s)
- Ling-Ling Wang
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, China;
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Yu Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Si-Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
- Department of Biology and Botanic Garden, University of Fribourg, 1700 Fribourg, Switzerland
- Natural History Museum Fribourg, 1700 Fribourg, Switzerland
| | - Jin Xu
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, China;
| | - Yi-Gang Song
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Y.L.); (S.-S.Z.); (G.K.)
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11
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Huang LJ, Yang W, Chen J, Yu P, Wang Y, Li N. Molecular identification and functional characterization of an environmental stress responsive glutaredoxin gene ROXY1 in Quercus glauca. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108367. [PMID: 38237422 DOI: 10.1016/j.plaphy.2024.108367] [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: 09/24/2023] [Revised: 12/03/2023] [Accepted: 01/10/2024] [Indexed: 03/16/2024]
Abstract
Quercus glauca is a valuable natural resource with both economic and ecological values. It is one of the dominant forest tree species widely distributed in Southern China. As a perennial broadleaf plant, Q. glauca inevitably encounters numerous stresses from environment. Glutaredoxins (GRXs) are a kind of small oxidoreductases that play an important role in response to oxidative stress. CC-type GRXs also known as ROXYs are specific to land plants. In this study, we isolated a CC-type GRX gene, QgROXY1, from Q. glauca. Expression of QgROXY1 is induced by a variety of environmental stimuli. QgROXY1 protein localizes to both cytoplasm and nucleus; whereas the nucleus localized QgROXY1 could physically interact with the basic region/leucine zipper motif (bZIP) transcription factor AtTGA2 from Arabidopsis thaliana. Transgenic A. thaliana ectopically expressing QgROXY1 is hypersensitive to exogenously applied salicylic acid. Induction of plant defense gene is significantly impaired in QgROXY1 transgenic plants that results in enhanced susceptibility to infection of Botrytis cinerea pathogen, indicating the evolutionary conserved function among ROXY homologs in weedy and woody plants. This is the first described function for the ROXYs in tree plants. Through this case study, we demonstrated the feasibility and efficacy of molecular technology applied to characterization of gene function in tree species.
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Affiliation(s)
- Li-Jun Huang
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Wenhai Yang
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Jiali Chen
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Peiyao Yu
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Yukun Wang
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ning Li
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China.
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12
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Qi M, Du FK, Guo F, Yin K, Tang J. Species identification through deep learning and geometrical morphology in oaks ( Quercus spp.): Pros and cons. Ecol Evol 2024; 14:e11032. [PMID: 38357593 PMCID: PMC10864717 DOI: 10.1002/ece3.11032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Plant phenotypic characteristics, especially leaf morphology of leaves, are an important indicator for species identification. However, leaf shape can be extraordinarily complex in some species, such as oaks. The great variation in leaf morphology and difficulty of species identification in oaks have attracted the attention of scientists since Charles Darwin. Recent advances in discrimination technology have provided opportunities to understand leaf morphology variation in oaks. Here, we aimed to compare the accuracy and efficiency of species identification in two closely related deciduous oaks by geometric morphometric method (GMM) and deep learning using preliminary identification of simple sequence repeats (nSSRs) as a prior. A total of 538 Asian deciduous oak trees, 16 Q. aliena and 23 Q. dentata populations, were firstly assigned by nSSRs Bayesian clustering analysis to one of the two species or admixture and this grouping served as a priori identification of these trees. Then we analyzed the shapes of 2328 leaves from the 538 trees in terms of 13 characters (landmarks) by GMM. Finally, we trained and classified 2221 leaf-scanned images with Xception architecture using deep learning. The two species can be identified by GMM and deep learning using genetic analysis as a priori. Deep learning is the most cost-efficient method in terms of time-consuming, while GMM can confirm the admixture individuals' leaf shape. These various methods provide high classification accuracy, highlight the application in plant classification research, and are ready to be applied to other morphology analysis.
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Affiliation(s)
- Min Qi
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Fang K. Du
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Fei Guo
- School of Computer Science and EngineeringCentral South UniversityChangshaHunanChina
| | - Kangquan Yin
- School of Grassland ScienceBeijing Forestry UniversityBeijingChina
| | - Jijun Tang
- Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdongChina
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13
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Wagner S, Seguin-Orlando A, Leplé JC, Leroy T, Lalanne C, Labadie K, Aury JM, Poirier S, Wincker P, Plomion C, Kremer A, Orlando L. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Mol Ecol 2024; 33:e16859. [PMID: 36748324 PMCID: PMC7615563 DOI: 10.1111/mec.16859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/08/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
Abstract
Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.
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Affiliation(s)
- Stefanie Wagner
- Plant Genomic Resources Center (CNRGV), INRAE, Castanet-Tolosan, France
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | | | - Thibault Leroy
- IRHS UMR1345, Université d’Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Patrick Wincker
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | | | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
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14
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Ma XG, Ren YB, Sun H. Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China. Cladistics 2024. [PMID: 38197450 DOI: 10.1111/cla.12570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 01/11/2024] Open
Abstract
Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.
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Affiliation(s)
- Xiang-Guang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yue-Bo Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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15
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De Luna-Bonilla OÁ, Valencia-Á S, Ibarra-Manríquez G, Morales-Saldaña S, Tovar-Sánchez E, González-Rodríguez A. Leaf morphometric analysis and potential distribution modelling contribute to taxonomic differentiation in the Quercus microphylla complex. JOURNAL OF PLANT RESEARCH 2024; 137:3-19. [PMID: 37740854 PMCID: PMC10764464 DOI: 10.1007/s10265-023-01495-z] [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: 06/06/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023]
Abstract
Mexico is a major center of evolutionary radiation for the genus Quercus, with oak species occurring across different habitat types and showing a wide variation in morphology and growth form. Despite representing about 20% of Mexican species, scrub oaks have received little attention and even basic aspects of their taxonomy and geographic distribution remain unresolved. In this study, we analyzed the morphological and climatic niche differentiation of scrub oak populations forming a complex constituted by six named species, Quercus cordifolia, Quercus frutex, Quercus intricata, Quercus microphylla, Quercus repanda, Quercus striatula and a distinct morphotype of Q. striatula identified during field and herbarium work (hereafter named Q. striatula II). Samples were obtained from 35 sites covering the geographic distribution of the complex in northern and central Mexico. Morphological differentiation was analyzed through geometric morphometrics of leaf shape and quantification of trichome traits. Our results indicated the presence of two main morphological groups with geographic concordance. The first was formed by Q. frutex, Q. microphylla, Q. repanda and Q. striatula, distributed in the Trans-Mexican Volcanic Belt, the Sierra Madre Occidental and a little portion of the south of the Mexican Altiplano (MA). The second group consists of Q. cordifola, Q. intricata and Q. striatula II, found in the Sierra Madre Oriental and the MA. Therefore, our evidence supports the distinctness of the Q. striatula II morphotype, indicating the need for a taxonomic revision. Within the two groups, morphological differentiation among taxa varied from very clear to low or inexistent (i.e. Q. microphylla-Q. striatula and Q. cordifolia-Q. striatula II) but niche comparisons revealed significant niche differentiation in all pairwise comparisons, highlighting the relevance of integrative approaches for the taxonomic resolution of complicated groups such as the one studied here.
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Affiliation(s)
- Oscar Ángel De Luna-Bonilla
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, México
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510, Ciudad de Mexico, México
| | - Susana Valencia-Á
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n, Ciudad Universitaria, Coyoacán, 04510, México City, México
| | - Guillermo Ibarra-Manríquez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, México
| | - Saddan Morales-Saldaña
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, México
| | - Efraín Tovar-Sánchez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, CP, 62209, Cuernavaca, Morelos, Mexico
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, México.
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16
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Sánchez-Acevedo V, González-Rodríguez A, Torres-Miranda CA, Rodríguez-Correa H, Valencia-Á S, De-la-Cruz IM, Oyama K. Nuclear and chloroplast DNA phylogeography reveals high genetic diversity and postglacial range expansion in Quercus mexicana. AMERICAN JOURNAL OF BOTANY 2023; 110:e16251. [PMID: 37843974 DOI: 10.1002/ajb2.16251] [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: 06/23/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023]
Abstract
PREMISE Phylogeographical studies are fundamental for understanding factors that influence the spatial distribution of genetic lineages within species. Population expansions and contractions, distribution shifts, and climate changes are among the most important factors shaping the genetic compositions of populations. METHODS We investigated the phylogeography of an endemic oak, Quercus mexicana (Fagaceae), which has a restricted distribution in northeastern Mexico along the Sierra Madre Oriental and adjacent areas. Nuclear and chloroplast DNA microsatellite markers were used to describe the genetic diversity and structure of 39 populations of Q. mexicana along its entire distribution area. We tested whether population expansion or contraction events influenced the genetic diversity and structure of the species. We also modeled the historical distributional range of Q. mexicana (for the Mid Holocene, the Last Glacial Maximum, and the Last Interglacial) to estimate the extent to which climate fluctuations have impacted the distribution of this oak species. RESULTS Our results revealed high genetic diversity and low genetic structure in Q. mexicana populations. Ecological niche models suggested historical fluctuations in the distributional range of Q. mexicana. Historical range changes, gene flow, and physical barriers seem to have played an important role in shaping the phylogeographic structure of Q. mexicana. CONCLUSIONS Our study indicates that the genetic structure of Q. mexicana may have been the result of responses of oak trees not only to heterogeneous environments present in the Sierra Madre Oriental and adjacent areas, but also to elevational and latitudinal shifts in response to climate changes in the past.
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Affiliation(s)
- Vanessa Sánchez-Acevedo
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
- Posgrado en Ciencias Biológicas, UNAM. Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P. 04510, CDMX, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM. Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
| | - César Andrés Torres-Miranda
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
| | - Hernando Rodríguez-Correa
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
| | - Susana Valencia-Á
- Facultad de Ciencias, UNAM. Av. Universidad 3000. Coyoacán, Ciudad de México, 04510, México
| | - Ivan M De-la-Cruz
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM). Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José del Cerrito, Morelia, Michoacán, México
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17
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Qian H, Kessler M, Zhang J, Jin Y, Soltis DE, Qian S, Zhou Y, Soltis PS. Angiosperm phylogenetic diversity is lower in Africa than South America. SCIENCE ADVANCES 2023; 9:eadj1022. [PMID: 37967173 PMCID: PMC10651126 DOI: 10.1126/sciadv.adj1022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
Although originating from a common Gondwanan flora, the diversity and composition of the floras of Africa and South America have greatly diverged since continental breakup of Africa from South America now having much higher plant species richness. However, the phylogenetic diversity of the floras and what this tells us about their evolution remained unexplored. We show that for a given species richness and considering land surface area, topography, and present-day climate, angiosperm phylogenetic diversity in South America is higher than in Africa. This relationship holds regardless of whether all climatically matched areas or only matched areas in tropical climates are considered. Phylogenetic diversity is high relative to species richness in refugial areas in Africa and in northwestern South America, once the gateway for immigration from the north. While species richness is strongly influenced by massive plant radiations in South America, we detect a pervasive influence of historical processes on the phylogenetic diversity of both the South American and African floras.
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Affiliation(s)
- Hong Qian
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Research and Collections Center, Illinois State Museum, 1011 East Ash Street, Springfield, IL 62703, USA
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Jian Zhang
- Center for Global Change and Complex Ecosystems, Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yi Jin
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Shenhua Qian
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
- College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yadong Zhou
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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18
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Chen X, Li B, Zhang X. Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis. Sci Rep 2023; 13:18731. [PMID: 37907468 PMCID: PMC10618267 DOI: 10.1038/s41598-023-45421-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
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Affiliation(s)
- Xiaoli Chen
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Buyu Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, 637009, China.
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McLay TGB, Fowler RM, Fahey PS, Murphy DJ, Udovicic F, Cantrill DJ, Bayly MJ. Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia. Mol Phylogenet Evol 2023; 187:107869. [PMID: 37423562 DOI: 10.1016/j.ympev.2023.107869] [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: 03/31/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/11/2023]
Abstract
Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.
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Affiliation(s)
- Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia.
| | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Patrick S Fahey
- Research Centre for Ecosystem Resilience, The Royal Botanic Garden Sydney, Sydney 2000, NSW, Australia; Qld Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia 4072, Qld, Australia
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia
| | - David J Cantrill
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
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20
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Denk T, Bouchal JM, Güner HT, Coiro M, Butzmann R, Pigg KB, Tiffney BH. Cenozoic migration of a desert plant lineage across the North Atlantic. THE NEW PHYTOLOGIST 2023; 238:2668-2684. [PMID: 36651063 DOI: 10.1111/nph.18743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/29/2022] [Indexed: 05/19/2023]
Abstract
Previous paleobotanical work concluded that Paleogene elements of the sclerophyllous subhumid vegetation of western Eurasia and western North America were endemic to these disjunct regions, suggesting that the southern areas of the Holarctic flora were isolated at that time. Consequently, molecular studies invoked either parallel adaptation to dry climates from related ancestors, or long-distance dispersal in explaining disjunctions between the two regions, dismissing the contemporaneous migration of dry-adapted lineages via land bridges as unlikely. We report Vauquelinia (Rosaceae), currently endemic to western North America, in Cenozoic strata of western Eurasia. Revision of North American fossils previously assigned to Vauquelinia confirmed a single fossil-species of Vauquelinia and one of its close relative Kageneckia. We established taxonomic relationships of fossil-taxa using diagnostic character combinations shared with modern species and constructed a time-calibrated phylogeny. The fossil record suggests that Vauquelinia, currently endemic to arid and subdesert environments, originated under seasonally arid climates in the Eocene of western North America and subsequently crossed the Paleogene North Atlantic land bridge (NALB) to Europe. This pattern is replicated by other sclerophyllous, dry-adapted and warmth-loving plants, suggesting that several of these taxa potentially crossed the North Atlantic via the NALB during Eocene times.
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Affiliation(s)
- Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden
| | - Johannes M Bouchal
- Department of Botany and Biodiversity Research, University of Vienna, 1030, Vienna, Austria
| | - H Tuncay Güner
- Department of Forest Botany, Faculty of Forestry, Istanbul University-Cerrahpaşa, 34473 Bahçeköy, Istanbul, Turkey
| | - Mario Coiro
- Department of Palaeontology, University of Vienna, 1090, Vienna, Austria
- Ronin Institute for Independent Scholarship, Montclair, NJ, 07043-2314, USA
| | - Rainer Butzmann
- Independent Researcher, Fuggerstraße 8, 81373, Munich, Germany
| | - Kathleen B Pigg
- School of Life Sciences and Biodiversity Knowledge Integration Center, Arizona State University, Box 874501, Tempe, AZ, 85287-4501, USA
| | - Bruce H Tiffney
- Department of Earth Science and College of Creative Studies, University of California, Santa Barbara, CA, 93106, USA
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21
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Denk T, Grimm GW, Hipp AL, Bouchal JM, Schulze ED, Simeone MC. Niche evolution in a northern temperate tree lineage: biogeographical legacies in cork oaks (Quercus section Cerris). ANNALS OF BOTANY 2023; 131:769-787. [PMID: 36805162 PMCID: PMC10184457 DOI: 10.1093/aob/mcad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/15/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Despite being a small clade, they display a range of leaf morphologies comparable to the largest sections (>100 spp.) in Quercus. Their fossil record extends back to the Eocene. Here, we explore how cork oaks achieved their modern ranges and how legacy effects might explain niche evolution in modern species of section Cerris and its sister section Ilex, the holly oaks. METHODS We inferred a dated phylogeny for cork and holly oaks using a reduced-representation next-generation sequencing method, restriction site-associated DNA sequencing (RAD-seq), and used D-statistics to investigate gene flow hypotheses. We estimated divergence times using a fossilized birth-death model calibrated with 47 fossils. We used Köppen profiles, selected bioclimatic parameters and forest biomes occupied by modern species to infer ancestral climatic and biotic niches. KEY RESULTS East Asian and Western Eurasian cork oaks diverged initially in the Eocene. Subsequently, four Western Eurasian lineages (subsections) differentiated during the Oligocene and Miocene. Evolution of leaf size, form and texture was correlated, in part, with multiple transitions from ancestral humid temperate climates to mediterranean, arid and continental climates. Distantly related but ecologically similar species converged on similar leaf traits in the process. CONCLUSIONS Originating in temperate (frost-free) biomes, Eocene to Oligocene ranges of the primarily deciduous cork oaks were restricted to higher latitudes (Siberia to north of Paratethys). Members of the evergreen holly oaks (section Ilex) also originated in temperate biomes but migrated southwards and south-westwards into then-(sub)tropical southern China and south-eastern Tibet during the Eocene, then westwards along existing pre-Himalayan mountain ranges. Divergent biogeographical histories and deep-time phylogenetic legacies (in cold and drought tolerance, nutrient storage and fire resistance) thus account for the modern species mosaic of Western Eurasian oak communities, which are composed of oaks belonging to four sections.
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Affiliation(s)
- Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | | | | | - Johannes M Bouchal
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | | | - Marco C Simeone
- Department of Agricultural and Forestry Sciences, University of Tuscia, 01100 Viterbo, Italy
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22
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Alonso-Forn D, Sancho-Knapik D, Fariñas MD, Nadal M, Martín-Sánchez R, Ferrio JP, de Dios VR, Peguero-Pina JJ, Onoda Y, Cavender-Bares J, Arenas TGÁ, Gil-Pelegrín E. Disentangling leaf structural and material properties in relationship to their anatomical and chemical compositional traits in oaks (Quercus L.). ANNALS OF BOTANY 2023; 131:789-800. [PMID: 36794926 PMCID: PMC10184456 DOI: 10.1093/aob/mcad030] [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: 11/02/2022] [Accepted: 02/15/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The existence of sclerophyllous plants has been considered an adaptive strategy against different environmental stresses. Given that it literally means 'hard-leaved', it is essential to quantify the leaf mechanical properties to understand sclerophylly. However, the relative importance of each leaf trait for mechanical properties is not yet well established. METHODS Genus Quercus is an excellent system to shed light on this because it minimizes phylogenetic variation while having a wide variation in sclerophylly. We measured leaf anatomical traits and cell wall composition, analysing their relationship with leaf mass per area and leaf mechanical properties in a set of 25 oak species. KEY RESULTS The upper epidermis outer wall makes a strong and direct contribution to the leaf mechanical strength. Moreover, cellulose plays a crucial role in increasing leaf strength and toughness. The principal component analysis plot based on leaf trait values clearly separates Quercus species into two groups corresponding to evergreen and deciduous species. CONCLUSIONS Sclerophyllous Quercus species are tougher and stronger owing to their thicker epidermis outer wall and/or higher cellulose concentration. Furthermore, section Ilex species share common traits, although they occupy different climates. In addition, evergreen species living in mediterranean-type climates share common leaf traits irrespective of their different phylogenetic origin.
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Affiliation(s)
- David Alonso-Forn
- Department of Agricultural and Forest Systems and the Environment, Agrifood Research and Technology Centre of Aragon (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Domingo Sancho-Knapik
- Department of Agricultural and Forest Systems and the Environment, Agrifood Research and Technology Centre of Aragon (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - María Dolores Fariñas
- Sensors and Ultrasonic Technologies Department, Information and Physics Technologies Institute, Spanish National Research Council (CSIC), Madrid, Spain
| | - Miquel Nadal
- Department of Agricultural and Forest Systems and the Environment, Agrifood Research and Technology Centre of Aragon (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Rubén Martín-Sánchez
- Department of Agricultural and Forest Systems and the Environment, Agrifood Research and Technology Centre of Aragon (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Juan Pedro Ferrio
- Department of Agricultural and Forest Systems and the Environment, Agrifood Research and Technology Centre of Aragon (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
- Aragon Agency for Research and Development (ARAID), E-50018 Zaragoza, Spain
| | - Víctor Resco de Dios
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
- Department of Crop and Forest Sciences, Universitat de Lleida, E-25198 Lleida, Spain
- JRU CTFC-Agrotecnio-CERCA Center, E-25198 Lleida, Spain
| | - José Javier Peguero-Pina
- Department of Agricultural and Forest Systems and the Environment, Agrifood Research and Technology Centre of Aragon (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Yusuke Onoda
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake, Kitashirakawa, Kyoto 606-8502, Japan
| | | | - Tomás Gómez Álvarez Arenas
- Sensors and Ultrasonic Technologies Department, Information and Physics Technologies Institute, Spanish National Research Council (CSIC), Madrid, Spain
| | - Eustaquio Gil-Pelegrín
- Department of Agricultural and Forest Systems and the Environment, Agrifood Research and Technology Centre of Aragon (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
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23
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Nie ZL, Hodel R, Ma ZY, Johnson G, Ren C, Meng Y, Ickert-Bond SM, Liu XQ, Zimmer E, Wen J. Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1183-1203. [PMID: 36772845 DOI: 10.1111/jipb.13466] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/08/2023] [Indexed: 05/13/2023]
Abstract
The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.
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Affiliation(s)
- Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Richard Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Stefanie M Ickert-Bond
- Herbarium (ALA), University of Alaska Museum of the North, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Elizabeth Zimmer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
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Adie H, Lawes MJ. Solutions to fire and shade: resprouting, growing tall and the origin of Eurasian temperate broadleaved forest. Biol Rev Camb Philos Soc 2023; 98:643-661. [PMID: 36444419 DOI: 10.1111/brv.12923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
Tree species of Eurasian broadleaved forest possess two divergent trait syndromes with contrasting patterns of resource allocation adapted to different selection environments: short-stature basal resprouters that divert resources to a bud bank adapted to frequent and severe disturbances such as fire and herbivory, and tall trees that delay reproduction by investing in rapid height growth to escape shading. Drawing on theory developed in savanna ecosystems, we propose a conceptual framework showing that the possession of contrasting trait syndromes is essential for the persistence of broadleaved trees in an open ecosystem that burns. Consistent with this hypothesis, trees of modern Eurasian broadleaved forest bear a suite of traits that are adaptive to surface and crown-fire regimes. We contend that limited opportunities in grassland restricts recruitment to disturbance-free refugia, and en masse establishment creates a wooded environment where shade limits the growth of light-demanding savanna plants. Rapid height growth, which involves investment in structural support and the switch from a multi-stemmed to a monopodial growth form, is adaptive in this shaded environment. Although clustering reduces surface fuel loads, these establishment nuclei are vulnerable to high-intensity crown fires. The lethal effects of canopy fire are avoided by seasonal leaf shedding, and aerial resprouting enhances rapid post-fire recovery of photosynthetic capacity. While these woody formations satisfy the structural definition of forest, their constituents are clearly derived from savanna. Contrasting trait syndromes thus represent the shift from consumer to resource regulation in savanna ecosystems. Consistent with global trends, the diversification of most contemporary broadleaved taxa coincided with the spread of grasslands, a surge in fire activity and a decline in wooded ecosystems in the late Miocene-Pliocene. Recognition that Eurasian broadleaved forest has savanna origins and persists as an alternative state with adjacent grassy ecosystems has far-reaching management implications in accordance with functional rather than structural criteria. Shade is a severe constraint to the regeneration and growth of both woody and herbaceous growth forms in consumer-regulated ecosystems. However, these ecosystems are highly resilient to disturbance, an essential process that maintains diversity especially among the species-rich herbaceous component that is vulnerable to shading when consumer behaviour is altered.
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Affiliation(s)
- Hylton Adie
- School of Life Sciences, University of KwaZulu-Natal, P/Bag X01, Scottsville, 3209, South Africa
| | - Michael J Lawes
- School of Life Sciences, University of KwaZulu-Natal, P/Bag X01, Scottsville, 3209, South Africa
- Institute of Biodiversity and Environmental Conservation (IBEC), Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
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25
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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26
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Ramírez-Valiente JA, Solé-Medina A, Robledo-Arnuncio JJ, Ortego J. Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks. Mol Ecol 2023; 32:983-999. [PMID: 36479963 DOI: 10.1111/mec.16816] [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: 08/31/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Improving our knowledge of how past climate-driven selection has acted on present-day trait population divergence is essential to understand local adaptation processes and improve our predictions of evolutionary trajectories in the face of altered selection pressures resulting from climate change. In this study, we investigated signals of selection on traits related to drought tolerance and growth rates in two Mediterranean oak species (Quercus faginea and Q. lusitanica) with contrasting distribution ranges and climatic niches. We genotyped 182 individuals from 24 natural populations of the two species using restriction-site-associated DNA sequencing and conducted a thorough functional characterization in 1602 seedlings from 21 populations cultivated in common garden experiments under contrasting watering treatments. Our genomic data revealed that both Q. faginea and Q. lusitanica have very weak population genetic structure, probably as a result of high rates of pollen-mediated gene flow among populations and large effective population sizes. In contrast, common garden experiments showed evidence of climate-driven divergent selection among populations on traits related to leaf morphology, physiology and growth in both species. Overall, our study suggests that climate is an important selective factor for Mediterranean oaks and that ecophysiological traits have evolved in drought-prone environments even in a context of very high rates of gene flow among populations.
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Affiliation(s)
- José Alberto Ramírez-Valiente
- Ecological and Forestry Applications Research Centre, CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
| | - Aida Solé-Medina
- Instituto de Ciencias Forestales (ICIFOR-INIA), CSIC, Madrid, Spain
| | | | - Joaquín Ortego
- Department of Ecology and Evolution, Estación Biológica de Doñana, EBD-CSIC, Seville, Spain
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27
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Qin SY, Zuo ZY, Guo C, Du XY, Liu SY, Yu XQ, Xiang XG, Rong J, Liu B, Liu ZF, Ma PF, Li DZ. Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change. Mol Ecol 2023; 32:2850-2868. [PMID: 36847615 DOI: 10.1111/mec.16904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related to the evolutionary processes of the component species under paleoclimatic change, and potentially reflected in the dynamic history of evergreen broadleaved forests (EBLFs) in East Asia. However, knowledge about the shift of evergreen versus deciduous leaf with the impact of paleoclimatic change using genomic data remains rare. Here, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of EBLFs, to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) with eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling and climate niche reconstruction were employed to estimate its origin and diversification pattern. Taking into account studies on other plant lineages dominating EBLFs of East Asia, it was revealed that the prototype of EBLFs in East Asia probably emerged in the Early Eocene (55-50 million years ago [Ma]), facilitated by the greenhouse warming. As a response to the cooling and drying climate in the Middle to Late Eocene (48-38 Ma), deciduous habits were evolved in the dominant lineages of the EBLFs in East Asia. Up to the Early Miocene (23 Ma), the prevailing of East Asian monsoon increased the extreme seasonal precipitation and accelerated the emergence of evergreen habits of the dominant lineages, and ultimately shaped the vegetation resembling that of today.
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Affiliation(s)
- Sheng-Yuan Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Yu Zuo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Centre for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Centre for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Zhi-Fang Liu
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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28
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Guan X, Wen Y, Zhang Y, Chen Z, Cao KF. Stem hydraulic conductivity and embolism resistance of Quercus species are associated with their climatic niche. TREE PHYSIOLOGY 2023; 43:234-247. [PMID: 36209451 DOI: 10.1093/treephys/tpac119] [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: 01/24/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
The hydraulic traits of a plant species may reflect its climate adaptations. Southwest China is considered as a biodiversity hotpot of the genus Quercus (oak). However, the hydraulic adaptations of Asian oaks to their climate niches remain unclear. Ten common garden-grown oak species with distinct natural distributions in eastern Asia were used to determine their stem xylem embolism resistance (water potential at 50% loss of hydraulic conductivity, P50), stem hydraulic efficiency (vessel anatomy and sapwood specific hydraulic conductivity (Ks)) and leaf anatomical traits. We also compiled four key functional traits: wood density, hydraulic-weighted vessel diameter, Ks and P50 data for 31 oak species from previous literature. We analyzed the relationship between hydraulic traits and climatic factors over the native ranges of 41 oak species. Our results revealed that the 10 Asian oak species, which are mainly distributed in humid subtropical habitats, possessed a stem xylem with low embolism resistance and moderate hydraulic efficiency. The deciduous and evergreen species of the 10 Asian oaks differed in the stem and leaf traits related to hydraulic efficiency. Ks differed significantly between the two phenological groups (deciduous and evergreens) in the 41-oak dataset. No significant difference in P50 between the two groups was found for the 10 Asian oaks or the 41-oak dataset. The oak species that can distribute in arid habitats possessed a stem xylem with high embolism resistance. Ks negatively related to the humidity of the native range of the 10 Asian oaks, but showed no trend when assessing the entire global oak dataset. Our study suggests that stem hydraulic conductivity and embolism resistance in Quercus species are shaped by their climate niche. Our findings assist predictions of oak drought resistance with future climate changes for oak forest management.
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Affiliation(s)
- Xinyi Guan
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilisation of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
| | - Yin Wen
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilisation of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
| | - Ya Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Zhao Chen
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilisation of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
| | - Kun-Fang Cao
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilisation of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
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29
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Otero A, Barcenas-Peña A, Lumbsch HT, Grewe F. Reference-Based RADseq Unravels the Evolutionary History of Polar Species in 'the Crux Lichenologorum' Genus Usnea (Parmeliaceae, Ascomycota). J Fungi (Basel) 2023; 9:99. [PMID: 36675920 PMCID: PMC9865703 DOI: 10.3390/jof9010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/03/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
Nearly 90% of fungal diversity, one of the most speciose branches in the tree of life, remains undescribed. Lichenized fungi as symbiotic associations are still a challenge for species delimitation, and current species diversity is vastly underestimated. The ongoing democratization of Next-Generation Sequencing is turning the tables. Particularly, reference-based RADseq allows for metagenomic filtering of the symbiont sequence and yields robust phylogenomic trees of closely related species. We implemented reference-based RADseq to disentangle the evolution of neuropogonoid lichens, which inhabit harsh environments and belong to Usnea (Parmeliaceae, Ascomycota), one of the most taxonomically intriguing genera within lichenized fungi. Full taxon coverage of neuropogonoid lichens was sampled for the first time, coupled with phenotype characterizations. More than 20,000 loci of 126 specimens were analyzed through concatenated and coalescent-based methods, including time calibrations. Our analysis addressed the major taxonomic discussions over recent decades. Subsequently, two species are newly described, namely U. aymondiana and U. fibriloides, and three species names are resurrected. The late Miocene and Pliocene-Pleistocene boundary is inferred as the timeframe for neuropogonoid lichen diversification. Ultimately, this study helped fill the gap of fungal diversity by setting a solid backbone phylogeny which raises new questions about which factors may trigger complex evolutionary scenarios.
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Affiliation(s)
- Ana Otero
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Science & Education, The Field Museum, Chicago, IL 60605, USA
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30
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Yuan S, Shi Y, Zhou BF, Liang YY, Chen XY, An QQ, Fan YR, Shen Z, Ingvarsson PK, Wang B. Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests. Mol Ecol 2023; 32:1639-1655. [PMID: 36626136 DOI: 10.1111/mec.16843] [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: 07/29/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Understanding the evolutionary processes that shape the landscape of genetic variation and influence the response of species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across the distribution range of a dominant forest tree, Quercus acutissima, in East Asia, and applied genome-wide analyses to track the evolutionary history and predict the fate of populations under future climate. We found two genetic groups (East and West) in Q. acutissima that diverged during Pliocene. We also found a heterogeneous landscape of genomic variation in this species, which may have been shaped by population demography and linked selections. Using genotype-environment association analyses, we identified climate-associated SNPs in a diverse set of genes and functional categories, indicating a model of polygenic adaptation in Q. acutissima. We further estimated three genetic offset metrics to quantify genomic vulnerability of this species to climate change due to the complex interplay between local adaptation and migration. We found that marginal populations are under higher risk of local extinction because of future climate change, and may not be able to track suitable habitats to maintain the gene-environment relationships observed under the current climate. We also detected higher reverse genetic offsets in northern China, indicating that genetic variation currently present in the whole range of Q. acutissima may not adapt to future climate conditions in this area. Overall, this study illustrates how evolutionary processes have shaped the landscape of genomic variation, and provides a comprehensive genome-wide view of climate maladaptation in Q. acutissima.
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Affiliation(s)
- Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yan-Ru Fan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Zhao Shen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
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31
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Ouyang ZY, Li ZH, Chen R, Jiang XL, Wu JY. The complete chloroplast genome sequence of Quercus kerrii (Fagaceae), and comparative analysis with related species. Mitochondrial DNA B Resour 2023; 8:527-531. [PMID: 37124995 PMCID: PMC10132218 DOI: 10.1080/23802359.2023.2204167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Quercus kerrii Craib 1911 (section Cyclobalanopsis) is a widespread tree species in the tropical seasonal forests of southwest China and Northern Indo-China areas. In this study, we sequenced, assembled and annotated the complete chloroplast genome of Q. kerrii. The circular genome was 160,743 bp in length and had a GC content of 36.89%. The Q. kerrii chloroplast genome has a typical quadripartite structure, including two inverted repeat regions (length, 25,825 bp; GC content, 42.76%), a large single-copy region (length, 90,196 bp; GC content, 34.74%), and a small single-copy region (length, 18,897 bp; GC content, 30.60%). Genome annotation has indicated that the Q. kerrii chloroplast genome contained 131 genes, including 86 protein-coding genes, 37 tRNA, and eight rRNA. The phylogenetic tree showed that Q. kerrii had a close relationship with Q. schottkyana Rehder & E.H.Wilson 1916.
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Affiliation(s)
- Ze-Yi Ouyang
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
- Hunan Botanical Garden, Changsha, China
| | - Zhi-Hui Li
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Ran Chen
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Xiao-Long Jiang
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
- CONTACT Xiao-Long Jiang College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ji-You Wu
- Hunan Academy of Forestry, Changsha, China
- Ji-You Wu Hunan Academy of Forestry, Changsha, Hunan, China
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32
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Rauschendorfer J, Rooney R, Külheim C. Strategies to mitigate shifts in red oak (Quercus sect. Lobatae) distribution under a changing climate. TREE PHYSIOLOGY 2022; 42:2383-2400. [PMID: 35867476 DOI: 10.1093/treephys/tpac090] [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: 11/24/2021] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Red oaks (Quercus sect. Lobatae) are a taxonomic group of hardwood trees, which occur in swamp forests, subtropical chaparral and savannahs from Columbia to Canada. They cover a wide range of ecological niches, and many species are thought to be able to cope with current trends in climate change. Genus Quercus encompasses ca. 500 species, of which ca. 80 make up sect. Lobatae. Species diversity is greatest within the southeastern USA and within the northern and eastern regions of Mexico. This review discusses the weak reproductive barriers between species of red oaks and the effects this has on speciation and niche range. Distribution and diversity have been shaped by drought adaptations common to the species of sect. Lobatae, which enable them to fill various xeric niches across the continent. Drought adaptive traits of this taxonomic group include deciduousness, deep tap roots, ring-porous xylem, regenerative stump sprouting, greater leaf thickness and smaller stomata. The complex interplay between these anatomical and morphological traits has given red oaks features of drought tolerance and avoidance. Here, we discuss physiological and genetic components of these adaptations to address how many species of sect. Lobatae reside within xeric sites and/or sustain normal metabolic function during drought. Although extensive drought adaptation appears to give sect. Lobatae a resilience to climate change, aging tree stands, oak life history traits and the current genetic structures place many red oak species at risk. Furthermore, oak decline, a complex interaction between abiotic and biotic agents, has severe effects on red oaks and is likely to accelerate species decline and fragmentation. We suggest that assisted migration can be used to avoid species fragmentation and increase climate change resilience of sect. Lobatae.
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Affiliation(s)
- James Rauschendorfer
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rebecca Rooney
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Carsten Külheim
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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33
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Yu T, Yang Q, Deng M, Cheng N, Yao K, Yang W, Ji X, Zheng H. Morphological characteristics of seed starch granules of Fagaceae in South China and their implication in paleodiet. FRONTIERS IN PLANT SCIENCE 2022; 13:977152. [PMID: 36452090 PMCID: PMC9702991 DOI: 10.3389/fpls.2022.977152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/14/2022] [Indexed: 06/13/2023]
Abstract
Nut fruits likely played a significant role before and during the origin of agriculture; however, relatively little research conducted on the morphological characteristics and statistical comparisons of nut fruit starch granule hinders the progress of paleodietary analysis of prehistorical society. For better species identification of starch granule remaining on tools discovered at archaeological sites, it is desirable to develop a more abundant morphology database of modern nut fruit starch granules as well as the establishment of relevant identification standards. Therefore, nuts from 40 species in four genera (Quercus, Lithocarpus, Castanea, and Castanopsis) of Fagaceae were collected from South China for statistical measurement and comparative analysis. Starch granules are highly accumulated in 34 species except for 6 species, whose shapes involve oval, subcircular, drop-shaped, rounded triangle, polygonal, spherical caps, and bell-shaped types, or a combination of several types, and the average length is between 10 and 20 μm. According to research on Quercus phylogeny relationships, it was found that the species in the same infragenious section produce similar morphological characteristics of starch granules. The result was applied in the identification of starch granules extracted from stone tools from the 20 to 10 ka cultural layer of Xiaodong Rockshelter, and some starch granules can be recognized to species level, revealing that nuts from Quercus and Lithocarpus were gathered and exploited by ancient people. This expansion of modern starch presentation and comparison of nuts helps to improve the accuracy of the identification of ancient starch and deepen the understanding of plant utilization of ancient humans.
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Affiliation(s)
- Tong Yu
- Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming, China
- Key Laboratory of Digital Human Technology R&D and Application of Yunnan Provincial Department of Education, School of History and Archival Science, Yunnan University, Kunming, China
| | - Qing Yang
- Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming, China
- Key Laboratory of Digital Human Technology R&D and Application of Yunnan Provincial Department of Education, School of History and Archival Science, Yunnan University, Kunming, China
| | - Min Deng
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Nan Cheng
- Key Laboratory of Digital Human Technology R&D and Application of Yunnan Provincial Department of Education, School of History and Archival Science, Yunnan University, Kunming, China
| | - Kaiping Yao
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Wanshu Yang
- Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming, China
| | - Xueping Ji
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Natural History Museum, Kunming, China
| | - Hongbo Zheng
- Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming, China
- School of Earth and Environmental Sciences, The University of Queensland, Bribane, QLD, Australia
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34
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Du FK, Qi M, Zhang YY, Petit RJ. Asymmetric character displacement in mixed oak stands. THE NEW PHYTOLOGIST 2022; 236:1212-1224. [PMID: 35706383 DOI: 10.1111/nph.18311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Ecological character displacement (ECD) refers to a pattern of increased divergence at sites where species ranges overlap caused by competition for resources. Although ECD is believed to be common, there are few in-depth studies that clearly establish its existence, especially in plants. Thus, we have compared leaf traits in allopatric and sympatric populations of two East Asian deciduous oaks: Quercus dentata and Quercus aliena. In contrast to previous studies, we define sympatry and allopatry at a local scale, thereby comparing populations that can or cannot directly interact. Using genetic markers, we found greater genetic divergence between the two oak species growing in mixed stands and inferred that long-term gene flow has predominantly occurred asymmetrically from the cold-tolerant species (Q. dentata) to the warm-demanding later colonizing species (Q. aliena). Analysis of leaf traits revealed greater divergence in mixed than in pure oak stands. This was mostly due to the later colonizing species being characterized by more resource-conservative traits in the presence of the other species. Controlling for relevant environmental differences did not alter these conclusions. These results suggest that asymmetric trait divergence can take place where species coexist, possibly due to the imbalance in demographic history of species resulting in asymmetric inter-specific selection pressures.
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Affiliation(s)
- Fang K Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Min Qi
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Rémy J Petit
- Université de Bordeaux, INRAE, BIOGECO, F-33610, Cestas, France
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35
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Zhou X, Liu N, Jiang X, Qin Z, Farooq TH, Cao F, Li H. A chromosome-scale genome assembly of Quercus gilva: Insights into the evolution of Quercus section Cyclobalanopsis (Fagaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:1012277. [PMID: 36212339 PMCID: PMC9539764 DOI: 10.3389/fpls.2022.1012277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/13/2022] [Indexed: 05/30/2023]
Abstract
Quercus gilva is an ecologically and economically important species of Quercus section Cyclobalanopsis and is a dominant species in evergreen broad-leaved forests in subtropical regions of East Asia. In the present study, we reported a high-quality chromosome-scale genome assembly of Q. gilva, the first reference genome for section Cyclobalanopsis, using the combination of Illumina and PacBio sequencing with Hi-C technologies. The assembled genome size of Q. gilva was 889.71 Mb, with a contig number of 773 and a contig N50 of 28.32 Mb. Hi-C scaffolding anchored 859.07 Mb contigs (96.54% of the assembled genome) onto 12 pseudochromosomes, with a scaffold N50 of 70.35 Mb. A combination of de novo, homology-based, and transcript-based predictions predicted a final set of 36,442 protein-coding genes distributed on 12 pseudochromosomes, and 97.73% of them were functionally annotated. A total of 535.64 Mb (60.20%) of repetitive sequences were identified. Genome evolution analysis revealed that Q. gilva was most closely related to Q. suber and they diverged at 40.35 Ma, and Q. gilva did not experience species-specific whole-genome duplication in addition to the ancient gamma (γ) whole-genome triplication event shared by core eudicot plants. Q. gilva underwent considerable gene family expansion and contraction, with 598 expanded and 6,509 contracted gene families detected. The first chromosome-scale genome of Q. gilva will promote its germplasm conservation and genetic improvement and provide essential resources for better studying the evolution of Quercus section Cyclobalanopsis.
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Affiliation(s)
- Xia Zhou
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Na Liu
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Xiaolong Jiang
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Zhikuang Qin
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Taimoor Hassan Farooq
- Bangor College China, A Joint Unit of Bangor University and Central South University of Forestry and Technology, Changsha, China
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - He Li
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
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36
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Ward AKG, Bagley RK, Egan SP, Hood GR, Ott JR, Prior KM, Sheikh SI, Weinersmith KL, Zhang L, Zhang YM, Forbes AA. Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both. Evolution 2022; 76:1849-1867. [PMID: 35819249 PMCID: PMC9541853 DOI: 10.1111/evo.14562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 01/22/2023]
Abstract
Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ∼1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae-primarily the oaks (genus Quercus; ∼435 sp.). The association of oak gall wasps with oaks is ancient (∼50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified the strong signal of host plant shifting among oak gall wasps that has been found in other phytophagous insect systems. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich. We collected 86 species of Nearctic oak gall wasps from most of the major clades of Nearctic oaks and sequenced >1000 Ultraconserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic wasp clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Although formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.
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Affiliation(s)
| | - Robin K. Bagley
- Department of BiologyUniversity of IowaIowa CityIowa52245,Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityLimaOhio45804
| | - Scott P. Egan
- Department of BioSciencesRice UniversityHoustonTexas77005
| | - Glen Ray Hood
- Department of BioSciencesRice UniversityHoustonTexas77005,Department of Biological ScienceWayne State UniversityDetroitMichigan48202
| | - James R. Ott
- Department of BiologyTexas State UniversitySan MarcosTexas78666
| | - Kirsten M. Prior
- Department of Biological SciencesBinghamton UniversityBinghamtonNew York13902
| | - Sofia I. Sheikh
- Department of BiologyUniversity of IowaIowa CityIowa52245,Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinois60637
| | | | - Linyi Zhang
- Department of BioSciencesRice UniversityHoustonTexas77005,Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM5S 3B2Canada
| | - Y. Miles Zhang
- Systematic Entomology Laboratory, USDA‐ARSc/o National Museum of Natural HistoryWashingtonD.C.20560
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Zhou W, Jenny Xiang QY. Phylogenomics and Biogeography of Castanea (Chestnut) and Hamamelis (Witch-hazel) - Choosing between RAD-seq and Hyb-Seq Approaches. Mol Phylogenet Evol 2022; 176:107592. [DOI: 10.1016/j.ympev.2022.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 10/31/2022]
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Li Y, Wang L, Zhang X, Kang H, Liu C, Mao L, Fang Y. Extensive sharing of chloroplast haplotypes among East Asian Cerris oaks: The imprints of shared ancestral polymorphism and introgression. Ecol Evol 2022; 12:e9142. [PMID: 35923946 PMCID: PMC9339761 DOI: 10.1002/ece3.9142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/27/2022] [Accepted: 07/01/2022] [Indexed: 11/08/2022] Open
Abstract
Shared ancestral polymorphism and introgression are two main causes of chloroplast DNA (cpDNA) haplotype sharing among closely related angiosperms. In this study, we explored the roles of these two processes in shaping the phylogeographic patterns of East Asian Cerris oaks by examining the geographic distributions of randomly and locally distributed shared haplotypes, which coincide with the expectations of shared ancestry and introgression, respectively. We sequenced 1340 bp of non‐coding cpDNA from Quercus acutissima (n = 418) and Q. chenii (n = 183) and compiled previously published sequence data of Q. variabilis (n = 439). The phylogenetic relationships among haplotypes were examined using a median‐joining network. The geographic patterns of interspecifically shared haplotypes were assessed to test whether nearby populations have a higher degree of interspecific cpDNA sharing than distant ones. We identified a total of 27 haplotypes that were grouped into three non‐species‐specific lineages with overlapping distributions. Ancestral haplotypes were extensively shared and randomly distributed across populations of the three species. Some young haplotypes were locally shared in mountainous areas that may have been shared refugia. The local exchange of cpDNA resulted in an excess of similar haplotypes between nearby populations. Our study demonstrated that the haplotype sharing pattern among East Asian Cerris oaks reflected the imprints of both shared ancestral polymorphism and introgression. This pattern was also associated with the relatively stable climates and complex landscapes in East Asia, which not only allowed the long‐term persistence of ancestral lineages but also connected the survived populations across refugia.
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Affiliation(s)
- Yao Li
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment, Nanjing Forestry University Nanjing China
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment, Nanjing Forestry University Nanjing China
| | - Xingwang Zhang
- School of Life Sciences Huaibei Normal University Huaibei China
| | - Hongzhang Kang
- School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Chunjiang Liu
- School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Lingfeng Mao
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment, Nanjing Forestry University Nanjing China
| | - Yanming Fang
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment, Nanjing Forestry University Nanjing China
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39
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Li Y, Wang TR, Kozlowski G, Liu MH, Yi LT, Song YG. Complete Chloroplast Genome of an Endangered Species Quercus litseoides, and Its Comparative, Evolutionary, and Phylogenetic Study with Other Quercus Section Cyclobalanopsis Species. Genes (Basel) 2022; 13:genes13071184. [PMID: 35885967 PMCID: PMC9316884 DOI: 10.3390/genes13071184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
Quercus litseoides, an endangered montane cloud forest species, is endemic to southern China. To understand the genomic features, phylogenetic relationships, and molecular evolution of Q. litseoides, the complete chloroplast (cp) genome was analyzed and compared in Quercus section Cyclobalanopsis. The cp genome of Q. litseoides was 160,782 bp in length, with an overall guanine and cytosine (GC) content of 36.9%. It contained 131 genes, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. A total of 165 simple sequence repeats (SSRs) and 48 long sequence repeats with A/T bias were identified in the Q. litseoides cp genome, which were mainly distributed in the large single copy region (LSC) and intergenic spacer regions. The Q. litseoides cp genome was similar in size, gene composition, and linearity of the structural region to those of Quercus species. The non-coding regions were more divergent than the coding regions, and the LSC region and small single copy region (SSC) were more divergent than the inverted repeat regions (IRs). Among the 13 divergent regions, 11 were in the LSC region, and only two were in the SSC region. Moreover, the coding sequence (CDS) of the six protein-coding genes (rps12, matK, atpF, rpoC2, rpoC1, and ndhK) were subjected to positive selection pressure when pairwise comparison of 16 species of Quercus section Cyclobalanopsis. A close relationship between Q. litseoides and Quercus edithiae was found in the phylogenetic analysis of cp genomes. Our study provided highly effective molecular markers for subsequent phylogenetic analysis, species identification, and biogeographic analysis of Quercus.
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Affiliation(s)
- Yu Li
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (Y.L.); (M.-H.L.)
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (T.-R.W.); (G.K.)
| | - Tian-Rui Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (T.-R.W.); (G.K.)
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (T.-R.W.); (G.K.)
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland
| | - Mei-Hua Liu
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (Y.L.); (M.-H.L.)
| | - Li-Ta Yi
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (Y.L.); (M.-H.L.)
- Correspondence: (L.-T.Y.); (Y.-G.S.)
| | - Yi-Gang Song
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (Y.L.); (M.-H.L.)
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (T.-R.W.); (G.K.)
- Correspondence: (L.-T.Y.); (Y.-G.S.)
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Saiz-Fernández I, Đorđević B, Kerchev P, Černý M, Jung T, Berka M, Fu CH, Horta Jung M, Brzobohatý B. Differences in the Proteomic and Metabolomic Response of Quercus suber and Quercus variabilis During the Early Stages of Phytophthora cinnamomi Infection. Front Microbiol 2022; 13:894533. [PMID: 35770156 PMCID: PMC9234522 DOI: 10.3389/fmicb.2022.894533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/11/2022] [Indexed: 12/23/2022] Open
Abstract
Phytophthora cinnamomi Rands is a cosmopolite pathogen of woody plants which during the last couple of centuries has spread all over the world from its center of origin in Southeast Asia. In contrast to Chinese cork oak (Quercus variabilis Blume) forests native to Asia, which are generally healthy despite the presence of the pathogen, the populations of Cork oaks (Quercus suber L.) in Europe have been severely decimated by P. cinnamomi. The present study aims at identifying the differences in the early proteomic and metabolomic response of these two tree species that lead to their differences in susceptibility to P. cinnamomi. By using micropropagated clonal plants, we tried to minimize the plant-to-plant differences in the defense response that is maximized by the high intraspecific genetic variability inherent to the Quercus genus. The evolution on the content of Phytophthora proteins in the roots during the first 36 h after inoculation suggests a slower infection process in Q. variabilis plants. These plants displayed a significant decrease in sugars in the roots, together with a downregulation of proteins related to carbon metabolism. In the leaves, the biggest changes in proteomic profiling were observed 16 h after inoculation, and included increased abundance of peroxidases, superoxide dismutases and glutathione S-transferases in Q. variabilis plants, which probably contributed to decrease its susceptibility to P. cinnamomi.
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Affiliation(s)
- Iñigo Saiz-Fernández
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Biljana Đorđević
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Thomas Jung
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Chuen-Hsu Fu
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Marília Horta Jung
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
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Baumel A, Nieto Feliner G, Médail F, La Malfa S, Di Guardo M, Bou Dagher Kharrat M, Lakhal-Mirleau F, Frelon V, Ouahmane L, Diadema K, Sanguin H, Viruel J. Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of a fruit tree in the Mediterranean. Mol Ecol 2022; 31:4095-4111. [PMID: 35691023 PMCID: PMC9541536 DOI: 10.1111/mec.16563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/13/2022] [Accepted: 06/08/2022] [Indexed: 12/22/2022]
Abstract
Intense research efforts over the last two decades have renewed our understanding of plant phylogeography and domestication in the Mediterranean basin. Here we aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome‐wide diversity and evolutionary patterns of the CEUs with 3557 single nucleotide polymorphisms generated by restriction‐site associated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, seminatural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic‐wide data allowed us to resolve west‐to‐east expansions from a single long‐term refugium probably located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range‐wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long‐distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in southwest Morocco, south Spain and eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees.
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Affiliation(s)
- Alex Baumel
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | | | - Frédéric Médail
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Magda Bou Dagher Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon
| | - Fatma Lakhal-Mirleau
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Valentine Frelon
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Lahcen Ouahmane
- Faculté des Sciences Semlalia, Laboratoire de Biotechnologies Microbiennes Agrosciences et Environnement, Université Cadi Ayyad Marrakech, Marrakech, Morocco
| | - Katia Diadema
- Conservatoire Botanique National Méditerranéen de Porquerolles (CBNMed), Hyères, France
| | - Hervé Sanguin
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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42
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Xia K, Daws MI, Peng LL. Climate drives patterns of seed traits in Quercus species across China. THE NEW PHYTOLOGIST 2022; 234:1629-1638. [PMID: 35306670 DOI: 10.1111/nph.18103] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/03/2022] [Indexed: 05/26/2023]
Abstract
Traits enabling seeds to survive post-dispersal desiccation and subsequently germinate are important aspects of plant regeneration for species with desiccation-sensitive seeds. However, how desiccation and germination-related traits co-vary and relate to patterns of climate variation are unknown. We investigated physiological traits related to desiccation and germination of desiccation-sensitive seeds from 19 Quercus species, which typically dominate subalpine, subtropical and temperate forests in China. The results demonstrate a strong relationship between climate and seed traits consistent with a hypothesis of minimizing seed death from desiccation. Seeds of subalpine species were most desiccation sensitive and died fastest when dried. These species avoided drought and cold by germinating rapidly. Subtropical and temperate oaks had more variable strategies to minimize the risk of mortality reflecting a continuum between traits that facilitate rapid germination (with the risk of rapid desiccation) and slow germination (and slow desiccation). Across the Quercus species, the relative level of seed desiccation sensitivity, which we predicted to be important for reducing the risk of drying related mortality, was independent of climate. For desiccation-sensitive seeds this suggests a more diverse range of strategies for minimizing desiccation risk than reported previously.
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Affiliation(s)
- Ke Xia
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, Yunnan, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, Yunnan University, Kunming, 650504, Yunnan, China
| | - Matthew I Daws
- Environment Department, Alcoa of Australia Ltd, Huntly Mine, off Del Park Road, PO Box 172, Pinjarra, WA, 6208, Australia
| | - Lin-Lin Peng
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, Yunnan, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, Yunnan University, Kunming, 650504, Yunnan, China
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43
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Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M, Salzberg SL. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nat Commun 2022; 13:2047. [PMID: 35440538 PMCID: PMC9018854 DOI: 10.1038/s41467-022-29584-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
The genus Quercus, which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata, revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since early Miocene. Analysis of 39,373 mapped protein-coding genes outlined copious duplications consistent with genetic and phenotypic diversity, both by retention of genes created during the ancient γ whole genome hexaploid duplication event and by tandem duplication within families, including numerous resistance genes and a very large block of duplicated DUF247 genes, which have been found to be associated with self-incompatibility in grasses. An additional surprising finding is that subcontext-specific patterns of DNA methylation associated with transposable elements reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses. Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA.
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Shawn J Cokus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Sorel T Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Aleksey V Zimin
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jesse A Garcia
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Ying Zhen
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Steven L Salzberg
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21218, USA
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44
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Ai W, Liu Y, Mei M, Zhang X, Tan E, Liu H, Han X, Zhan H, Lu X. A chromosome-scale genome assembly of the Mongolian oak (Quercus mongolica). Mol Ecol Resour 2022; 22:2396-2410. [PMID: 35377556 DOI: 10.1111/1755-0998.13616] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/13/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022]
Abstract
Mongolian oak (Quercus mongolica Fisch.) is an ecologically and economically important white oak species native to and widespread in the temperate zone of East Asia. Here, we present a chromosome-scale reference genome assembly of Q. mongolica, a representative white oak species, by combining Illumina and PacBio data with Hi-C mapping technologies that is the first reference genome created for an Asian oak. Our results showed that the PacBio draft genome size was 809.84 Mb, with a BUSCO complete gene percentage of 92.71%. Hi-C scaffolding anchored 774.59 Mb contigs (95.65% of draft assembly) onto 12 pseudochromosomes. The contig N50 and scaffold N50 were 2.64 Mb and 66.74 Mb, respectively. Of the 36,553 protein-coding genes predicted in the study, approximately 95% had functional annotations in public databases. A total of 435.34 Mb (53.75% of the genome) of repetitive sequences were predicted in the assembled genome. Genome evolution analysis showed that Q. mongolica is closely related to Q. robur from Europe, and they shared a common ancestor ~11.8 million years ago. Gene family evolution analysis of Q. mongolica revealed that the nucleotide-binding site (NBS)-encoding gene family related to disease resistance was significantly contracted, whereas the ECERIFERUM 1 (CER1) homologous genes related to cuticular wax biosynthesis was significantly expanded. This pioneering Asian oak genome resource represents an important supplement to the oak genomics community and will improve our understanding of Asian white oak biology and evolution.
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Affiliation(s)
- Wanfeng Ai
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yanqun Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Mei Mei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.,Biotechnology and Analysis Test Center, Liaoning Academy of Forest Science, Shenyang, 110032, Liaoning, China
| | - Xiaolin Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Enguang Tan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hanzhang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Xiaoyi Han
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hao Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Xiujun Lu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.,College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
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45
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Zhou BF, Yuan S, Crowl AA, Liang YY, Shi Y, Chen XY, An QQ, Kang M, Manos PS, Wang B. Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nat Commun 2022; 13:1320. [PMID: 35288565 PMCID: PMC8921187 DOI: 10.1038/s41467-022-28917-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses of nuclear and plastid genomes to investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. Innovation related to seed dispersal is implicated in triggering waves of continental radiations beginning with the rapid diversification of major lineages and resulting in unparalleled transformation of forest dynamics within 15 million years following the K-Pg extinction. We detect introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, which may have further amplified the diversification of white oaks across Eurasia. Fagaceae are diverse family including trees of ecological and economic importance. This phylogenomic analysis of nuclear and plastid genomes reconstructs evolutionary history and finds evidence of multiple adaptive introgression events in this important plant family.
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Tree functional traits, forest biomass, and tree species diversity interact with site properties to drive forest soil carbon. Nat Commun 2022; 13:1097. [PMID: 35233020 PMCID: PMC8888738 DOI: 10.1038/s41467-022-28748-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 02/02/2022] [Indexed: 01/04/2023] Open
Abstract
Forests constitute important ecosystems in the global carbon cycle. However, how trees and environmental conditions interact to determine the amount of organic carbon stored in forest soils is a hotly debated subject. In particular, how tree species influence soil organic carbon (SOC) remains unclear. Based on a global compilation of data, we show that functional traits of trees and forest standing biomass explain half of the local variability in forest SOC. The effects of functional traits on SOC depended on the climatic and soil conditions with the strongest effect observed under boreal climate and on acidic, poor, coarse-textured soils. Mixing tree species in forests also favours the storage of SOC, provided that a biomass over-yielding occurs in mixed forests. We propose that the forest carbon sink can be optimised by (i) increasing standing biomass, (ii) increasing forest species richness, and (iii) choosing forest composition based on tree functional traits according to the local conditions. Forests constitute important ecosystems in the global carbon cycle. This study investigates how tree species influence soil organic carbon using a global dataset, showing the importance of tree functional traits and forest standing biomass to optimise forest carbon sink.
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Hara M. Phytogeography and history of Japanese beech forests: Recent advances and implications for vegetation ecology. Ecol Res 2022. [DOI: 10.1111/1440-1703.12298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cardoni S, Piredda R, Denk T, Grimm GW, Papageorgiou AC, Schulze E, Scoppola A, Salehi Shanjani P, Suyama Y, Tomaru N, Worth JRP, Cosimo Simeone M. 5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:909-926. [PMID: 34808015 PMCID: PMC9299691 DOI: 10.1111/tpj.15601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 11/02/2021] [Accepted: 11/18/2021] [Indexed: 05/31/2023]
Abstract
Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.
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Affiliation(s)
- Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Roberta Piredda
- Department of Veterinary MedicineUniversity of Bari ‘Aldo Moro’Valenzano70010Italy
| | - Thomas Denk
- Swedish Museum of Natural HistoryStockholm10405Sweden
| | | | | | | | - Anna Scoppola
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Parvin Salehi Shanjani
- Natural Resources Gene Bank, Research Institute of Forests and RangelandsAgricultural Research, Education and Extension OrganizationTehranIran
| | - Yoshihisa Suyama
- Graduate School of Agricultural ScienceTohoku UniversityOsakiMiyagi989‐6711Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaAichi464‐8601Japan
| | - James R. P. Worth
- Ecological Genetics LaboratoryForestry and Forest Products Research Institute (FFPRI)TsukubaIbaraki305‐8687Japan
| | - Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
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Li Y, Zhang X, Wang L, Sork VL, Mao L, Fang Y. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China. ANNALS OF BOTANY 2022; 129:231-245. [PMID: 34893791 PMCID: PMC8796672 DOI: 10.1093/aob/mcab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. METHODS We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. KEY RESULTS More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. CONCLUSIONS Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.
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Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xingwang Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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Liang YY, Shi Y, Yuan S, Zhou BF, Chen XY, An QQ, Ingvarsson PK, Plomion C, Wang B. Linked selection shapes the landscape of genomic variation in three oak species. THE NEW PHYTOLOGIST 2022; 233:555-568. [PMID: 34637540 DOI: 10.1111/nph.17793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('FST -islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that FST -islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.
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Affiliation(s)
- Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | | | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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