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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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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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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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Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biol 2021; 22:254. [PMID: 34479604 PMCID: PMC8414701 DOI: 10.1186/s13059-021-02467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/12/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. RESULTS By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce's disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. CONCLUSIONS Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | | | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Andrew M. Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
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Tamaki I, Obora T, Ohsawa T, Matsumoto A, Saito Y, Ide Y. Different population size change and migration histories created genetic diversity of three oaks in Tokai region, central Japan. JOURNAL OF PLANT RESEARCH 2021; 134:933-946. [PMID: 34155542 DOI: 10.1007/s10265-021-01323-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
To understand genetic diversity in focal species, it is important to consider the possibility of speciation with gene flow, especially in species with porous genomes such as oaks. We studied genetic diversity and structure in three oaks, Quercus mongolica var. mongolicoides (QM), Q. mongolica var. crispula (QC) and Q. serrata (QS), growing in the Tokai region, central Japan. QM is semi-endemic to the region while the others are common taxa. We also conducted demographic modeling to infer their population size change and migration histories using an approximate Bayesian computation (ABC) approach. The three taxa showed distinct genetic structures but there was genetic admixture among the taxa, especially between QM and QC. ABC analysis of population size change revealed that the population size of QM was stable during and after the last glacial period, while QC and QS showed population expansion after the last glacial maximum. ABC analysis of population divergence and migration revealed that continuous gene flow between QM and QC after their divergence was supported, while between QM and QS, and between QC and QS, secondary contact after sufficient isolation was supported. These historical migration patterns among the three taxa indicate that QM and QC are currently in the early stage or gray zone of speciation, whereas speciation of the other two taxon pairs is considered to have almost been established. Observed gene flow patterns and strength between QM and QC, and between QM and QS, were explained by both flowering patterns and historical distributions, but those between QC and QS were not.
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Affiliation(s)
- Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan.
| | - Tomohiro Obora
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan
| | - Takafumi Ohsawa
- Ministry of the Environment, 1-2-2 Kasumigaseki, Chiyoda-ku, Tokyo, 100-8975, Japan
| | - Asako Matsumoto
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoko Saito
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuji Ide
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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Li
X, Wei G, El-Kassaby YA, Fang Y. Hybridization and introgression in sympatric and allopatric populations of four oak species. BMC PLANT BIOLOGY 2021; 21:266. [PMID: 34107871 PMCID: PMC8188795 DOI: 10.1186/s12870-021-03007-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/05/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant members in the Northern hemisphere, that are used to studying the introgression of species boundaries and adaptive processes. China is the second-largest distribution center of Quercus, but there are limited studies on introgressive hybridization. RESULTS Here, we screened 17 co-dominant nuclear microsatellite markers to investigate the hybridization and introgression of four oaks (Quercus acutissima, Quercus variabilis, Quercus fabri, and Quercus serrata) in 10 populations. We identified 361 alleles in the four-oak species across 17 loci, and all loci were characterized by high genetic variability (HE = 0.844-0.944) and moderate differentiation (FST = 0.037-0.156) levels. A population differentiation analysis revealed the following: allopatric homologous (FST = 0.064) < sympatric heterogeneous (FST = 0.071) < allopatric heterogeneous (FST = 0.084). A Bayesian admixture analysis determined four types of hybrids (Q. acutissima × Q. variabilis, Q. fabri × Q. serrata, Q. acutissima × Q. fabri, and Q. acutissima × Q. variabilis × Q. fabri) and their asymmetric introgression. Our results revealed that interspecific hybridization is commonly observed within the section Quercus, with members having tendency to hybridize. CONCLUSIONS Our study determined the basic hybridization and introgression states among the studied four oak species and extended our understanding of the evolutionary role of hybridization. The results provide useful theoretical data for formulating conservation strategies.
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Affiliation(s)
- Xuan 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, 159 Longpan Road, Nanjing, 210037 PR China
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Gaoming Wei
- 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, 159 Longpan Road, Nanjing, 210037 PR China
- School of Physics and Electronics Henan University, Jinming Avenue, Jinming District, Kaifeng, 475001 PR China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - 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, 159 Longpan Road, Nanjing, 210037 PR China
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Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods. FORESTS 2021. [DOI: 10.3390/f12020222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.
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Yang J, Guo YF, Chen XD, Zhang X, Ju MM, Bai GQ, Liu ZL, Zhao GF. Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1024. [PMID: 32823635 PMCID: PMC7464331 DOI: 10.3390/plants9081024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022]
Abstract
Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak's lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene-Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak's lineage.
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Affiliation(s)
- Jia Yang
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Yu-Fan Guo
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Xiao-Dan Chen
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Xiao Zhang
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Miao-Miao Ju
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Guo-Qing Bai
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
- Institute of Botany of Shaanxi Province, Xi’an 710061, China
| | - Zhan-Lin Liu
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Gui-Fang Zhao
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
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Plomion C, Martin F. Oak genomics is proving its worth. THE NEW PHYTOLOGIST 2020; 226:943-946. [PMID: 32301515 DOI: 10.1111/nph.16560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
| | - Francis Martin
- INRAE, UMR IAM, Centre INRAE-Grand Est, Université de Lorraine, F-54280, Champenoux, France
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