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Huang K, Li B, Chen X, Qin C, Zhang X. Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1430191. [PMID: 39224852 PMCID: PMC11366656 DOI: 10.3389/fpls.2024.1430191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.
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Affiliation(s)
| | | | | | | | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, China
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Ji HY, Ye C, Chen YQ, Li JW, Hidayat A, Miao JL, Li JH, Wu JY, Zhai JW, Lan SR, Jin XH. Phylogenomics and biogeographical diversification of Collabieae (Orchidaceae) and its implication in the reconstruction of the dynamic history of Asian evergreen broadleaved forests. Mol Phylogenet Evol 2024; 196:108084. [PMID: 38688440 DOI: 10.1016/j.ympev.2024.108084] [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: 05/31/2023] [Revised: 02/16/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
The tribe Collabieae (Epidendroideae, Orchidaceae) comprises approximately 500 species. Generic delimitation within Collabieae are confusing and phylogenetic interrelationships within the Collabieae have not been well resolved. Plastid genomes and nuclear internal transcribed spacer (ITS) sequences were used to estimate the phylogenetic relationships, ancestral ranges, and diversification rates of Collabieae. The results showed that Collabieae was subdivided into nine clades with high support. We proposed to combine Ancistrochilus and Pachystoma into Spathoglottis, merge Collabium and Chrysoglossum into Diglyphosa, and separate Pilophyllum and Hancockia as distinctive genera. The diversification of the nine clades of Collabieae might be associated with the uplift of the Himalayas during the Late Oligocene/Early Miocene. The enhanced East Asian summer monsoon in the Late Miocene may have promoted the rapid diversification of Collabieae at a sustained high diversification rate. The increased size of terrestrial pseudobulbs may be one of the drivers of Collabieae diversification. Our results suggest that the establishment and development of evergreen broadleaved forests facilitated the diversification of Collabieae.
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Affiliation(s)
- Hong-Yu Ji
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Ye
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yan-Qiong Chen
- College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Jian-Wu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Arief Hidayat
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong, Indonesia
| | - Jiang-Lin Miao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Jian-Yong Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), China
| | - Jun-Wen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Xiao-Hua Jin
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China; China National Botanical Garden, Beijing, China.
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Li B, Huang K, Chen X, Qin C, Zhang X. Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis. BMC Genom Data 2024; 25:57. [PMID: 38858616 PMCID: PMC11165809 DOI: 10.1186/s12863-024-01232-y] [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: 06/29/2023] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
The Quercus L. species is widely recognized as a significant group in the broad-leaved evergreen forests of tropical and subtropical East Asia. These plants hold immense economic value for their use as firewood, furniture, and street trees. However, the identification of Quercus species is considered challenging, and the relationships between these species remain unclear. In this study, we sequenced and assembled the chloroplast (cp.) genomes of four Quercus section Cyclobalanopsis species (Quercus disciformis, Quercus dinghuensis, Quercus blackei, and Quercus hui). Additionally, we retrieved six published cp. genome sequences of Cyclobalanopsis species (Quercus fleuryi, Quercus pachyloma, Quercus ningangensis, Quercus litseoides, Quercus gilva, and Quercus myrsinifolia). Our aim was to perform comparative genomics and phylogenetic analyses of the cp. whole genome sequences of ten Quercus section Cyclobalanopsis species. The results revealed that: (1) Quercus species exhibit a typical tetrad structure, with the cp. genome lengths of the newly sequenced species (Q. disciformis, Q. dinghuensis, Q. blakei, and Q. hui) being 160,805 bp, 160,801 bp, 160,787 bp, and 160,806 bp, respectively; (2) 469 SSRs were detected, among which A/T base repeats were the most common; (3) no rearrangements or inversions were detected within the chloroplast genomes. Genes with high nucleotide polymorphism, such as rps14-psaB, ndhJ-ndhK, rbcL-accD, and rps19-rpl2_2, provided potential reference loci for molecular identification within the Cyclobalanopsis section; (4) phylogenetic analysis showed that the four sections of Cyclobalanopsis were grouped into sister taxa, with Q. hui being the first to diverge from the evolutionary branch and Q. disciformis being the most closely related to Q. blackei. The results of this study form the basis for future studies on taxonomy and phylogenetics.
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Affiliation(s)
- Buyu Li
- College of Life Science, China West Normal University, Nanchong, 637000, China
| | - Ke Huang
- College of Life Science, China West Normal University, Nanchong, 637000, China
| | - Xiaoli Chen
- College of Life Science, China West Normal University, Nanchong, 637000, China
| | - Chun Qin
- College of Life Science, China West Normal University, Nanchong, 637000, China
| | - Xuemei Zhang
- College of Life Science, China West Normal University, Nanchong, 637000, China.
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Zhang Q, Yang Y, Liu B, Lu L, Sauquet H, Li D, Chen Z. Meta-analysis provides insights into the origin and evolution of East Asian evergreen broad-leaved forests. THE NEW PHYTOLOGIST 2024; 242:2369-2379. [PMID: 38186378 DOI: 10.1111/nph.19524] [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: 08/30/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Evergreen broad-leaved forests (EBLFs) are dominated by a monsoon climate and form a distinct biome in East Asia with notably high biodiversity. However, the origin and evolution of East Asian EBLFs (EAEBLFs) remain elusive despite the estimation of divergence times for various representative lineages. Using 72 selected generic-level characteristic lineages, we constructed an integrated lineage accumulation rate (LAR) curve based on their crown ages. According to the crown-based LAR, the EAEBLF origin was identified at least as the early Oligocene (c. 31.8 million years ago (Ma)). The accumulation rate of the characteristic genera peaked at 25.2 and 6.4 Ma, coinciding with the two intensification periods of the Asian monsoon at the Oligocene - Miocene and the Miocene - Pliocene boundaries, respectively. Moreover, the LAR was highly correlated with precipitation in the EAEBLF region and negatively to global temperature, as revealed through time-lag cross-correlation analyses. An early Oligocene origin is suggested for EAEBLFs, bridging the gap between paleobotanical and molecular dating studies and solving conflicts among previous estimates based on individual representative lineages. The strong correlation between the crown-based LAR and the precipitation brought about by the Asian monsoon emphasizes its irreplaceable role in the origin and development of EAEBLFs.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yuchang Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Limin Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dezhu Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhiduan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
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Liu X, Zhang W, Zhang Y, Yang J, Zeng P, Tian Z, Sun W, Cai J. Chromosome-scale genomes of Quercus sichourensis and Quercus rex provide insights into the evolution and adaptation of Fagaceae. J Genet Genomics 2024; 51:554-565. [PMID: 38575109 DOI: 10.1016/j.jgg.2024.03.012] [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: 12/26/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
The Fagaceae, a plant family with a wide distribution and diverse adaptability, has garnered significant interest as a subject of study in plant speciation and adaptation. Meanwhile, certain Fagaceae species are regarded as highly valuable wood resources due to the exceptional quality of their wood. In this study, we present two high-quality, chromosome-scale genome sequences for Quercus sichourensis (848.75 Mb) and Quercus rex (883.46 Mb). Comparative genomics analysis reveals that the difference in the number of plant disease resistance genes and the nonsynonymous and synonymous substitution ratio (Ka/Ks) of protein-coding genes among Fagaceae species are related to different environmental adaptations. Interestingly, most genes related to starch synthesis in the investigated Quercoideae species are located on a single chromosome, as compared to the outgroup species, Fagus sylvatica. Furthermore, resequencing and population analysis of Q. sichourensis and Q. rex reveal that Q. sichourensis has lower genetic diversity and higher deleterious mutations compared to Q. rex. The high-quality, chromosome-level genomes and the population genomic analysis of the critically endangered Q. sichourensis and Q. rex will provide an invaluable resource as well as insights for future study in these two species, even the genus Quercus, to facilitate their conservation.
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Affiliation(s)
- Xue Liu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Weixiong Zhang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Yongting Zhang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Jing Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Peng Zeng
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Zunzhe Tian
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Jing Cai
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China.
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Zhu H, Tan Y. The Origin of Evergreen Broad-Leaved Forests in East Asia from the Evidence of Floristic Elements. PLANTS (BASEL, SWITZERLAND) 2024; 13:1106. [PMID: 38674515 PMCID: PMC11054231 DOI: 10.3390/plants13081106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
Arguments about the origin and evolution of the evergreen broad-leaved forests in East Asia exist generally, and are even contradictory in some cases. The origin and evolution of the flora of East Asia, especially in the evolutionary process, the formation time of the Asian monsoon, the implications of phylogenetic and biogeographic studies on some important taxa, and the implications of palaeobotanical evidence are debatable. Most research from different disciplines suggests that the monsoon in the Miocene was key to the diversification of East Asian flora and its evergreen broad-leaved forests. The common view is that the evergreen broad-leaved forests of East Asia are closely related to the monsoon's intensity and developments, which were caused by the uplift of Himalaya-Tibet during or after the mid-Miocene. Analysis of the floristic elements show that the present subtropical evergreen broad-leaved forests in East Asia could have an early or ancient tropical origin and a tropical Asian affinity, but that their species are dominated by endemic Chinese or East Asian ones, many of which have tropical Asian affinity or are tropical sister species. The time of Himalayan uplift and the intensity of the monsoon climate are believed to be key to the formation of the evergreen broad-leaved forests in East Asia. Combined with existing paleobotanical findings, the uplift of the Himalayas and the formation of the monsoon climate, as well as floristic elements of the subtropical evergreen broad-leaved forests, we believe that they evolved from an Asian tropical rainforest after the mid-Miocene in the southeastern region of East Asia, while the ancient subtropical evergreen broad-leaved forests in the southwestern region continuously evolved into the present subtropical ones.
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Affiliation(s)
- Hua Zhu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan International Joint Laboratory of Southeast Asia Biodiversity Conservation, Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Mengla 666303, China;
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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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Shi J, Xia M, He G, Gonzalez NCT, Zhou S, Lan K, Ouyang L, Shen X, Jiang X, Cao F, Li H. Predicting Quercus gilva distribution dynamics and its response to climate change induced by GHGs emission through MaxEnt modeling. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 357:120841. [PMID: 38581898 DOI: 10.1016/j.jenvman.2024.120841] [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: 12/18/2023] [Revised: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
Quercus gilva, an evergreen tree species in Quercus section Cyclobalanopsis, is an ecologically and economically valuable species in subtropical regions of East Asia. Predicting the impact of climate change on potential distribution of Q. gilva can provide a scientific basis for the conservation and utilization of its genetic resources, as well as for afforestation. In this study, 74 distribution records of Q. gilva and nine climate variables were obtained after data collection and processing. Current climate data downloaded from WorldClim and future climate data predicted by four future climate scenarios (2040s SSP1-2.6, 2040s SSP5-8.5, 2060s SSP1-2.6, and 2060s SSP5-8.5) mainly based on greenhouse gases emissions of distribution sites were used in MaxEnt model with optimized parameters to predict distribution dynamics of Q. gilva and its response to climate change. The results showed that the predicted current distribution was consistent with natural distribution of Q. gilva, which was mainly located in Hunan, Jiangxi, Zhejiang, Fujian, Guizhou, and Taiwan provinces of China, as well as Japan and Jeju Island of South Korea. Under current climate conditions, precipitation factors played a more significant role than temperature factors on distribution of Q. gilva, and precipitation of driest quarter (BIO17) is the most important restriction factor for its current distribution (contribution rate of 57.35%). Under future climate conditions, mean temperature of driest quarter (BIO9) was the essential climate factor affecting future change in potential distribution of Q. gilva. As the degree of climatic anomaly increased in the future, the total area of predicted distribution of Q. gilva showed a shrinking trend (decreased by 12.24%-45.21%) and Q. gilva would migrate to high altitudes and latitudes. The research results illustrated potential distribution range and suitable climate conditions of Q. gilva, which can provide essential theoretical references for the conservation, development, and utilization of Q. gilva and other related species.
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Affiliation(s)
- Jingye Shi
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Muxuan Xia
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Guoqin He
- Bangor College China, a Joint Unit of Bangor University and Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Norela C T Gonzalez
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Sheng Zhou
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Kun Lan
- Bangor College China, a Joint Unit of Bangor University and Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Lei Ouyang
- Fujian Academy of Forestry, Fuzhou, 350012, Fujian, China
| | - Xiangbao Shen
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Xiaolong Jiang
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - He Li
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.
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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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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: 2] [Impact Index Per Article: 2.0] [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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12
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Lin L, Jiang XL, Guo KQ, Byrne A, Deng M. Climate change impacts the distribution of Quercus section Cyclobalanopsis (Fagaceae), a keystone lineage in East Asian evergreen broadleaved forests. PLANT DIVERSITY 2023; 45:552-568. [PMID: 37936812 PMCID: PMC10625921 DOI: 10.1016/j.pld.2023.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 11/09/2023]
Abstract
East Asian evergreen broadleaved forests (EBFLs) harbor high species richness, but these ecosystems are severely impacted by global climate change and deforestation. Conserving and managing EBLFs requires understanding dominant tree distribution dynamics. In this study, we used 29 species in Quercus section Cyclobalanopsis-a keystone lineage in East Asian EBLFs-as proxies to predict EBLF distribution dynamics using species distribution models (SDMs). We examined climatic niche overlap, similarity, and equivalency among seven biogeographical regions' species using 'ecospat'. We also estimated the effectiveness of protected areas in the predicted range to elucidate priority conservation regions. Our results showed that the climatic niches of most geographical groups differ. The western species under the Indian summer monsoon regime were mainly impacted by temperature factors, whereas precipitation impacted the eastern species under the East Asian summer monsoon regime. Our simulation predicted a northward range expansion of section Cyclobalanopsis between 2081 and 2100, except for the ranges of the three Himalayan species analyzed, which might shrink significantly. The greatest shift of highly suitable areas was predicted for the species in the South Pacific, with a centroid shift of over 300 km. Remarkably, only 7.56% of suitable habitat is currently inside protected areas, and the percentage is predicted to continue declining in the future. To better conserve Asian EBLFs, establishing nature reserves in their northern distribution ranges, and transplanting the populations with predicted decreasing numbers and degraded habitats to their future highly suitable areas, should be high-priority objectives.
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Affiliation(s)
- Lin Lin
- School of Ecology and Environmental Sciences, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming 650500, Yunnan, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of BioResources in Yunnan, Yunnan University, Kunming 650500, Yunnan, China
| | - Xiao-Long Jiang
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Kai-Qi Guo
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
- Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Amy Byrne
- The Morton Arboretum, Lile, IL 60532-1293, USA
| | - Min Deng
- School of Ecology and Environmental Sciences, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming 650500, Yunnan, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of BioResources in Yunnan, Yunnan University, Kunming 650500, Yunnan, China
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13
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Chen Z, Zhou Z, Guo ZM, Van Do T, Sun H, Niu Y. Historical development of karst evergreen broadleaved forests in East Asia has shaped the evolution of a hemiparasitic genus Brandisia (Orobanchaceae). PLANT DIVERSITY 2023; 45:501-512. [PMID: 37936821 PMCID: PMC10625920 DOI: 10.1016/j.pld.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/14/2023] [Accepted: 03/17/2023] [Indexed: 11/09/2023]
Abstract
Brandisia is a shrubby genus of about eight species distributed basically in East Asian evergreen broadleaved forests (EBLFs), with distribution centers in the karst regions of Yunnan, Guizhou, and Guangxi in southwestern China. Based on the hemiparasitic and more or less liana habits of this genus, we hypothesized that its evolution and distribution were shaped by the development of EBLFs there. To test our hypothesis, the most comprehensive phylogenies of Brandisia hitherto were constructed based on plastome and nuclear loci (nrDNA, PHYA and PHYB); then divergence time and ancestral areas were inferred using the combined nuclear loci dataset. Phylogenetic analyses reconfirmed that Brandisia is a member of Orobanchaceae, with unstable placements caused by nuclear-plastid incongruences. Within Brandisia, three major clades were well supported, corresponding to the three subgenera based on morphology. Brandisia was inferred to have originated in the early Oligocene (32.69 Mya) in the Eastern Himalayas-SW China, followed by diversification in the early Miocene (19.45 Mya) in karst EBLFs. The differentiation dates of Brandisia were consistent with the origin of keystone species of EBLFs in this region (e.g., Fagaceae, Lauraceae, Theaceae, and Magnoliaceae) and the colonization of other characteristic groups (e.g., Gesneriaceae and Mahonia). These findings indicate that the distribution and evolution of Brandisia were facilitated by the rise of the karst EBLFs in East Asia. In addition, the woody and parasitic habits, and pollination characteristics of Brandisia may also be the important factors affecting its speciation and dispersal.
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Affiliation(s)
- Zhe Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Ze-Min Guo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay 10000, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay 10000, Hanoi, Vietnam
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Yang Niu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
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14
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Liu XY, Song HZ, Wu XK, Hu JR, Huang WY, Quan C, Jin JH. Late Oligocene fossil acorns and nuts of Quercus section Cyclobalanopsis from the Nanning Basin, Guangxi, South China. PLANT DIVERSITY 2023; 45:434-445. [PMID: 37601538 PMCID: PMC10435911 DOI: 10.1016/j.pld.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 07/15/2022] [Accepted: 08/12/2022] [Indexed: 08/22/2023]
Abstract
Quercus is the largest genus within the Fagaceae and has a rich fossil record. Most of the fossil material is attributed to the subgenus Quercus based on leaves, pollen or rarely acorns and nuts. Fossil records of Q. section Cyclobalanopsis characterized by ring-cupped acorns are relatively few and especially those described based on nuts are scant. In this study, we described four new species of Quercus section Cyclobalanopsis based on mummified acorns and nuts: Q. paleodisciformis X.Y. Liu et J.H. Jin sp. nov., Q. paleohui X.Y. Liu et J.H. Jin sp. nov., Q. nanningensis X.Y. Liu et J.H. Jin sp. nov. and Q. yongningensis X.Y. Liu et J.H. Jin sp. nov. These species closely resemble the extant species Q. disciformis, Q. hui, Q. kerrii, and Q. dinghuensis. The occurrence of Q. section Cyclobalanopsis in the Oligocene stratum of Guangxi, South China, suggests that the section has diversified within its extant distribution center since the Oligocene. By combining records from other areas, we propose that the section first appeared in the middle Eocene of East Asia (Sino-Japan), has diversified in situ with a few elements scattering into West Asia and southern Europe since the Oligocene and Pliocene, respectively, and finally became restricted in East Asia since the Pleistocene. This indicates that the section originated and diversified in East Asia, before spreading into West Asia no later than the Oligocene and into southern Europe by the Pliocene. Subsequently it disappeared from South Europe and West Asia due to the appearance of the (summer dry) Mediterranean climate and widespread cooling during the Pleistocene.
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Affiliation(s)
- Xiao-Yan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- School of Geography, South China Normal University, Guangzhou 510631, China
| | - Han-Zhang Song
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xin-Kai Wu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Jia-Rong Hu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei-Ye Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Cheng Quan
- School of Earth Science and Resources, Chang'an University, Xi'an 710054, China
| | - Jian-Hua Jin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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15
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Tóth EG, Cseke K, Benke A, Lados BB, Tomov VT, Zhelev P, Kámpel JD, Borovics A, Köbölkuti ZA. Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data. Heredity (Edinb) 2023:10.1038/s41437-023-00629-2. [PMID: 37316726 PMCID: PMC10382515 DOI: 10.1038/s41437-023-00629-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023] Open
Abstract
Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north-southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4-16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.
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Affiliation(s)
- Endre Gy Tóth
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Botond B Lados
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Vladimir T Tomov
- Department of Landscape Architecture, Faculty of Ecology and Landscape Architecture, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - Petar Zhelev
- Department of Dendrology, Faculty of Forestry, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - József D Kámpel
- Ottó Herman Environmental and Agricultural Technical School, Vocational School and College (Agricultural Vocational Centre of the Kisalföld Region), Ernuszt Kelemen 1, Szombathely, 9700, Hungary
| | - Attila Borovics
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Zoltán A Köbölkuti
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
- Departement of Applied Forest Genetics Research, Bavarian Office for Forest Genetics (AWG), Forstamtsplatz 1, Teisendorf, 83317, Germany
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16
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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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17
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Zan T, He YT, Zhang M, Yonezawa T, Ma H, Zhao QM, Kuo WY, Zhang WJ, Huang CH. Phylogenomic analyses of Camellia support reticulate evolution among major clades. Mol Phylogenet Evol 2023; 182:107744. [PMID: 36842731 DOI: 10.1016/j.ympev.2023.107744] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023]
Abstract
Camellia (Theaceae) is a morphologically highly diverse genus of flowering plants and includes many famous species with high economic value, and the phylogeny of this genus is not fully resolved. We used 95 transcriptomes from 87 Camellia species and identified 1481 low-copy genes to conduct a detailed analysis of the phylogeny of this genus according to various data-screening criteria. The results show that, very different from the two existing classification systems of Camellia, 87 species are grouped into 8 main clades and two independent species, and that all 8 clades except Clade 8 were strongly supported by almost all the coalescent or concatenated trees using different gene subsets. However, the relationships among these clades were weakly supported and different from analyses using different gene subsets; furthermore, they do not agree with the phylogeny from chloroplast genomes of Camellia. Additional analyses support reticulate evolution (probably resulting from introgression or hybridization) among some major Camellia lineages, providing explanation for extensive gene tree conflicts. Furthermore, we inferred that together with the formation of East Asian subtropical evergreen broad-leaved forests, Camellia underwent a radiative divergence of major clades at 23 ∼ 19 Ma in the late Miocene then had a subsequent species burst at 10 ∼ 5 Ma. Principal component and cluster analyses provides new insights into morphological changes underlying the evolution of Camellia and a reference to further clarify subgenus and sections of this genus. The comprehensive study here including a nuclear phylogeny and other analyses reveal the rapid evolutionary history of Camellia.
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Affiliation(s)
- Ting Zan
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Yi-Tao He
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi, Kanagawa 14 243-0034, Japan.
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
| | - Qiang-Min Zhao
- Guangzhou Zongke Horticulture Development Co., Ltd., Guangzhou 511300, China.
| | - Wen-Yu Kuo
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Wen-Ju Zhang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Chien-Hsun Huang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
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18
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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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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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20
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Lyu R, Xiao J, Li M, Luo Y, He J, Cheng J, Xie L. Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data. Int J Mol Sci 2023; 24:3056. [PMID: 36769378 PMCID: PMC9917980 DOI: 10.3390/ijms24033056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/29/2023] [Indexed: 02/09/2023] Open
Abstract
The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.
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Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Mingyang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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21
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Du ZY, Jenny Xiang QY, Cheng J, Zhou W, Wang QF, Soltis DE, Soltis PS. An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data. AMERICAN JOURNAL OF BOTANY 2023; 110:e16116. [PMID: 36480351 DOI: 10.1002/ajb2.16116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
PREMISE A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group. METHODS We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis. RESULTS A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode. CONCLUSIONS Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.
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Affiliation(s)
- Zhi-Yuan Du
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jin Cheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qing-Feng Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611 FL, USA
- Department of Biology, University of Florida, Gainesville, 32611 FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611 FL, USA
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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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Xie C, Tian E, Jim CY, Liu D, Hu Z. Effects of climate-change scenarios on the distribution patterns of Castanea henryi. Ecol Evol 2022; 12:e9597. [PMID: 36514555 PMCID: PMC9731913 DOI: 10.1002/ece3.9597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Castanea henryi, with edible nuts and timber value, is a key tree species playing essential roles in China's subtropical forest ecosystems. However, natural and human perturbations have nearly depleted its wild populations. The study identified the dominant environmental variables enabling and limiting its distribution and predicted its suitable habitats and distribution. The 212 occurrence records covering the whole distribution range of C. henryi in China and nine main bioclimatic variables were selected for detailed analysis. We applied the maximum entropy model (MaxEnt) and QGIS to predict potentially suitable habitats under the current and four future climate-change scenarios. The limiting factors for distribution were accessed by Jackknife, percent contribution, and permutation importance. We found that the current distribution areas were concentrated in the typical subtropical zone, mainly Central and South China provinces. The modeling results indicated temperature as the critical determinant of distribution patterns, including mean temperature of the coldest quarter, isothermality, and mean diurnal range. Winter low temperature imposed an effective constraint on its spread. Moisture served as a secondary factor in species distribution, involving precipitation seasonality and annual precipitation. Under future climate-change scenarios, excellent habitats would expand and shift northwards, whereas range contraction would occur on the southern edge. Extreme climate change could bring notable range shrinkage. This study provided a basis for protecting the species' germplasm resources. The findings could guide the management, cultivation, and conservation of C. henryi, assisted by a proposed three-domain operation framework: preservation areas, loss areas, and new areas, each to be implemented using tailor-made strategies.
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Affiliation(s)
- Chunping Xie
- College of Science Qiongtai Normal University Haikou China
| | - Erlin Tian
- College of Science Qiongtai Normal University Haikou China
| | - Chi Yung Jim
- Department of Social Sciences Education University of Hong Kong Tai Po Hong Kong China
| | - Dawei Liu
- Nanjing Forest Police College Nanjing China
| | - Zhaokai Hu
- Guangdong Ocean University Zhanjiang China
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Ye JW, Tian B, Li DZ. Monsoon intensification in East Asia triggered the evolution of its flora. FRONTIERS IN PLANT SCIENCE 2022; 13:1046538. [PMID: 36507402 PMCID: PMC9733597 DOI: 10.3389/fpls.2022.1046538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION East Asia (EA), which falls within the region of the Asian monsoon that is composed of the East Asia monsoon (EAM) and the Indian monsoon (IM), is known for its high species diversity and endemism. This has been attributed to extreme physiographical heterogeneity in conjunction with climate and sea-level changes during the Pleistocene, this hypothesis has been widely proven by phylogeographic studies. Recently, dated phylogenies have indicated that the origins (stem age) of the flora occurred after the Oligocene-Miocene boundary and are related to the establishment of the EAM. METHODS Hence, this study further examined whether the strengthening of the monsoons triggered floral evolution via a meta-analysis of the tempo-spatial pattern of evolutionary radiation dates (crown ages) of 101 endemic seed plant genera. RESULTS Taxonomic diversification began during the late Eocene, whereas the accumulated number of diversifications did not significantly accelerate until the late Miocene. The distribution of the weighted mean and the average divergence times in the EAM, IM, or transitional regions all fall within the mid-late Miocene. Fossils of the Tertiary relict genera are mostly and widely distributed outside EA and only half of the earliest fossils in the EA region are not older than Miocene, while their divergence times are mostly after the late Miocene. The pattern of divergence time of monotypic and polytypic taxa suggest the climatic changes after the late Pliocene exert more influence on monotypic taxa. DISCUSSION The two key stages of floral evolution coincide with the intensifications of the EAM and IM, especially the summer monsoon which brings a humid climate. An integrated review of previous studies concerning flora, genus, and species levels further supports our suggestion that monsoon intensification in EA triggered the evolution of its flora.
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Affiliation(s)
- Jun-Wei Ye
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Bin Tian
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Liu D, Xie X, Tong B, Zhou C, Qu K, Guo H, Zhao Z, El-Kassaby YA, Li W, Li W. A high -quality genome assembly and annotation of Quercus acutissima Carruth. FRONTIERS IN PLANT SCIENCE 2022; 13:1068802. [PMID: 36507419 PMCID: PMC9729791 DOI: 10.3389/fpls.2022.1068802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered as an excellent tree for soil and water conservation. METHODS Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble Q. acutissima genome. RESULTS We generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome. Ab initio, homology-based and RNA sequence-based gene prediction identified 29,889 protein-coding genes, of which 82.6% could be functionally annotated. Phylogenetic analysis showed that Q. acutissima and Q. variabilis were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication. CONCLUSION The assembled and annotated high-quality Q. acutissima genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.
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Affiliation(s)
- Dan Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Xiaoman Xie
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Chengcheng Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai Qu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Haili Guo
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Zhiheng Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Wei Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wenqing Li
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
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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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Ye J, Li D. Diversification of East Asian subtropical evergreen broadleaved forests over the last 8 million years. Ecol Evol 2022; 12:e9451. [PMID: 36329812 PMCID: PMC9618824 DOI: 10.1002/ece3.9451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
The evolution of subtropical evergreen broadleaved forests (EBLFs) in East Asia is interesting while complicated. Genus-level phylogenies indicate that the origins of EBLFs could trace back to the Oligocene-Miocene boundary or even the Eocene, while population-level phylogeographic evidence suggests that they diversified after the Miocene, particularly in the Pleistocene. Here, we review the origins of dominant plant species to better understand the evolution of EBLFs. We compiled published estimates of the timing of origin of dominant species and diversification of evergreen relict genera from East Asian EBLFs. We also traced and visualized the evolution of EBLFs in the region using dated phylogenies and geographic distributions of the reviewed taxa. Most (76.1%) of the dominant species originated after the late Miocene, ca. 8 million years ago. Of the 10 evergreen relict genera, eight diverged near the late Miocene-Pliocene boundary or during the late Pliocene, and the remaining two diverged during the Pleistocene. Over the past 8 million years, geo-climatic changes have triggered origins of most of the dominant EBLF species and provided refugia for evergreen relict genera. Three pulsed phases of evolution are suggested by genetic studies at the genus, species, and population levels. Fossil evidence and spatiotemporal investigations should be integrated to fully understand the evolution of EBLFs in East Asia.
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Affiliation(s)
- Jun‐Wei Ye
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of EducationSouthwest Forestry UniversityKunmingChina
| | - De‐Zhu Li
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
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28
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Hai L, Li XQ, Zhang JB, Xiang XG, Li RQ, Jabbour F, Ortiz RDC, Lu AM, Chen ZD, Wang W. Assembly dynamics of East Asian subtropical evergreen broadleaved forests: New insights from the dominant Fagaceae trees. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2126-2134. [PMID: 36083596 DOI: 10.1111/jipb.13361] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
The dominant species of a biome can be regarded as its genuine indicator. Evergreen broadleaved forests (EBLFs) in subtropical East Asia harbor high levels of species biodiversity and endemism and are vital to regional carbon storage and cycling. However, the historical assembly of this unique biome is still controversial. Fagaceae is the most essential family in East Asian subtropical EBLFs and its dominant species are vital for the existence of this biome. Here, we used the dominant Fagaceae species to shed light on the dynamic process of East Asian subtropical EBLFs over time. Our results indicate high precipitation in summer and low temperature in winter are the most influential climatic factors for the distribution of East Asian subtropical EBLFs. Modern East Asian subtropical EBLFs did not begin to appear until 23 Ma, subsequently experienced a long-lasting development in the Miocene and markedly deteriorated at about 4 Ma, driven jointly by orogenesis and paleoclimate. We also document that there is a lag time between when one clade invaded the region and when its members become dominant species within the region. This study may improve our ability to predict and mitigate the threats to biodiversity of East Asian subtropical EBLFs and points to a new path for future studies involving multidisciplinary methods to explore the assembly of regional biomes.
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Affiliation(s)
- Lisi Hai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Qian Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing-Bo Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, 75005, France
| | | | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Corrales A, Koch RA, Vasco-Palacios AM, Smith ME, Ge ZW, Henkel TW. Diversity and distribution of tropical ectomycorrhizal fungi. Mycologia 2022; 114:919-933. [PMID: 36194092 DOI: 10.1080/00275514.2022.2115284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
The tropics were long considered to have few ectomycorrhizal fungi, presumably due to a paucity of ectomycorrhizal host plants relative to higher-latitude ecosystems. However, an increase in research in tropical regions over the past 30 years has greatly expanded knowledge about the occurrence of tropical ectomycorrhizal fungi. To assess their broad biogeographic and diversity patterns, we conducted a comprehensive review and quantitative data analysis of 49 studies with 80 individual data sets along with additional data from GlobalFungi to elucidate tropical diversity patterns and biogeography of ectomycorrhizal fungi across the four main tropical regions: the Afrotropics, the Neotropics, Southeast Asia, and Oceania. Generalized linear models were used to explore biotic and abiotic influences on the relative abundance of the 10 most frequently occurring lineages. We also reviewed the available literature and synthesized current knowledge about responses of fungi to anthropogenic disturbances, and their conservation status and threats. We found that /russula-lactarius and /tomentella-thelephora were the most abundant lineages in the Afrotropics, the Neotropics, and Southeast Asia, whereas /cortinarius was the most abundant lineage in Oceania, and that /russula-lactarius, /inocybe, and /tomentella-thelephora were the most species-rich lineages across all of the tropical regions. Based on these analyses, we highlight knowledge gaps for each tropical region. Increased sampling of tropical regions, collaborative efforts, and use of molecular methodologies are needed for a more comprehensive view of the ecology and diversity of tropical ectomycorrhizal fungi.
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Affiliation(s)
- Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Carrera 26 # 63B - 48, Bogotá 111221, Colombia
| | - Rachel A Koch
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd., Storrs, Connecticut 06269, USA
| | - Aída M Vasco-Palacios
- Grupo BioMicro y de Microbiología Ambiental, Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-2, Medellín, Colombia. Asociación Colombiana de Micología, ASCOLMIC
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, 2550 Hull Road, Gainesville, Florida 32611, USA
| | - Zai-Wei Ge
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Kunming 650201, China
| | - Terry W Henkel
- Department of Biological Sciences, California State Polytechnic University, Humboldt, 1 Harpst St., Arcata, California 95521, USA
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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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Zhao N, Park S, Zhang YQ, Nie ZL, Ge XJ, Kim S, Yan HF. Fingerprints of climatic changes through the late Cenozoic in southern Asian flora: Magnolia section Michelia (Magnoliaceae). ANNALS OF BOTANY 2022; 130:41-52. [PMID: 35460565 PMCID: PMC9295916 DOI: 10.1093/aob/mcac057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Ongoing global warming is a challenge for humankind. A series of drastic climatic changes have been proven to have occurred throughout the Cenozoic based on a variety of geological evidence, which helps to better understand our planet's future climate. Notably, extant biomes have recorded drastic environmental shifts. The climate in southern Asia, which hosts high biodiversity, is deeply impacted by the Asian monsoon. The origins and evolutionary dynamics of biomes occurring between the tropics and sub-tropics in southern Asia have probably been deeply impacted by climatic changes; however, these aspects remain poorly studied. We tested whether the evolutionary dynamics of the above biomes have recorded the drastic, late Cenozoic environmental shifts, by focusing on Magnolia section Michelia of the family Magnoliaceae. METHODS We established a fine time-calibrated phylogeny of M. section Michelia based on complete plastid genomes and inferred its ancestral ranges. Finally, we estimated the evolutionary dynamics of this section through time, determining its diversification rate and the dispersal events that occurred between tropical and sub-tropical areas. KEY RESULTS The tropical origin of M. section Michelia was dated to the late Oligocene; however, the diversification of its core group (i.e. M. section Michelia subsection Michelia) has occurred mainly from the late Miocene onward. Two key evolutionary shifts (dated approx. 8 and approx. 3 million years ago, respectively) were identified, each of them probably in response to drastic climatic changes. CONCLUSION Here, we inferred the underlying evolutionary dynamics of biomes in southern Asia, which probably reflect late Cenozoic climatic changes. The occurrence of modern Asian monsoons was probably fundamental for the origin of M. section Michelia; moreover, the occurrence of asymmetric dispersal events between the tropics and sub-tropics hint at an adaptation strategy of M. section Michelia to global cooling, in agreement with the tropical conservatism hypothesis.
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Affiliation(s)
| | | | - Yu-Qu Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi’an 712046, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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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: 10] [Impact Index Per Article: 5.0] [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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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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Menolli N, Sánchez-Ramírez S, Sánchez-García M, Wang C, Patev S, Ishikawa NK, Mata JL, Lenz AR, Vargas-Isla R, Liderman L, Lamb M, Nuhn M, Hughes KW, Xiao Y, Hibbett DS. Global phylogeny of the Shiitake mushroom and related Lentinula species uncovers novel diversity and suggests an origin in the Neotropics. Mol Phylogenet Evol 2022; 173:107494. [PMID: 35490968 DOI: 10.1016/j.ympev.2022.107494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 01/18/2023]
Abstract
Lentinula (Basidiomycota, Agaricales) includes the most widely cultivated mushroom in the world, Lentinula edodes, also known as shiitake (Japanese) or xiang-gu (Chinese). At present, nine species are recognized in the genus, based on morphology, mating criteria, and geographic distributions. However, analyses of internal transcribed spacers (ITS) of ribosomal RNA genes have suggested that there are cryptic lineages. We analyzed a global-scale phylogenetic dataset from 325 Lentinula individuals from 24 countries in Asia-Australasia and the Americas plus Madagascar, with 325 sequences of ITS, 80 LSU sequences, and 111 sequences of translation elongation factor (tef1-α) genes. We recovered 15 independent lineages (Groups 1-15) that may correspond to species. Lineages in Asia-Australasia (Groups 1-5) and the Americas plus Madagascar (Groups 6-15) formed sister clades. Four lineages are represented only by sequences from single individuals and require further molecular sampling, including L. aff. raphanica (Group 7), L. ixodes (Group 8), L. boryana (Group 12), and L. aff. aciculospora (Group 14). Groups 1 and 5 are here referred to L. edodes and L. aff. edodes, respectively. However, these groups most likely represent the same species and are only recognized as (unsupported) monophyletic lineages by maximum likelihood analyses of ITS alone. Other putative species resolved here include L. lateritia (Group 2), L. novae-zelandieae (Group 3), L. aff. lateritia (Group 4), L. raphanica (Group 6), L. aff. detonsa (Group 9), L. detonsa (Group 10), L. guzmanii sp. nov. (Group 11), L. aciculospora (Group 13), and L. madagasikarensis (Group 15). Groups 9-12 represent the "L. boryana complex". Molecular clock and historical biogeographic analyses suggest that the most recent common ancestor (MRCA) of Lentinula can be placed in the middle Oligocene, ca. 30 million years ago (Ma), and had a likely presence in neotropical America. The MRCA of Lentinula in the Americas and Madagascar lived ca. 22 Ma in the Neotropics and the MRCA of Lentinula in Asia-Australasia lived ca. 6 Ma in Oceania. Given the current knowledge about plate tectonics and paleoclimatic models of the last 30 Myr, our phylogenetic hypothesis suggests that the extant distribution of Lentinula is likely to have arisen, in large part, due to long-distance dispersal. Lentinula collections include at least four dubious taxa that need further taxonomic studies: L. reticeps from the USA (Ohio); L. guarapiensis from Paraguay; Lentinus puiggarii from Brazil (São Paulo); and "L. platinedodes" from Vietnam. Approximately ten of the fifteen Groups are reported on Fagaceae, which appears to be the ancestral substrate of Lentinula.
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Affiliation(s)
- Nelson Menolli
- IFungiLab, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Departamento de Ciências da Natureza e Matemática (DCM) / Subárea de Biologia (SAB), Rua Pedro Vicente 625, São Paulo, SP 01109-010, Brazil.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada
| | - Marisol Sánchez-García
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-75005, Sweden
| | - Chaoqun Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou 510070, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sean Patev
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Noemia Kazue Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Juan L Mata
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alexandre Rafael Lenz
- Departamento de Ciências Exatas e da Terra, Colegiado de Sistemas de Informação, Campus I, Universidade do Estado da Bahia (UNEB), Salvador, BA, Brazil
| | - Ruby Vargas-Isla
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Lauren Liderman
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Meriel Lamb
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Mitchell Nuhn
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Karen W Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - David S Hibbett
- Biology Department, Clark University, Worcester, MA 01610, USA
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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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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] [Key Words] [MESH Headings] [Grants] [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.
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Affiliation(s)
- Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Andrew A Crowl
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Paul S Manos
- Department of Biology, Duke University, Durham, NC, 27708, USA.
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 510650, Guangzhou, China.
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Xiao TW, Yan HF, Ge XJ. Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests. BMC PLANT BIOLOGY 2022; 22:32. [PMID: 35027008 PMCID: PMC8756638 DOI: 10.1186/s12870-021-03413-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/17/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential plant groups, the tribe Perseeae (Lauraceae). RESULTS Our plastid tree topologies were robust to analyses based on different plastid regions and different strategies for data partitioning, nucleotide substitution saturation, and gap handling. We found that tribe Perseeae comprised six major clades and began to colonize the subtropical EBLFs of East Asia in the early Miocene. The diversification rates of tribe Perseeae accelerated twice in the late Miocene. CONCLUSIONS Our findings suggest that the intensified precipitation in East Asia in the early Miocene may have facilitated range expansions of the subtropical EBLFs and establishment of tribe Perseeae within this biome. By the late Miocene, species assembly and diversification within the EBLFs had become rapid.
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Affiliation(s)
- Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
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Phylotranscriptomics reveals the evolutionary history of subtropical East Asian white pines: further insights into gymnosperm diversification. Mol Phylogenet Evol 2022; 168:107403. [PMID: 35031461 DOI: 10.1016/j.ympev.2022.107403] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/15/2021] [Accepted: 12/25/2021] [Indexed: 11/20/2022]
Abstract
Floristic composition within a geographic area is driven by a wide array of factors from local biotic interactions to biogeographical processes. Subtropical East Asia is a key biodiversity hotspot of the world, and harbors the most families of extant gymnosperms and a large number of endemic genera with ancient origins, but rare phylogenetic studies explored whether it served as a diversification center for gymnosperms. Here, we investigated the evolutionary and biogeographical history of subtropical East Asian white pines using an integrative approach that combines phylotranscriptomic and ecological analyses. Using 2,606 orthologous nuclear genes, we reconstructed a fully resolved and dated phylogeny of these species. Two main clades first diverged in the early Miocene, and by the late Miocene, all species appeared. Two white pines endemic to Taiwan Island experienced independent colonization events and regional extinction, which resulted in the present disjunctive distribution from mainland China. Ecological and biogeographical analyses indicate that the monsoon-driven assembly of evergreen broadleaved forests (EBLFs) might have significantly affected the diversification of subtropical East Asian white pines. Our study highlights the interactions of biotic and abiotic forces in the diversification and speciation of subtropical East Asian white pines. These findings indicate that subtropical East Asia is not only a floristic museum, but also a diversification center for gymnosperms. Our study also demonstrates the importance of phylotranscriptomics on species delimitation and biodiversity conservation, particularly for closely related species.
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Chen S, Zhang W, Li Y, Ge X, Zhou X, Hu Y, Ding H. The complete chloroplast genome sequence of Quercus sessilifolia Blume (Fagaceae). Mitochondrial DNA B Resour 2022; 7:182-184. [PMID: 35028413 PMCID: PMC8751490 DOI: 10.1080/23802359.2021.2017366] [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] [Indexed: 11/23/2022] Open
Abstract
Quercus sessilifolia Blume is one of the dominant tree species in East Asian evergreen broadleaved forests. In this study, we assembled and characterized the plastome of Q. sessilifolia using Illumina paired-end data. The circular genome is 160,813 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,862 bp, one large single-copy (LSC) region of 90,218 bp, and one small single-copy (SSC) region of 18,871 bp. It encodes a total of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 28 chloroplast genome sequences indicated that Q. sessilifolia was most closely related to Q. myrsinifolia with 90% bootstrap support.
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Affiliation(s)
- Shuifei Chen
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Wenwen Zhang
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - 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, China
| | - Xiaomin Ge
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Xu Zhou
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Yaping Hu
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Hui Ding
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, 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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Wen H, Luo T, Wang Y, Wang S, Liu T, Xiao N, Zhou J. Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China. Integr Zool 2021; 17:311-325. [PMID: 34958525 DOI: 10.1111/1749-4877.12624] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modern accumulations of genetic data offer unprecedented opportunities for understanding the systematic classification and origins of specific groups of organisms. The genus Sinocyclocheilus is among the most cave abundant genera in Cyprinidae, with 76 recognized species, belonging to four species groups. Recent phylogenetic studies have shown that the classification of species groups within the genus Sinocyclocheilus remains controversial. In this study, we constructed a sequence supermatrix of 26 species from four species groups of the genus Sinocyclocheilus using the mitochondrial genome to reveal phylogenetic relationships, historical biogeography and patterns of species diversification in the genus Sinocyclocheilus. Phylogenetic analysis strongly supports the monophyletic groups of the three species groups (S. jii, S. cyphotergous, and S. tingi groups) except the S. angularis group. Phylogenetic analysis showed that S. anshuiensis and S. microphthalmus, which were recognized as numbers of S. angularis group, formed a strongly supported independent clade. Therefore, we propose a new species group, the S. microphthalmus group, which contains S. anshuiensis and S. microphthalmus. Biogeographic reconstruction suggests that the living Sinocyclocheilus may have originated in north-central Guangxi at the late Eocene and dispersed outward after a vicariance at 32.31 Million years ago (Ma). Early diversification is focused on the late Oligocene (ca. 25 Ma), which is related to the second uplift of the Qinghai-Tibetan Plateau and the lateral extrusion of the Indochina at the Oligocene/Miocene boundary. Our results suggest that two uplifts of the Qinghai-Tibetan Plateau and climate change in the Miocene may have influenced the diversification of the Sinocyclocheilus lineage. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Huamei Wen
- School of Life Sciences, Central China Normal University, Wuhan, China.,School of Karst Sciences, Guizhou Normal University, Guiyang, China
| | - Tao Luo
- School of Karst Sciences, Guizhou Normal University, Guiyang, China
| | - Yali Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Siwei Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Tao Liu
- Liupanshui No. 4 Higth School, Liupanshui, China
| | - Ning Xiao
- Guiyang Nursing Vocational College, Guiyang, China
| | - Jiang Zhou
- School of Karst Sciences, Guizhou Normal University, Guiyang, China
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Wang W, Xiang XG, Xiang KL, Ortiz RDC, Jabbour F, Chen ZD. A dated phylogeny of Lardizabalaceae reveals an unusual long-distance dispersal across the Pacific Ocean and the rapid rise of East Asian subtropical evergreen broadleaved forests in the late Miocene. Cladistics 2021; 36:447-457. [PMID: 34618951 DOI: 10.1111/cla.12414] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2020] [Indexed: 01/08/2023] Open
Abstract
Temperate South American-Asian disjunct distributions are the most unusual in organisms, and challenging to explain. Here, we address the origin of this unusual disjunction in Lardizabalaceae using explicit models and molecular data. The family (c.40 species distributed in ten genera) also provides an opportunity to explore the historical assembly of East Asian subtropical evergreen broadleaved forests, a typical and luxuriant vegetation in East Asia. DNA sequences of five plastid loci of 42 accessions representing 23 species of Lardizabalaceae (c. 57.5% of estimated species diversity), and 19 species from the six other families of Ranunculales, were used to perform phylogenetic analyses. By dating the branching events and reconstructing ancestral ranges, we infer that extant Lardizabalaceae dated to the Upper Cretaceous of East Asia and that the temperate South American lineage might have split from its East Asian sister group at c. 24.4 Ma. A trans-Pacific dispersal possibly by birds from East Asia to South America is plausible to explain the establishment of the temperate South American-East Asian disjunction in Lardizabalaceae. Diversification rate analyses indicate that net diversification rates of Lardizabalaceae experienced a significant increase around c. 7.5 Ma. Our findings suggest that the rapid rise of East Asian subtropical evergreen broadleaved forests occurred in the late Miocene, associated with the uplift of the Tibetan Plateau and the intensified East Asian monsoon, as well as the higher winter temperature and atmospheric CO2 levels.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rosa Del C Ortiz
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63166-0299, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, 57 rue Cuvier, CP39, Paris, 75005, France
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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43
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Li X, Li Y, Sylvester SP, Zang M, El‐Kassaby YA, Fang Y. Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus. Ecol Evol 2021; 11:13401-13414. [PMID: 34646478 PMCID: PMC8495791 DOI: 10.1002/ece3.8063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein-coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein-coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH-psbA, trnK_UUU-rps16, trnfM_CAU-rps14, trnS_GCU-trnG_GCC, and atpF-atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.
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Affiliation(s)
- Xuan Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yongfu Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Steven Paul Sylvester
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Mingyue Zang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yanming Fang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
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Genetic Differentiation and Demographic History of Three Cerris Oak Species in China Based on Nuclear Microsatellite Makers. FORESTS 2021. [DOI: 10.3390/f12091164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Knowledge of interspecific divergence and population expansions/contractions of dominant forest trees in response to geological events and climatic oscillations is of major importance to understand their evolution and demography. However, the interspecific patterns of genetic differentiation and spatiotemporal population dynamics of three deciduous Cerris oak species (Q. acutissima, Q. variabilis and Q. chenii) that are widely distributed in China remain poorly understood. In this study, we genotyped 16 nuclear loci in 759 individuals sampled from 44 natural populations of these three sibling species to evaluate the plausible demographical scenarios of the closely related species. We also tested the hypothesis that macro- and microevolutionary processes of the three species had been triggered and molded by Miocene–Pliocene geological events and Quaternary climatic change. The Bayesian cluster analysis showed that Q. acutissima and Q. chenii were clustered in the same group, whereas Q. variabilis formed a different genetic cluster. An approximate Bayesian computation (ABC) analyses suggested that Q. variabilis and Q. acutissima diverged from their most common ancestor around 19.84 Ma, and subsequently Q. chenii diverged from Q. acutissima at about 9.6 Ma, which was significantly associated with the episodes of the Qinghai–Tibetan Plateau (QTP). In addition, ecological niche modeling and population history analysis showed that these three Cerris oak species repeatedly underwent considerable ‘expansion–contraction’ during the interglacial and glacial periods of the Pleistocene, although they have varying degrees of tolerance for the climatic change. Overall, these findings indicated geological and climatic changes during the Miocene–Pliocene and Pleistocene as causes of species divergence and range shifts of dominant tree species in the subtropical and warm temperature areas in China.
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Maslova NP, Karasev EV, Xu SL, Spicer RA, Liu XY, Kodrul TM, Spicer TEV, Jin JH. Variations in morphological and epidermal features of shade and sun leaves of two species: Quercus bambusifolia and Q. myrsinifolia. AMERICAN JOURNAL OF BOTANY 2021; 108:1441-1463. [PMID: 34431508 DOI: 10.1002/ajb2.1706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Microclimatic differences between the periphery and the interior of tree crowns result in a variety of adaptive leaf macromorphological and anatomical features. Our research was designed to reveal criteria for sun/shade leaf identification in two species of evergreen oaks, applicable to both modern and fossil leaves. We compared our results with those in other species similarly studied. METHODS For both Quercus bambusifolia and Q. myrsinifolia (section Cyclobalanopsis), leaves from single mature trees with well-developed crowns were collected in the South China Botanical Garden, Guangzhou, China. We focus on leaf characters often preserved in fossil material. SVGm software was used for macromorphological measurement. Quantitative analyses were performed and box plots generated using R software with IDE Rstudio. Leaf cuticles were prepared using traditional botanical techniques. RESULTS Principal characters for distinguishing shade and sun leaves in the studied oaks were identified as leaf lamina length to width ratio (L/W), and the degree of development of venation networks. For Q. myrsinifolia, shade and sun leaves differ in tooth morphology and the ratio of toothed lamina length to overall lamina length. The main epidermal characters are ordinary cell size and anticlinal wall outlines. For both species, plasticity within shade leaves exceeds that of sun leaves. CONCLUSIONS Morphological responses to sun and shade in the examined oaks are similar to those in other plant genera, pointing to useful generalizations for recognizing common foliar polymorphisms that must be taken into account when determining the taxonomic position of both modern and fossil plants.
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Affiliation(s)
- Natalia P Maslova
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, 117647, Russia
| | - Eugeny V Karasev
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, 117647, Russia
- Kazan Federal University, Kazan, Respublika Tatarstan, 420000, Russia
| | - Sheng-Lan Xu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Robert A Spicer
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, MK7 6AA, UK
| | - Xiao-Yan Liu
- School of Geography, South China Normal University, Guangzhou, 510631, China
| | - Tatiana M Kodrul
- Geological Institute, Russian Academy of Sciences, Moscow, 119017, Russia
| | - Teresa E V Spicer
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Jian-Hua Jin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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Abstract
Quercus species (oaks) have been an integral part of the landscape in the northern hemisphere for millions of years. Their ability to adapt and spread across different environments and their contributions to many ecosystem services is well documented. Human activity has placed many oak species in peril by eliminating or adversely modifying habitats through exploitative land usage and by practices that have exacerbated climate change. The goal of this review is to compile a list of oak species of conservation concern, evaluate the genetic data that is available for these species, and to highlight the gaps that exist. We compiled a list of 124 Oaks of Concern based on the Red List of Oaks 2020 and the Conservation Gap Analysis for Native U.S. Oaks and their evaluations of each species. Of these, 57% have been the subject of some genetic analysis, but for most threatened species (72%), the only genetic analysis was done as part of a phylogenetic study. While nearly half (49%) of published genetic studies involved population genetic analysis, only 16 species of concern (13%) have been the subject of these studies. This is a critical gap considering that analysis of intraspecific genetic variability and genetic structure are essential for designing conservation management strategies. We review the published population genetic studies to highlight their application to conservation. Finally, we discuss future directions in Quercus conservation genetics and genomics.
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Jiang XL, Mou HL, Luo CS, Xu GB. The complete chloroplast genome sequence of Quercus chungii (Fagaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1789-1790. [PMID: 34104776 PMCID: PMC8168737 DOI: 10.1080/23802359.2021.1931505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Quercus chungii F.P.Metcalf, a rare oak with endemic to southern China, belongs to the compound trichome base (CTB) lineage in the Cyclobalanopsis section. The complete chloroplast genome of the species was assembled and annotated in this study. The circular genome was 160,731 bp in size, presenting a typical quadripartite structure including one large single-copy region (LSC, 90,140 bp), one small single-copy region (SSC, 18,911 bp), and two copies of inverted repeat regions (IRs, 25,840 bp). It encoded a total of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The maximum-likelihood (ML) phylogenetic tree reconstructed by IQ-TREE indicated that Q. chungii was more closely related to Q. myrsinifolia and Q. sichourensis.
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Affiliation(s)
- Xiao-Long Jiang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, China
| | - Hong-Lin Mou
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, China
| | - Chang-Sha Luo
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, China
| | - Gang-Biao Xu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, China
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48
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Yang Y, Zhou T, Qian Z, Zhao G. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing. Genomics 2021; 113:1438-1447. [PMID: 33744343 DOI: 10.1016/j.ygeno.2021.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 01/29/2023]
Abstract
China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree supported Quercus section Ilex as not monophyletic, in which Quercus section Cyclobalanopsis and Quercus section Cerris were nested. Most likely, incomplete lineage sorting and/or introgression among ancestral lineages in these three sections resulted in this complex pattern. The current distribution, diversification and molecular differentiation of Q. sect. Ilex in China are likely consequences of local adaptation to the geographic and paleoclimatic changes, which were driven by the uplift of Tibetan Plateau, the Hengduan Mountains and the Himalayas.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China; School of Biological Science and Technology, Baotou Teachers' College, Baotou, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zengqiang Qian
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.
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Cho WB, Han EK, Choi IS, Kwak M, Kim JH, Kim BY, Lee JH. The complete plastid genome sequence of Quercus acuta (Fagaceae), an evergreen broad-leaved oak endemic to East Asia. Mitochondrial DNA B Resour 2021; 6:320-322. [PMID: 33659663 PMCID: PMC7872549 DOI: 10.1080/23802359.2020.1866449] [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] [Indexed: 10/31/2022] Open
Abstract
We are reporting the complete plastid genome (plastome) of Quercus acuta, an evergreen broad-leaved oak endemic to East Asia. This species is important for maintaining the warm-temperate evergreen forest biome in East Asia. The Q. acuta plastome is 160,522 base pairs (bp) long, with two inverted repeat (IR) regions (25,839 bp each) that separate a large single copy (LSC) region (90,199 bp) and a small single copy (SSC) region (18,645 bp). The phylogenetic tree shows that Quercus acuta is closely related to Quercus sichourensis with strong bootstrap support.
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Affiliation(s)
- Won-Bum Cho
- Department of Biology Education, Chonnam National University, Gwangju, Republic of Korea
| | - Eun-Kyeong Han
- Department of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Myounghai Kwak
- Biological and Genetic Resources Utilization Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Jung-Hyun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju, Republic of Korea
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Feng Y, Comes HP, Qiu YX. Phylogenomic insights into the temporal-spatial divergence history, evolution of leaf habit and hybridization in Stachyurus (Stachyuraceae). Mol Phylogenet Evol 2020; 150:106878. [DOI: 10.1016/j.ympev.2020.106878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/07/2020] [Accepted: 06/01/2020] [Indexed: 12/14/2022]
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