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Sezen UU, Shue JE, Worthy SJ, Davies SJ, McMahon SM, Swenson NG. Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech. Proc Biol Sci 2024; 291:20232338. [PMID: 38593851 PMCID: PMC11003779 DOI: 10.1098/rspb.2023.2338] [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: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 04/11/2024] Open
Abstract
Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33 042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the single nucleotide polymorphism-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-autumn transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologues we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed gene ontology terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech.
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Affiliation(s)
- U. Uzay Sezen
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
| | - Jessica E. Shue
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
| | - Samantha J. Worthy
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Stuart J. Davies
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Gamboa, Panama
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA
| | - Sean M. McMahon
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Nathan G. Swenson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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2
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Wang L, Dang QL. Elevated CO 2 and ammonium nitrogen promoted the plasticity of two maple in great lakes region by adjusting photosynthetic adaptation. FRONTIERS IN PLANT SCIENCE 2024; 15:1367535. [PMID: 38654907 PMCID: PMC11035798 DOI: 10.3389/fpls.2024.1367535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
Introduction Climate change-related CO2 increases and different forms of nitrogen deposition are thought to affect the performance of plants, but their interactions have been poorly studied. Methods This study investigated the responses of photosynthesis and growth in two invasive maple species, amur maple (Acer ginnala Maxim.) and boxelder maple (Acer negundo L.), to elevated CO2 (400 µmol mol-1 (aCO2) vs. 800 µmol mol-1 (eCO2) and different forms of nitrogen fertilization (100% nitrate, 100% ammonium, and an equal mix of the two) with pot experiment under controlled conditions. Results and discussion The results showed that eCO2 significantly promoted photosynthesis, biomass, and stomatal conductance in both species. The biochemical limitation of photosynthesis was switched to RuBP regeneration (related to Jmax) under eCO2 from the Rubisco carboxylation limitation (related to Vcmax) under aCO2. Both species maximized carbon gain by lower specific leaf area and higher N concentration than control treatment, indicating robust morphological plasticity. Ammonium was not conducive to growth under aCO2, but it significantly promoted biomass and photosynthesis under eCO2. When nitrate was the sole nitrogen source, eCO2 significantly reduced N assimilation and growth. The total leaf N per tree was significantly higher in boxelder maple than in amur maple, while the carbon and nitrogen ratio was significantly lower in boxelder maple than in amur maple, suggesting that boxelder maple leaf litter may be more favorable for faster nutrient cycling. The results suggest that increases in ammonium under future elevated CO2 will enhance the plasticity and adaptation of the two maple species.
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Affiliation(s)
- Lei Wang
- Jiyang College, Zhejiang A&F University, Zhuji, Zhejiang, China
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON, Canada
| | - Qing-Lai Dang
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON, Canada
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McEvoy SL, Grady PGS, Pauloski N, O'Neill RJ, Wegrzyn JL. Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology. Evol Appl 2024; 17:e13669. [PMID: 38633133 PMCID: PMC11022628 DOI: 10.1111/eva.13669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 04/19/2024] Open
Abstract
DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.
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Affiliation(s)
- Susan L. McEvoy
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Department of Forest SciencesUniversity of HelsinkiHelsinkiFinland
| | - Patrick G. S. Grady
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Nicole Pauloski
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
| | - Rachel J. O'Neill
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
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Zhang H, Zhang H, Wang Y, Wang M, Guo H, Chan Y, Cong R, Zhao S, Xie J. High-quality maple genome reveals duplication-facilitated leaf color diversity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111917. [PMID: 37944703 DOI: 10.1016/j.plantsci.2023.111917] [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: 07/24/2023] [Revised: 10/05/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
Acer truncatum is a horticultural tree species with individuals that display either yellow or red leaves in autumn, giving it high ornamental and economic value. 'Lihong' of A. truncatum is an excellent cultivar due to its characteristic of having autumn leaves that turn a bright and beautiful shade of red, while its closely related cultivar 'Bunge' does not. However, the molecular mechanism underlying the color change in the cultivar 'Lihong' is still unclear. Here, we assembled a high-quality genome sequence of Acer truncatum 'Lihong' (genome size = 688 Mb, scaffold N50 = 9.14 Mb) with 28,438 protein-coding genes predicted. Through comparative genomic analysis, we found that 'Lihong' had experienced more tandem duplication events although it's a high degree of collinearity with 'Bunge'. Especially, the expansion of key enzymes in the anthocyanin synthesis pathway was significantly uneven between the two varieties, with 'Lihong' genome containing a significantly higher number of tandem/dispersed duplication key genes. Further transcriptomic, metabolomic, and molecular functional analyses demonstrated that several UFGT genes, mainly resulting from tandem/dispersed duplication, followed by the promoter sequence variation, may contribute greatly to the leaf color phenotype, which provides new insights into the mechanism of divergent anthocyanin accumulation process in the 'Lihong' and 'Bunge' with yellow leaves in autumn. Further, constitutive expression of two UFGT genes, which showed higher expression in 'Lihong', elevated the anthocyanin content. We proposed that the small-scale duplication events could contribute to phenotype innovation.
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Affiliation(s)
- Hua Zhang
- Beijing Key Laboratory of Greening Plants Breeding,Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China.
| | - Haoyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Yongge Wang
- Beijing Key Laboratory of Greening Plants Breeding,Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Maoliang Wang
- Beijing Key Laboratory of Greening Plants Breeding,Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Hao Guo
- Heilongjiang Bayi Agricultural University, Heilongjiang, China
| | - Yuan Chan
- Heilongjiang Bayi Agricultural University, Heilongjiang, China
| | - Richen Cong
- Beijing Key Laboratory of Greening Plants Breeding,Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Shiwei Zhao
- Beijing Key Laboratory of Greening Plants Breeding,Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Jianbo Xie
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi Province, China.
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Chromosomal-level genome and multi-omics dataset provides new insights into leaf pigmentation in Acer palmatum. Int J Biol Macromol 2023; 227:93-104. [PMID: 36470439 DOI: 10.1016/j.ijbiomac.2022.11.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022]
Abstract
Acer palmatum (A. palmatum), a deciduous shrub or small arbour which belongs to Acer of Aceraceae, is an excellent greening species as well as a beautiful ornamental plant. In this study, a high-quality chromosome-level reference genome for A. palmatum was constructed using Oxford Nanopore sequencing and Hi-C technology. The assembly genome was ∼745.78 Mb long with a contig N50 length of 3.20 Mb, and 95.30 % (710.71 Mb) of the assembly was anchored into 13 pseudochromosomes. A total of 28,559 protein-coding genes were obtained, ∼90.02 % (25,710) of which could be functionally annotated. The genomic evolutionary analysis revealed that A. palmatum is most closely related to A. yangbiense and A. truncatum, and underwent only an ancient gamma whole-genome duplication event. Despite lacking a recent independent WGD, 25,795 (90.32 %) genes of A. palmatum were duplicated, and the unique/expanded gene families were linked with genes involved in plant-pathogen interaction and several metabolic pathways, which might underpin adaptability. A combined genomic, transcriptomic, and metabolomic analysis related to the biosynthesis of anthocyanin in leaves during the different season were characterized. The results indicate that the dark-purple colouration of the leaves in spring was caused by a high amount of anthocyanins, especially delphinidin and its derivatives; and the red colouration of the leaves in autumn by a high amount of cyanidin 3-O-glucoside. In conclusion, these valuable multi-omic resources offer important foundations to explore the molecular regulation mechanism in leaf colouration and also provide a platform for the scientific and efficient utilization of A. palmatum.
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Mulozi L, Vennapusa AR, Elavarthi S, Jacobs OE, Kulkarni KP, Natarajan P, Reddy UK, Melmaiee K. Transcriptome profiling, physiological, and biochemical analyses provide new insights towards drought stress response in sugar maple ( Acer saccharum Marshall) saplings. FRONTIERS IN PLANT SCIENCE 2023; 14:1150204. [PMID: 37152134 PMCID: PMC10154611 DOI: 10.3389/fpls.2023.1150204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023]
Abstract
Sugar maple (Acer saccharum Marshall) is a temperate tree species in the northeastern parts of the United States and is economically important for its hardwood and syrup production. Sugar maple trees are highly vulnerable to changing climatic conditions, especially drought, so understanding the physiological, biochemical, and molecular responses is critical. The sugar maple saplings were subjected to drought stress for 7, 14, and 21 days and physiological data collected at 7, 14, and 21 days after stress (DAS) showed significantly reduced chlorophyll and Normalized Difference Vegetation Index with increasing drought stress time. The drought stress-induced biochemical changes revealed a higher accumulation of malondialdehyde, proline, and peroxidase activity in response to drought stress. Transcriptome analysis identified a total of 14,099 differentially expressed genes (DEGs); 328 were common among all stress periods. Among the DEGs, transcription factors (including NAC, HSF, ZFPs, GRFs, and ERF), chloroplast-related and stress-responsive genes such as peroxidases, membrane transporters, kinases, and protein detoxifiers were predominant. GO enrichment and KEGG pathway analysis revealed significantly enriched processes related to protein phosphorylation, transmembrane transport, nucleic acids, and metabolic, secondary metabolite biosynthesis pathways, circadian rhythm-plant, and carotenoid biosynthesis in response to drought stress. Time-series transcriptomic analysis revealed changes in gene regulation patterns in eight different clusters, and pathway analysis by individual clusters revealed a hub of stress-responsive pathways. In addition, qRT-PCR validation of selected DEGs revealed that the expression patterns were consistent with transcriptome analysis. The results from this study provide insights into the dynamics of physiological, biochemical, and gene responses to progressive drought stress and reveal the important stress-adaptive mechanisms of sugar maple saplings in response to drought stress.
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Affiliation(s)
- Lungowe Mulozi
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Amaranatha R. Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Sathya Elavarthi
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
- *Correspondence: Kalpalatha Melmaiee, ; Sathya Elavarthi,
| | - Oluwatomi E. Jacobs
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Krishnanand P. Kulkarni
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Purushothaman Natarajan
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Umesh K. Reddy
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Kalpalatha Melmaiee
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
- *Correspondence: Kalpalatha Melmaiee, ; Sathya Elavarthi,
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Li X, Cai K, Han Z, Zhang S, Sun A, Xie Y, Han R, Guo R, Tigabu M, Sederoff R, Pei X, Zhao C, Zhao X. Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change. FRONTIERS IN PLANT SCIENCE 2022; 13:850054. [PMID: 35310631 PMCID: PMC8927880 DOI: 10.3389/fpls.2022.850054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Acer pseudosieboldianum (Pax) Komarov is an ornamental plant with prominent potential and is naturally distributed in Northeast China. Here, we obtained a chromosome-scale genome assembly of A. pseudosieboldianum combining HiFi and Hi-C data, and the final assembled genome size was 690.24 Mb and consisted of 287 contigs, with a contig N50 value of 5.7 Mb and a BUSCO complete gene percentage of 98.4%. Genome evolution analysis showed that an ancient duplication occurred in A. pseudosieboldianum. Phylogenetic analyses revealed that Aceraceae family could be incorporated into Sapindaceae, consistent with the present Angiosperm Phylogeny Group system. We further construct a gene-to-metabolite correlation network and identified key genes and metabolites that might be involved in anthocyanin biosynthesis pathways during leaf color change. Additionally, we identified crucial teosinte branched1, cycloidea, and proliferating cell factors (TCP) transcription factors that might be involved in leaf morphology regulation of A. pseudosieboldianum, Acer yangbiense and Acer truncatum. Overall, this reference genome is a valuable resource for evolutionary history studies of A. pseudosieboldianum and lays a fundamental foundation for its molecular breeding.
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Affiliation(s)
- Xiang Li
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Zhiming Han
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Shikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Anran Sun
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Ying Xie
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Rui Han
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Ruixue Guo
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Mulualem Tigabu
- Southern Swedish Forest Research Centre, Faculty of Forest Science, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Xiaona Pei
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Chunli Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
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