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Peláez P, Lorenzana GP, Baesen K, Montes JR, De La Torre AR. Spatially heterogeneous selection and inter-varietal differentiation maintain population structure and local adaptation in a widespread conifer. BMC Ecol Evol 2024; 24:117. [PMID: 39227766 DOI: 10.1186/s12862-024-02304-4] [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: 12/12/2023] [Accepted: 08/28/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) plays a critical role in the ecology and economy of Western North America. This conifer species comprises two distinct varieties: the coastal variety (var. menziesii) along the Pacific coast, and the interior variety (var. glauca) spanning the Rocky Mountains into Mexico, with instances of inter-varietal hybridization in Washington and British Columbia. Recent investigations have focused on assessing environmental pressures shaping Douglas-fir's genomic variation for a better understanding of its evolutionary and adaptive responses. Here, we characterize range-wide population structure, estimate inter-varietal hybridization levels, identify candidate loci for climate adaptation, and forecast shifts in species and variety distribution under future climates. RESULTS Using a custom SNP-array, we genotyped 540 trees revealing four distinct clusters with asymmetric admixture patterns in the hybridization zone. Higher genetic diversity observed in coastal and hybrid populations contrasts with lower diversity in inland populations of the southern Rockies and Mexico, exhibiting a significant isolation by distance pattern, with less marked but still significant isolation by environment. For both varieties, we identified candidate loci associated with local adaptation, with hundreds of genes linked to processes such as stimulus response, reactions to chemical compounds, and metabolic functions. Ecological niche modeling revealed contrasting potential distribution shifts among the varieties in the coming decades, with interior populations projected to lose habitat and become more vulnerable, while coastal populations are expected to gain suitable areas. CONCLUSIONS Overall, our findings provide crucial insights into the population structure and adaptive potential of Douglas-fir, with the coastal variety being the most likely to preserve its evolutionary path throughout the present century, which carry implications for the conservation and management of this species across their range.
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Affiliation(s)
- Pablo Peláez
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Kailey Baesen
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Jose Ruben Montes
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Delourme D, Brémaud L, Plazanet I, Pélissier P, Label P, Boizot N, Breton C, Durand S, Costa G. Transcriptomic monitoring of Douglas-fir heartwood formation. BMC Genom Data 2023; 24:69. [PMID: 37986039 PMCID: PMC10662504 DOI: 10.1186/s12863-023-01172-z] [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: 07/07/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
OBJECTIVES Molecular cues linked to heartwood formation open new (complementary) perspectives to genetic breeding programs of Douglas-fir, a tree species largely cultivated in Europe for the natural durability and civil engineering properties of its wood. DATA DESCRIPTION RNAs from a single genotype of Douglas-fir, extracted from three distinct wood zones (outer sapwood, inner sapwood and transition zone) at four vegetative seasons to generate an extensive RNA-seq dataset used to apprehend the in-wood dynamic and seasonality of heartwood formation in this hardwood model species. Previously published data collected on somatic embryos of the same genotype could be merged with the present dataset to upgrade grade the Douglas-fir reference transcriptome.
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Affiliation(s)
- Didier Delourme
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Laure Brémaud
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Idelette Plazanet
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Patrick Pélissier
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | | | | | | | - Stéphanie Durand
- Université de Limoges, CAPTuR, UMR INSERM/CHU 1308, 2 Rue du Docteur Marcland, Limoges, F-87025, France
| | - Guy Costa
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France.
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3
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Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions. PLoS One 2023; 18:e0277797. [PMID: 36795783 PMCID: PMC9934357 DOI: 10.1371/journal.pone.0277797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/03/2022] [Indexed: 02/17/2023] Open
Abstract
Environmental responses are critical for plant growth and survival under different climate conditions. To elucidate the underlying biological mechanisms of environmental responses in Japanese cedar (Cryptomeria japonica D. Don), the annual transcriptome dynamics of common clonal trees (Godai1) planted at three different climate sites (Yamagata, Ibaraki, and Kumamoto Prefectures) were analyzed using microarrays. Both principal component analysis (PCA) and hierarchical clustering of the microarray data indicated the transition to dormant transcriptome status occurred earlier and the transition to active growth status later in the colder region. Interestingly, PCA also indicated that the transcriptomes of trees grown under three different conditions were similar during the growth period (June to September), whereas the transcriptomes differed between sites during the dormant period (January to March). In between-site comparisons, analyses of the annual expression profiles of genes for sites 'Yamagata vs. Kumamoto', 'Yamagata vs. Ibaraki', and 'Ibaraki vs. Kumamoto' identified 1,473, 1,137, and 925 targets exhibiting significantly different expression patterns, respectively. The total of 2,505 targets that exhibited significantly different expression patterns in all three comparisons may play important roles in enabling cuttings to adapt to local environmental conditions. Partial least-squares regression analysis and Pearson correlation coefficient analysis revealed that air temperature and day length were the dominant factors controlling the expression levels of these targets. GO and Pfam enrichment analyses indicated that these targets include genes that may contribute to environmental adaptation, such as genes related to stress and abiotic stimulus responses. This study provided fundamental information regarding transcripts that may play an important role in adaptation to environmental conditions at different planting sites.
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Velasco VME, Ferreira A, Zaman S, Noordermeer D, Ensminger I, Wegrzyn JL. A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir). G3 (BETHESDA, MD.) 2023; 13:jkac304. [PMID: 36454025 PMCID: PMC10468028 DOI: 10.1093/g3journal/jkac304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/13/2021] [Accepted: 10/19/2022] [Indexed: 12/02/2022]
Abstract
Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.
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Affiliation(s)
| | - Alyssa Ferreira
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
| | - Sumaira Zaman
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
| | - Devin Noordermeer
- Department of Biology, University of Toronto,
Mississauga, ON L5L 1C8, Canada
- Graduate Department of Cell and Systems Biology, University of
Toronto, Toronto, ON M5S, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto,
Mississauga, ON L5L 1C8, Canada
- Graduate Department of Cell and Systems Biology, University of
Toronto, Toronto, ON M5S, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of
Toronto, Toronto, ON M5S, Canada
| | - Jill L Wegrzyn
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
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Compton S, Stackpole C, Dixit A, Sekhwal MK, Kolb T, De la Torre AR. Differences in heat tolerance, water use efficiency and growth among Douglas-fir families and varieties evidenced by GWAS and common garden studies. AOB PLANTS 2023; 15:plad008. [PMID: 37007611 PMCID: PMC10052383 DOI: 10.1093/aobpla/plad008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Severe and frequent heat and drought events challenge the survival and development of long-generation trees. In this study, we investigated the genomic basis of heat tolerance, water use efficiency and growth by performing genome-wide association studies in coastal Douglas-fir (Pseudotsuga menziesii) and intervarietal (menziesii × glauca) hybrid seedlings. GWAS results identified 32 candidate genes involved in primary and secondary metabolism, abiotic stress and signaling, among other functions. Water use efficiency (inferred from carbon isotope discrimination), photosynthetic capacity (inferred from %N), height and heat tolerance (inferred from electrolyte leakage in a heat stress experiment) were significantly different among Douglas-fir families and varieties. High-elevation seed sources had increased water use efficiency, which could be a result of higher photosynthetic capacity. Similarly, families with greater heat tolerance also had higher water use efficiency and slower growth, suggesting a conservative growth strategy. Intervarietal hybrids showed increased heat tolerance (lower electrolyte leakage at 50 and 55 °C) and higher water use efficiency compared with coastal families, suggesting that hybridization might be a source of pre-adapted alleles to warming climates and should be considered for large-scale reforestation projects under increasingly arid conditions.
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Affiliation(s)
| | | | - Aalap Dixit
- Department of Forestry, New Mexico Highlands University, Las Vegas, NM 87701, USA
| | - Manoj K Sekhwal
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, AZ 86011, USA
| | - Thomas Kolb
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, AZ 86011, USA
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6
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Response of Poplar Leaf Transcriptome to Changed Management and Environmental Conditions in Pure and Mixed with Black Locust Stands. FORESTS 2022. [DOI: 10.3390/f13020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Mixed cropping in short rotation coppice can be an alternative to monocultures. To design optimized mixtures, field trials are needed. Poplar, as an economically important and fast-growing species, and black locust, as a nitrogen-fixing species, are promising candidates for such studies. RNA sequencing (RNA-seq) was used to monitor effects of mixed and pure cultivations on the gene expression of poplar along with growth measurements during 2017 and 2018. Both biomass production and leaf transcriptomes revealed a strong competition pressure of black locust and the abiotic environment on poplar trees. Gene expression differed between the two study sites and pure and mixed stands. Shading effects from black locust caused the downregulation of photosynthesis and upregulation of shade avoidance genes in mixed stands in 2017. As a result of higher light availability after cutting black locust, plant organ development genes were upregulated in mixed stands in 2018. Drought conditions during the summer of 2018 and competition for water between the two species caused the upregulation of drought stress response genes in mixed stands and at the unfavorable growing site. Further investigations are required to discover the mechanisms of interspecific competition and to develop stand designs, which could increase the success and productivity of mixed plantations.
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7
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Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio. PLoS One 2021; 16:e0246615. [PMID: 33784314 PMCID: PMC8009359 DOI: 10.1371/journal.pone.0246615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/17/2021] [Indexed: 12/20/2022] Open
Abstract
Global warming is predicted to exert negative impacts on plant growth due to the damaging effect of high temperatures on plant physiology. Revealing the genetic architecture underlying the heat stress response is therefore crucial for the development of conservation strategies, and for breeding heat-resistant plant genotypes. Here we investigated the transcriptional changes induced by heat in Nothofagus pumilio, an emblematic tree species of the sub-Antarctic forests of South America. Through the performance of RNA-seq of leaves of plants exposed to 20°C (control) or 34°C (heat shock), we generated the first transcriptomic resource for the species. We also studied the changes in protein-coding transcripts expression in response to heat. We found 5,214 contigs differentially expressed between temperatures. The heat treatment resulted in a down-regulation of genes related to photosynthesis and carbon metabolism, whereas secondary metabolism, protein re-folding and response to stress were up-regulated. Moreover, several transcription factor families like WRKY or ERF were promoted by heat, alongside spliceosome machinery and hormone signaling pathways. Through a comparative analysis of gene regulation in response to heat in Arabidopsis thaliana, Populus tomentosa and N. pumilio we provide evidence of the existence of shared molecular features of heat stress responses across angiosperms, and identify genes of potential biotechnological application.
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8
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Gaafar ARZ, Al-Qurainy F, Alshameri A, Khan S, Nadeem M, Tarroum M, Alansi S, Shaikhaldein HO, Salih AM, Arrak Alenezi N. High RNA quality extracted from the tolerant crop Cyamopsis tetragonoloba (L.) despite possession of low RNA integrity number. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1910567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
| | - Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Aref Alshameri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Nadeem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Alansi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan O. Shaikhaldein
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdalrhaman M. Salih
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Norah Arrak Alenezi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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9
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Chang CYY, Bräutigam K, Hüner NPA, Ensminger I. Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers. THE NEW PHYTOLOGIST 2021; 229:675-691. [PMID: 32869329 DOI: 10.1111/nph.16904] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.
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Affiliation(s)
- Christine Yao-Yun Chang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Norman P A Hüner
- Department of Biology and The Biotron Experimental Climate Change Research Centre, Western University, London, ON, N6A5B7, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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10
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Estravis-Barcala M, Mattera MG, Soliani C, Bellora N, Opgenoorth L, Heer K, Arana MV. Molecular bases of responses to abiotic stress in trees. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3765-3779. [PMID: 31768543 PMCID: PMC7316969 DOI: 10.1093/jxb/erz532] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 05/05/2023]
Abstract
Trees are constantly exposed to climate fluctuations, which vary with both time and geographic location. Environmental changes that are outside of the physiological favorable range usually negatively affect plant performance and trigger responses to abiotic stress. Long-living trees in particular have evolved a wide spectrum of molecular mechanisms to coordinate growth and development under stressful conditions, thus minimizing fitness costs. The ongoing development of techniques directed at quantifying abiotic stress has significantly increased our knowledge of physiological responses in woody plants. However, it is only within recent years that advances in next-generation sequencing and biochemical approaches have enabled us to begin to understand the complexity of the molecular systems that underlie these responses. Here, we review recent progress in our understanding of the molecular bases of drought and temperature stresses in trees, with a focus on functional, transcriptomic, epigenetic, and population genomic studies. In addition, we highlight topics that will contribute to progress in our understanding of the plastic and adaptive responses of woody plants to drought and temperature in a context of global climate change.
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Affiliation(s)
- Maximiliano Estravis-Barcala
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, (Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad Nacional del Comahue), San Carlos de Bariloche, Rio Negro, Argentina
| | - María Gabriela Mattera
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
| | - Carolina Soliani
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
| | - Nicolás Bellora
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, (Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad Nacional del Comahue), San Carlos de Bariloche, Rio Negro, Argentina
| | - Lars Opgenoorth
- Department of Ecology, Philipps University Marburg, Marburg, Germany
- Swiss Federal Research Institute WSL, BirmensdorfSwitzerland
| | - Katrin Heer
- Department of Conservation Biology, Philipps University Marburg, Marburg Germany
| | - María Verónica Arana
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
- Correspondence:
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11
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Mohl JE, Fetcher N, Stunz E, Tang J, Moody ML. Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event. Sci Rep 2020; 10:8990. [PMID: 32488082 PMCID: PMC7265556 DOI: 10.1038/s41598-020-65693-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/05/2020] [Indexed: 11/25/2022] Open
Abstract
Tussock cottongrass (Eriophorum vaginatum) is a foundation species for much of the arctic moist acidic tundra, which is currently experiencing extreme effects of climate change. The Arctic is facing higher summer temperatures and extreme weather events are becoming more common. We used Illumina RNA-Seq to analyse cDNA libraries for differential expression of genes from leaves of ecologically well-characterized ecotypes of tussock cottongrass found along a latitudinal gradient in the Alaskan Arctic and transplanted into a common garden. Plant sampling was performed on a typical summer day and during an extreme heat event. We obtained a de novo assembly that contained 423,353 unigenes. There were 363 unigenes up-regulated and 1,117 down-regulated among all ecotypes examined during the extreme heat event. Of these, 26 HSP unigenes had >log2-fold up-regulation. Several TFs associated with heat stress in previous studies were identified that had >log2-fold up- or down-regulation during the extreme heat event (e.g., DREB, NAC). There was consistent variation in DEGs among ecotypes, but not specifically related to whether plants originated from taiga or tundra ecosystems. As the climate changes it is essential to determine ecotypic diversity at the genomic level, especially for widespread species that impact ecosystem function.
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Affiliation(s)
- Jonathon E Mohl
- Bioinformatics Program, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Ned Fetcher
- Institute for Environmental Science and Sustainability, Wilkes University, Wilkes-Barre, PA, 18766, USA
| | - Elizabeth Stunz
- Biological Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Jianwu Tang
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Michael L Moody
- Biological Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA.
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12
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Nose M, Kurita M, Tamura M, Matsushita M, Hiraoka Y, Iki T, Hanaoka S, Mishima K, Tsubomura M, Watanabe A. Effects of day length- and temperature-regulated genes on annual transcriptome dynamics in Japanese cedar (Cryptomeria japonica D. Don), a gymnosperm indeterminate species. PLoS One 2020; 15:e0229843. [PMID: 32150571 PMCID: PMC7062269 DOI: 10.1371/journal.pone.0229843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 02/15/2020] [Indexed: 11/29/2022] Open
Abstract
Seasonal phenomena in plants are primarily affected by day length and temperature. The shoot transcriptomes of trees grown in the field and a controlled-environment chamber were compared to characterize genes that control annual rhythms and the effects of day length- and temperature-regulated genes in the gymnosperm Japanese cedar (Cryptomeria japonica D. Don), which exhibits seasonally indeterminate growth. Annual transcriptome dynamics were clearly demonstrated by principal component analysis using microarray data obtained under field-grown conditions. Analysis of microarray data from trees grown in a controlled chamber identified 2,314 targets exhibiting significantly different expression patterns under short-day (SD) and long-day conditions, and 2,045 targets exhibited significantly different expression patterns at 15°C (LT; low temperature) versus 25°C. Interestingly, although growth was suppressed under both SD and LT conditions, approximately 80% of the SD- and LT-regulated targets differed, suggesting that each factor plays a unique role in the annual cycle. The top 1,000 up-regulated targets in the growth/dormant period in the field coincided with more than 50% of the SD- and LT-regulated targets, and gene co-expression network analysis of the annual transcriptome indicated a close relationship between the SD- and LT-regulated targets. These results indicate that the respective effects of day length and temperature interact to control annual transcriptome dynamics. Well-known upstream genes of signaling pathways responsive to environmental conditions, such as the core clock (LHY/CjLHYb and CCA1/CjLHYa) and PEBP family (MFT) genes, exhibited unique expression patterns in Japanese cedar compared with previous reports in other species, suggesting that these genes control differences in seasonal regulation mechanisms between species. The results of this study provide new insights into seasonal regulation of transcription in Japanese cedar.
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Affiliation(s)
- Mine Nose
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Manabu Kurita
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Miho Tamura
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Michinari Matsushita
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Yuichiro Hiraoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Taiichi Iki
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - So Hanaoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Atsushi Watanabe
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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13
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RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress. BMC Genomics 2019; 20:724. [PMID: 31601194 PMCID: PMC6785863 DOI: 10.1186/s12864-019-6098-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 09/11/2019] [Indexed: 01/29/2023] Open
Abstract
Background Clerodendrum inerme (L.) Gaertn, a halophyte, usually grows on coastal beaches as an important mangrove plant. The salt-tolerant mechanisms and related genes of this species that respond to short-term salinity stress are unknown for us. The de novo transcriptome of C. inerme roots was analyzed using next-generation sequencing technology to identify genes involved in salt tolerance and to better understand the response mechanisms of C. inerme to salt stress. Results Illumina RNA-sequencing was performed on root samples treated with 400 mM NaCl for 0 h, 6 h, 24 h, and 72 h to investigate changes in C. inerme in response to salt stress. The de novo assembly identified 98,968 unigenes. Among these unigenes, 46,085 unigenes were annotated in the NCBI non-redundant protein sequences (NR) database, 34,756 sequences in the Swiss-Prot database and 43,113 unigenes in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database. 52 Gene Ontology (GO) terms and 31 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were matched to those unigenes. Most differentially expressed genes (DEGs) related to the GO terms “single-organism process”, “membrane” and “catalytic activity” were significantly enriched while numerous DEGs related to the plant hormone signal transduction pathway were also significantly enriched. The detection of relative expression levels of 9 candidate DEGs by qRT-PCR were basically consistent with fold changes in RNA sequencing analysis, demonstrating that transcriptome data can accurately reflect the response of C. inerme roots to salt stress. Conclusions This work revealed that the response of C. inerme roots to saline condition included significant alteration in response of the genes related to plant hormone signaling. Besides, our findings provide numerous salt-tolerant genes for further research to improve the salt tolerance of functional plants and will enhance research on salt-tolerant mechanisms of halophytes.
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Junker-Frohn LV, Kleiber A, Jansen K, Gessler A, Kreuzwieser J, Ensminger I. Differences in isoprenoid-mediated energy dissipation pathways between coastal and interior Douglas-fir seedlings in response to drought. TREE PHYSIOLOGY 2019; 39:1750-1766. [PMID: 31287896 DOI: 10.1093/treephys/tpz075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 02/21/2019] [Accepted: 05/12/2019] [Indexed: 06/09/2023]
Abstract
Plants have evolved energy dissipation pathways to reduce photooxidative damage under drought when photosynthesis is hampered. Non-volatile and volatile isoprenoids are involved in non-photochemical quenching of excess light energy and scavenging of reactive oxygen species. A better understanding of trees' ability to cope with and withstand drought stress will contribute to mitigate the negative effects of prolonged drought periods expected under future climate conditions. Therefore we investigated if Douglas-fir (Pseudotsuga menziesii(Mirb.)) provenances from habitats with contrasting water availability reveal intraspecific variation in isoprenoid-mediated energy dissipation pathways. In a controlled drought experiment with 1-year-old seedlings of an interior and a coastal Douglas-fir provenance, we assessed the photosynthetic capacity, pool sizes of non-volatile isoprenoids associated with the photosynthetic apparatus, as well as pool sizes and emission of volatile isoprenoids. We observed variation in the amount and composition of non-volatile and volatile isoprenoids among provenances, which could be linked to variation in photosynthetic capacity under drought. The coastal provenance exhibited an enhanced biosynthesis and emission of volatile isoprenoids, which is likely sustained by generally higher assimilation rates under drought. In contrast, the interior provenance showed an enhanced photoprotection of the photosynthetic apparatus by generally higher amounts of non-volatile isoprenoids and increased amounts of xanthophyll cycle pigments under drought. Our results demonstrate that there is intraspecific variation in isoprenoid-mediated energy dissipation pathways among Douglas-fir provenances, which may be important traits when selecting provenances suitable to grow under future climate conditions.
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Affiliation(s)
- Laura Verena Junker-Frohn
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON, Canada
- Forstliche Versuchs- und Forschungsanstalt Baden-Württemberg, Wonnhaldestr. 4, 79100 Freiburg, Germany
| | - Anita Kleiber
- Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 53, 79110 Freiburg, Germany
| | - Kirstin Jansen
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany
| | - Arthur Gessler
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany
- Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zürich, Switzerland
- Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903 Birmensdorf, Switzerland
| | - Jürgen Kreuzwieser
- Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 53, 79110 Freiburg, Germany
| | - Ingo Ensminger
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON, Canada
- Forstliche Versuchs- und Forschungsanstalt Baden-Württemberg, Wonnhaldestr. 4, 79100 Freiburg, Germany
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15
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Du B, Kreuzwieser J, Dannenmann M, Junker LV, Kleiber A, Hess M, Jansen K, Eiblmeier M, Gessler A, Kohnle U, Ensminger I, Rennenberg H, Wildhagen H. Foliar nitrogen metabolism of adult Douglas-fir trees is affected by soil water availability and varies little among provenances. PLoS One 2018; 13:e0194684. [PMID: 29566035 PMCID: PMC5864041 DOI: 10.1371/journal.pone.0194684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/07/2018] [Indexed: 12/29/2022] Open
Abstract
The coniferous forest tree Douglas-fir (Pseudotsuga menziesii) is native to the pacific North America, and is increasingly planted in temperate regions worldwide. Nitrogen (N) metabolism is of great importance for growth, resistance and resilience of trees. In the present study, foliar N metabolism of adult trees of three coastal and one interior provenance of Douglas-fir grown at two common gardens in southwestern Germany (Wiesloch, W; Schluchsee, S) were characterized in two subsequent years. Both the native North American habitats of the seed sources and the common garden sites in Germany differ in climate conditions. Total and mineral soil N as well as soil water content were higher in S compared to W. We hypothesized that i) provenances differ constitutively in N pool sizes and composition, ii) N pools are affected by environmental conditions, and iii) that effects of environmental factors on N pools differ among interior and coastal provenances. Soil water content strongly affected the concentrations of total N, soluble protein, total amino acids (TAA), arginine and glutamate. Foliar concentrations of total N, soluble protein, structural N and TAA of trees grown at W were much higher than in trees at S. Provenance effects were small but significant for total N and soluble protein content (interior provenance showed lowest concentrations), as well as arginine, asparagine and glutamate. Our data suggest that needle N status of adult Douglas-fir is independent from soil N availability and that low soil water availability induces a re-allocation of N from structural N to metabolic N pools. Small provenance effects on N pools suggest that local adaptation of Douglas-fir is not dominated by N conditions at the native habitats.
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Affiliation(s)
- Baoguo Du
- College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, China
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Jürgen Kreuzwieser
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Michael Dannenmann
- Karlsruhe Institute of Technology (KIT) Campus Alpin, Institute of Meteorology and Climate Research (IMK), Atmospheric Environmental Research (IMK-IFU), Garmisch-Partenkirchen, Germany
| | - Laura Verena Junker
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Anita Kleiber
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Moritz Hess
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
- Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
| | - Kirstin Jansen
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Institute of Ecology, Leuphana University of Lüneburg, Lüneburg, Germany
| | - Monika Eiblmeier
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Arthur Gessler
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Ulrich Kohnle
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Ingo Ensminger
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- King Saud University, Riyadh, Saudi Arabia
| | - Henning Wildhagen
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
- * E-mail:
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16
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Dal Santo S, Zenoni S, Sandri M, De Lorenzis G, Magris G, De Paoli E, Di Gaspero G, Del Fabbro C, Morgante M, Brancadoro L, Grossi D, Fasoli M, Zuccolotto P, Tornielli GB, Pezzotti M. Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G×E) on the berry transcriptome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1143-1159. [PMID: 29381239 DOI: 10.1111/tpj.13834] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/14/2017] [Accepted: 01/04/2018] [Indexed: 05/20/2023]
Abstract
Changes in the performance of genotypes in different environments are defined as genotype × environment (G×E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G×E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G×E-related. The G×E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G×E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.
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Affiliation(s)
- Silvia Dal Santo
- Department of Biotechnology, University of Verona, I-37034, Verona, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, I-37034, Verona, Italy
| | - Marco Sandri
- Department of Biotechnology, University of Verona, I-37034, Verona, Italy
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milano, I-20133, Milano, Italy
| | | | - Emanuele De Paoli
- Department of Agricultural Food, Environmental and Animal Sciences (DI4A), University of Udine, I-33100, Udine, Italy
| | | | - Cristian Del Fabbro
- Department of Agricultural Food, Environmental and Animal Sciences (DI4A), University of Udine, I-33100, Udine, Italy
| | | | - Lucio Brancadoro
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milano, I-20133, Milano, Italy
| | - Daniele Grossi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milano, I-20133, Milano, Italy
| | - Marianna Fasoli
- Department of Biotechnology, University of Verona, I-37034, Verona, Italy
| | - Paola Zuccolotto
- Department of Economics and management, University of Brescia, I-25121, Brescia, Italy
| | | | - Mario Pezzotti
- Department of Biotechnology, University of Verona, I-37034, Verona, Italy
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Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR. Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. BMC Genomics 2017; 18:558. [PMID: 28738815 PMCID: PMC5525293 DOI: 10.1186/s12864-017-3916-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/30/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. RESULTS We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/- 2 h from sunrise and sunset, and +/- 20 days from winter and summer solstices. Comparisons with published studies from other conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. CONCLUSIONS Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone conifers, and for identifying cyclic transcriptome components in other conifer species.
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Affiliation(s)
- Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
| | - Peter C Dolan
- University of Minnesota - Morris, Morris, MN, 56267, USA
| | - Sanjuro Jogdeo
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - David B Neale
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - J Bradley St Clair
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
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Holliday JA, Aitken SN, Cooke JEK, Fady B, González-Martínez SC, Heuertz M, Jaramillo-Correa JP, Lexer C, Staton M, Whetten RW, Plomion C. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Mol Ecol 2017; 26:706-717. [PMID: 27997049 DOI: 10.1111/mec.13963] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022]
Abstract
Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.
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Affiliation(s)
- Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 304 Cheatham Hall, Blacksburg, VA 24061, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T1Z4, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, 5-108 Centennial Centre for Interdisciplinary Science, Edmonton, AB T6G2E9, Canada
| | - Bruno Fady
- Mediterranean Forest Ecology (URFM), Institut National de la Recherche Agronomique (INRA), Domaine St Paul, Site Agroparc, 84914 Avignon, France
| | | | - Myriam Heuertz
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Juan-Pablo Jaramillo-Correa
- Institute of Ecology, Universidad Nacional Autonoma de Mexico (UNAM) Circuito Exterior s/n, Apartado Postal 70-275, 04510 Ciudad de México, Mexico City, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna Faculty of Life SciencesRennweg 14, Room 217, A-1030, Vienna, Austria
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 EJ Chapman Drive, Knoxville, TN 37996, USA
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University Jordan Hall Addition 5231, Raleigh, NC 27695, USA
| | - Christophe Plomion
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
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Shimmura S, Nozoe M, Kitora S, Kin S, Matsutani S, Ishizaki Y, Nakahira Y, Shiina T. Comparative Analysis of Chloroplast psbD Promoters in Terrestrial Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1186. [PMID: 28751898 PMCID: PMC5508017 DOI: 10.3389/fpls.2017.01186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/21/2017] [Indexed: 05/15/2023]
Abstract
The transcription of photosynthesis genes encoded by the plastid genome is mainly mediated by a prokaryotic-type RNA polymerase called plastid-encoded plastid RNA polymerase (PEP). Standard PEP-dependent promoters resemble bacterial sigma-70-type promoters containing the so-called -10 and -35 elements. On the other hand, an unusual light- and stress-responsive promoter (psbD LRP) that is regulated by a 19-bp AAG-box immediately upstream of the -35 element has been mapped upstream of the psbD-psbC operon in some angiosperms. However, the occurrence of the AAG-box containing psbD LRP in plant evolution remains elusive. We have mapped the psbD promoters in eleven embryophytes at different evolutionary stages from liverworts to angiosperms. The psbD promoters were mostly mapped around 500-900 bp upstream of the psbD translational start sites, indicating that the psbD mRNAs have unusually long 5'-UTR extensions in common. The -10 elements of the psbD promoter are well-conserved in all embryophytes, but not the -35 elements. We found that the AAG-box sequences are highly conserved in angiosperms and gymnosperms except for gnetaceae plants. Furthermore, partial AAG-box-like sequences have been identified in the psbD promoters of some basal embryophytes such as moss, hornwort, and lycophyte, whereas liverwort has the standard PEP promoter without the AAG-box. These results suggest that the AAG-box sequences of the psbD LRP may have evolved from a primitive type of AAG-box of basal embryophytes. On the other hand, monilophytes (ferns) use another type of psbD promoter composed of a distinct cis-element upstream of the potential -35 element. Furthermore, we found that psbD expression is not regulated by light in gymnosperms or basal angiosperms, although they have the well-conserved AAG-box sequences. Thus, it is unlikely that acquisition of the AAG-box containing psbD promoter is directly associated with light-induced transcription of the psbD-psbC operon. Light- and stress-induced transcription may have evolved independently and multiple times during terrestrial plant evolution.
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Affiliation(s)
- Shuichi Shimmura
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Mikio Nozoe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- AMITA Institute for Sustainable Economies Co., Ltd.Kyoto, Japan
| | - Shota Kitora
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Satoko Kin
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Shigeru Matsutani
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- Kyoto Botanical GardenKyoto, Japan
| | - Yoko Ishizaki
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Yoichi Nakahira
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- College of Agriculture, Ibaraki UniversityIbaraki, Japan
| | - Takashi Shiina
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- *Correspondence: Takashi Shiina,
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Hess M, Wildhagen H, Junker LV, Ensminger I. Erratum to: Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat. BMC Genomics 2016; 17:780. [PMID: 27716042 PMCID: PMC5053107 DOI: 10.1186/s12864-016-3144-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/30/2016] [Indexed: 12/02/2022] Open
Affiliation(s)
- Moritz Hess
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100, Freiburg i. Brsg., Germany.,Institute for Biology III, Faculty of Biology, Albert Ludwigs University Freiburg, Schänzlestrasse 1, D-79104, Freiburg i. Brsg., Germany.,Present Address: Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Obere Zahlbacher Strasse 69, 55131, Mainz, Germany
| | - Henning Wildhagen
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100, Freiburg i. Brsg., Germany.,Present Address: Department of Forest Botany and Tree Physiology, Büsgen-Institute, Georg-August-University Göttingen, Büsgenweg 2, D-37077, Göttingen, Germany
| | - Laura Verena Junker
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100, Freiburg i. Brsg., Germany.,Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
| | - Ingo Ensminger
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100, Freiburg i. Brsg., Germany. .,Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada.
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