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Modica A, Lalagüe H, Muratorio S, Scotti I. Rolling down that mountain: microgeographical adaptive divergence during a fast population expansion along a steep environmental gradient in European beech. Heredity (Edinb) 2024; 133:99-112. [PMID: 38890557 PMCID: PMC11286953 DOI: 10.1038/s41437-024-00696-z] [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: 02/07/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Forest tree populations harbour high genetic diversity thanks to large effective population sizes and strong gene flow, allowing them to diversify through adaptation to local environmental pressures within dispersal distance. Many tree populations also experienced historical demographic fluctuations, including spatial population contraction or expansions at various temporal scales, which may constrain their ability to adapt to environmental variations. Our aim is to investigate how recent contraction and expansion events interfere with local adaptation, by studying patterns of adaptive divergence between closely related stands undergoing environmentally contrasted conditions, and having or not recently expanded. To investigate genome-wide signatures of local adaptation while accounting for demography, we analysed divergence in a European beech population by testing pairwise differentiation among four tree stands at ~35k Single Nucleotide Polymorphisms from ~9k genomic regions. We applied three divergence outlier search methods resting on different assumptions and targeting either single SNPs or contiguous genomic regions, while accounting for the effect of population size variations on genetic divergence. We found 27 signals of selective signatures in 19 target regions. Putatively adaptive divergence involved all stand pairs. We retrieved signals both when comparing old-growth stands and recently colonised areas and when comparing stands within the old-growth area. Therefore, adaptive divergence processes have taken place both over short time spans, under strong environmental contrasts, and over short ecological gradients, in populations that have been stable in the long term. This suggests that standing genetic variation supports local, microgeographic divergence processes, which can maintain genetic diversity at the landscape level.
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Affiliation(s)
- Andrea Modica
- INRAE, URFM, 228, Route de l'Aérodrome, 84914, Avignon, France
| | - Hadrien Lalagüe
- INRAE, EcoFoG, Campus agronomique, 97310, Kourou, French Guiana
| | - Sylvie Muratorio
- INRAE, EcoBioP, 173, Route de Saint-Jean-de-Luz RD 918, 64310, Saint-Pée-sur-Nivelle, France
| | - Ivan Scotti
- INRAE, URFM, 228, Route de l'Aérodrome, 84914, Avignon, France.
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2
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Neycken A, Wohlgemuth T, Frei ER, Klesse S, Baltensweiler A, Lévesque M. Slower growth prior to the 2018 drought and a high growth sensitivity to previous year summer conditions predisposed European beech to crown dieback. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169068. [PMID: 38049004 DOI: 10.1016/j.scitotenv.2023.169068] [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: 08/07/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
The record-breaking drought in 2018 caused premature leaf discoloration and shedding (early browning) in many beech (Fagus sylvatica L.) dominated forests in Central Europe. However, a high degree of variability in drought response among individual beech trees was observed. While some trees were severely impacted by the prolonged water deficits and high temperatures, others remained vital with no or only minor signs of crown vitality loss. Why some beech trees were more susceptible to drought-induced crown damage than others and whether growth recovery is possible are poorly understood. Here, we aimed to identify growth characteristics associated with the variability in drought response between individual beech trees based on a sample of 470 trees in northern Switzerland. By combining tree growth measurements and crown condition assessments, we also investigated the possible link between crown dieback and growth recovery after drought. Beech trees with early browning exhibited an overall lower growth vigor before the 2018 drought than co-occurring vital beech trees. This lower vigor is mainly indicated by lower overall growth rates, stronger growth declines in the past decades, and higher growth-climate sensitivity. Particularly, warm previous year summer conditions negatively affected current growth of the early-browning trees. These findings suggest that the affected trees had less access to critical resources and were physiologically limited in their growth predisposing them to early browning. Following the 2018 drought, observed growth recovery potential corresponded to the amount of crown dieback and the local climatic water balance. Overall, our findings emphasize that beech-dominated forests in Central Europe are under increasing pressure from severe droughts, ultimately reducing the competitive ability of this species, especially on lowland sites with shallow soils and low water holding capacity.
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Affiliation(s)
- Anna Neycken
- Silviculture Group, Institute of Terrestrial Ecosystems, ETH Zurich, Universitätsstrasse 16, Zurich 8092, Switzerland.
| | - Thomas Wohlgemuth
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Esther R Frei
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland; Alpine Environment and Natural Hazards, WSL Institute for Snow and Avalanche Research SLF, Flüelastrasse 11, 7260 Davos Dorf, Switzerland; Climate Change and Extremes in Alpine Regions Research Centre CERC, 7260 Davos Dorf, Switzerland
| | - Stefan Klesse
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland; Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Andri Baltensweiler
- Forest Resources and Management, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Mathieu Lévesque
- Silviculture Group, Institute of Terrestrial Ecosystems, ETH Zurich, Universitätsstrasse 16, Zurich 8092, Switzerland
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3
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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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4
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Mishra B, Ulaszewski B, Meger J, Aury JM, Bodénès C, Lesur-Kupin I, Pfenninger M, Da Silva C, Gupta DK, Guichoux E, Heer K, Lalanne C, Labadie K, Opgenoorth L, Ploch S, Le Provost G, Salse J, Scotti I, Wötzel S, Plomion C, Burczyk J, Thines M. A Chromosome-Level Genome Assembly of the European Beech ( Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs. Front Genet 2022; 12:691058. [PMID: 35211148 PMCID: PMC8862710 DOI: 10.3389/fgene.2021.691058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 12/14/2021] [Indexed: 01/14/2023] Open
Abstract
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
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Affiliation(s)
- Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Bartosz Ulaszewski
- Department of Genetics, ul. Chodkiewicza 30, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Joanna Meger
- Department of Genetics, ul. Chodkiewicza 30, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Isabelle Lesur-Kupin
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France.,HelixVenture, Mérignac, France.,Faculty of Biology, Plant Ecology and Geobotany, Philipps University Marburg, Marburg, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Corinne Da Silva
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Deepak K Gupta
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | | | - Katrin Heer
- Faculty of Biology, Plant Ecology and Geobotany, Philipps University Marburg, Marburg, Germany.,Forest Genetics, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Lars Opgenoorth
- Faculty of Biology, Plant Ecology and Geobotany, Philipps University Marburg, Marburg, Germany
| | - Sebastian Ploch
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | | | | | | | - Stefan Wötzel
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | | | - Jaroslaw Burczyk
- Department of Genetics, ul. Chodkiewicza 30, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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5
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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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6
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Pfenninger M, Reuss F, Kiebler A, Schönnenbeck P, Caliendo C, Gerber S, Cocchiararo B, Reuter S, Blüthgen N, Mody K, Mishra B, Bálint M, Thines M, Feldmeyer B. Genomic basis for drought resistance in European beech forests threatened by climate change. eLife 2021; 10:65532. [PMID: 34132196 PMCID: PMC8266386 DOI: 10.7554/elife.65532] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/07/2021] [Indexed: 12/30/2022] Open
Abstract
In the course of global climate change, Central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought-damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated single-nucleotide polymorphisms (SNPs) throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. An SNP assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding. Climate change is having a serious impact on many ecosystems. In the summer of 2018 and 2019, around two thirds of European beech trees were damaged or killed by extreme drought. It is critical to keep these beech woods healthy, as they are central to the survival of over 6,000 other species of animals and plants. The level of damage caused by the drought varied between forests. However, not all the trees in each forest responded in the same way, with severely damaged trees often sitting next to fully healthy ones. This suggests that the genetic make-up of each tree determines how well it can adapt to drought rather than its local environment. To investigate this further, Pfenninger et al. studied the genome of over 400 European beech trees from the Hesse region in Germany. The samples came from pairs of neighbouring trees that had responded differently to the droughts. The analysis found more than 80 parts of the genome that differed between healthy and damaged trees. Pfenninger et al. then used this information to create a genetic test which can quickly and inexpensively predict how well an individual beech tree might survive in a drought. Applying this test to another 92 trees revealed that it can reliably detect which ones were healthy and which ones were damaged. Beech forests are typically managed by private owners, agencies or breeders that could use this genetic test to select and reproduce trees that are better adapted to drought. The goal now is to develop the test so that it can be used more widely to manage European beech trees and potentially other species.
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Affiliation(s)
- Markus Pfenninger
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Friederike Reuss
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Angelika Kiebler
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Philipp Schönnenbeck
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Cosima Caliendo
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Berardino Cocchiararo
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Sabrina Reuter
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Nico Blüthgen
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Karsten Mody
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Department of Applied Ecology, Hochschule Geisenheim University, Geisenheim, Germany
| | - Bagdevi Mishra
- Biological Archives, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Functional Environmental Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Agricultural Sciences, Nutritional Sciences, and Environmental Management, Universität Giessen, Giessen, Germany
| | - Marco Thines
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Biological Archives, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Barbara Feldmeyer
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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Park S, Wijeratne AJ, Moon Y, Waterland NL. Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing. PLoS One 2021; 16:e0250284. [PMID: 33901201 PMCID: PMC8075263 DOI: 10.1371/journal.pone.0250284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Water deficit limits plant growth and development, resulting in quality loss of horticultural crops. However, there is limited information on gene regulation and signaling pathways related to water deficit stress response at multiple time points. The objective of this research was to investigate global gene expression patterns under water deficit stress to provide an insight into how petunia (Petunia ×hybrida 'Mitchell Diploid') responded in the process of stress. Nine-week-old petunias were irrigated daily or placed under water stress by withholding water. Stressed plants reduced stomatal conductance after five days of water deficit, indicating they perceived stress and initiated stress response mechanisms. To analyze transcriptomic changes at the early stage of water deficit, leaf tissue samples were collected 1, 3, and 5 days after water was withheld for RNA sequencing. Under water deficit stress, 154, 3611, and 980 genes were upregulated and 41, 2806, and 253 genes were downregulated on day 1, 3, and 5, respectively. Gene Ontology analysis revealed that redox homeostasis processes through sulfur and glutathione metabolism pathways, and hormone signal transduction, especially abscisic acid and ethylene, were enriched under water deficit stress. Thirty-four transcription factor families were identified, including members of AP2/ERF, NAC, MYB-related, C2H2, and bZIP families, and TFs in AP2/ERF family was the most abundant in petunia. Interestingly, only one member of GRFs was upregulated on day 1, while most of TFs were differentially expressed on day 3 and/or 5. The transcriptome data from this research will provide valuable molecular resources for understanding the early stages of water stress-responsive networks as well as engineering petunia with enhanced water stress tolerance.
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Affiliation(s)
- Suejin Park
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Asela J. Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Youyoun Moon
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Nicole L. Waterland
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
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8
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Mora-Márquez F, Chano V, Vázquez-Poletti JL, López de Heredia U. TOA: A software package for automated functional annotation in non-model plant species. Mol Ecol Resour 2020; 21:621-636. [PMID: 33070442 DOI: 10.1111/1755-0998.13285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 01/05/2023]
Abstract
The increase of sequencing capacity provided by high-throughput platforms has made it possible to routinely obtain large sets of genomic and transcriptomic sequences from model and non-model organisms. Subsequent genomic analysis and gene discovery in next-generation sequencing experiments are, however, bottlenecked by functional annotation. One common way to perform functional annotation of sets of sequences obtained from next-generation sequencing experiments, is by searching for homologous sequences and accessing the related functional information deposited in genomic databases. Functional annotation is especially challenging for non-model organisms, like many plant species. In such cases, existing free and commercial general-purpose applications may not offer complete and accurate results. We present TOA (Taxonomy-oriented annotation), a Python-based user-friendly open source application designed to establish functional annotation pipelines geared towards non-model plant species that can run in Linux/Mac computers, HPCs and cloud servers. TOA performs homology searches against proteins stored in the PLAZA databases, NCBI RefSeq Plant, Nucleotide Database and Non-Redundant Protein Sequence Database, and outputs functional information from several ontology systems: Gene Ontology, InterPro, EC, KEGG, Mapman and MetaCyc. The software performance was validated by comparing the runtimes, total number of annotated sequences and accuracy of the functional information obtained for several plant benchmark data sets with TOA and other functional annotation solutions. TOA outperformed the other software in terms of number of annotated sequences and accuracy of the annotation and constitutes a good alternative to improve functional annotation in plants. TOA is especially recommended for gymnosperms or for low quality sequence data sets of non-model plants.
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Affiliation(s)
- Fernando Mora-Márquez
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Víctor Chano
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - José Luis Vázquez-Poletti
- GI Arquitectura de Sistemas Distribuidos, Dpto. Arquitectura de Computadores y Automática, Facultad de Informática, Universidad Complutense de Madrid, Madrid, Spain
| | - Unai López de Heredia
- GI Sistemas Naturales e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
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9
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Soltani N, Best T, Grace D, Nelms C, Shumaker K, Romero-Severson J, Moses D, Schuster S, Staton M, Carlson J, Gwinn K. Transcriptome profiles of Quercus rubra responding to increased O 3 stress. BMC Genomics 2020; 21:160. [PMID: 32059640 PMCID: PMC7023784 DOI: 10.1186/s12864-020-6549-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/31/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3). Ozone is formed by the interaction of sunlight, molecular oxygen and by the reactions of chemicals commonly found in industrial and automobile emissions such as nitrogen oxides and volatile organic compounds. Although it is well known that productivity of Northern red oak (Quercus rubra) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O3, limited information is available on its responses to exogenous stimuli at the level of gene expression. RESULTS RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, of which more than 42,000 sequences could be annotated through homology-based searches. A total of 4140 differential expressed genes (DEGs) were detected in response to O3 stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O3-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction. CONCLUSION This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O3. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.
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Affiliation(s)
- Nourolah Soltani
- The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Teo Best
- The Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dantria Grace
- Department of Biological & Environmental Sciences, University of West Alabama, Livingston, AL, 35470, USA
| | - Christen Nelms
- Department of Biological & Environmental Sciences, University of West Alabama, Livingston, AL, 35470, USA
| | - Ketia Shumaker
- Department of Biological & Environmental Sciences, University of West Alabama, Livingston, AL, 35470, USA
| | | | - Daniela Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Nanyang Technological University, Nanyang Avenue, 637551, Singapore
| | - Stephan Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Nanyang Technological University, Nanyang Avenue, 637551, Singapore
| | - Margaret Staton
- The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
| | - John Carlson
- The Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Kimberly Gwinn
- The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
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10
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Müller M, Gailing O. Abiotic genetic adaptation in the Fagaceae. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:783-795. [PMID: 31081234 DOI: 10.1111/plb.13008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Fagaceae can be found in tropical and temperate regions and contain species of major ecological and economic importance. In times of global climate change, tree populations need to adapt to rapidly changing environmental conditions. The predicted warmer and drier conditions will potentially result in locally maladapted populations. There is evidence that major genera of the Fagaceae are already negatively affected by climate change-related factors such as drought and associated biotic stressors. Therefore, knowledge of the mechanisms underlying adaptation is of great interest. In this review, we summarise current literature related to genetic adaptation to abiotic environmental conditions. We begin with an overview of genetic diversity in Fagaceae species and then summarise current knowledge related to drought stress tolerance, bud burst timing and frost tolerance in the Fagaceae. Finally, we discuss the role of hybridisation, epigenetics and phenotypic plasticity in adaptation.
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Affiliation(s)
- M Müller
- Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, University of Goettingen, Göttingen, Germany
| | - O Gailing
- Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
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11
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Johnson LK, Alexander H, Brown CT. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience 2019; 8:giy158. [PMID: 30544207 PMCID: PMC6481552 DOI: 10.1093/gigascience/giy158] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/18/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or "pipelines," on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. RESULTS New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. CONCLUSIONS Given current bioinformatics approaches, there is no single "best" reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
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Affiliation(s)
- Lisa K Johnson
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Harriet Alexander
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - C Titus Brown
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Genome Center, University of California Davis, 451 Health Sciences Dr, Davis, CA 95616, USA
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12
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Physiological and Transcriptomic Analysis of Tree Peony (Paeonia section Moutan DC.) in Response to Drought Stress. FORESTS 2019. [DOI: 10.3390/f10020135] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tree peony (Paeonia section Moutan DC.) is a famous ornamental plant, and P. ostii has been used for seed oil production in China because it is rich in α-linolenic acid. P. ostii has some resistance to drought, but lack of water can severely hinder its growth and development in arid areas. In order to clarify drought stress induced physiological and molecular changes of P. ostia, its physiological and transcriptomic analyses were performed under drought stress, and we found that P. ostii leaves drooped significantly 12 days after treatment and observed a significant increase in all detected physiological indices in response to drought treatment except leaf water content, chlorophyll, and carotenoid content. Meanwhile, the activity of three antioxidant enzymes basically increased under drought treatment. Moreover, drought treatment significantly reduced photosynthetic and chlorophyll fluorescence parameters except non-photochemical quenching (qN), and maintained more intact mesophyll cell structures. Additionally, many differentially expressed genes (DEGs) were found by transcriptome sequencing, which play an important role in P. ostia drought tolerance by controlling a variety of biological processes, including the reactive oxygen species (ROS) system, chlorophyll degradation and photosynthetic competency, fatty acid metabolism, proline metabolism, biosynthesis of secondary metabolism, and plant hormone metabolism. These results provide a better understanding of P. ostii responses to drought stress.
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13
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Mishra B, Gupta DK, Pfenninger M, Hickler T, Langer E, Nam B, Paule J, Sharma R, Ulaszewski B, Warmbier J, Burczyk J, Thines M. A reference genome of the European beech (Fagus sylvatica L.). Gigascience 2018; 7:5017772. [PMID: 29893845 PMCID: PMC6014182 DOI: 10.1093/gigascience/giy063] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/19/2018] [Indexed: 01/09/2023] Open
Abstract
Background The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany. Findings Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum. Conclusions The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
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Affiliation(s)
- Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Deepak K Gupta
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Johannes Gutenberg Universität, Fachbereich Biologie, Institut für Organismische und Molekulare Evolutionsbiologie (iOME), Gresemundweg 2, 55128 Mainz
| | - Thomas Hickler
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Geology, Institute of Geography, Max-von-Laue-Str. 23, D-60438 Frankfurt am Main, Germany
| | - Ewald Langer
- University of Kassel, FB 10, Department of Ecology, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| | - Bora Nam
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Juraj Paule
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Botany and Molecular Evolution, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Rahul Sharma
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Bartosz Ulaszewski
- Kazimierz Wielki University, Department of Genetics, ul. Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Joanna Warmbier
- Kazimierz Wielki University, Department of Genetics, ul. Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Kazimierz Wielki University, Department of Genetics, ul. Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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Wang J, Lin J, Kan J, Wang H, Li X, Yang Q, Li H, Chang Y. Genome-Wide Identification and Functional Prediction of Novel Drought-Responsive lncRNAs in Pyrus betulifolia. Genes (Basel) 2018; 9:E311. [PMID: 29925818 PMCID: PMC6027255 DOI: 10.3390/genes9060311] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/14/2018] [Accepted: 06/14/2018] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence shows that long noncoding RNAs (lncRNAs) play important roles in developmental regulation and many other biological processes in plants. However, identification of lncRNAs in Pyrus betulifolia is limited compared with studies of functional gene expression. Using high-throughput sequencing technology, the transcriptome of P. betulifolia under drought stress was analyzed to identify lncRNAs. A total of 14,478 lncRNAs were identified, of which 251 were found to be drought-responsive. The putative target genes of these differentially expressed lncRNAs were significantly enriched in metabolic processes, organic substance metabolic processes, macromolecule metabolic processes, and heterocyclic compound binding. Real-time quantitative polymerase chain reaction validation suggested that the results of the RNA sequencing data analysis were reliable. This study will provide genetic resources for pear breeding and provide reference to other pomological studies.
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Affiliation(s)
- Jinxing Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Jing Lin
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Jialiang Kan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Hong Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Xiaogang Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Qingsong Yang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Hui Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Youhong Chang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
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