1
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Kapoor B, Jenkins J, Schmutz J, Zhebentyayeva T, Kuelheim C, Coggeshall M, Heim C, Lasky JR, Leites L, Islam-Faridi N, Romero-Severson J, DeLeo VL, Lucas SM, Lazic D, Gailing O, Carlson J, Staton M. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3 (BETHESDA, MD.) 2023; 13:jkad209. [PMID: 37708394 PMCID: PMC10627279 DOI: 10.1093/g3journal/jkad209] [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: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]
Abstract
Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. Single major QTL regions were identified for vegetative bud break and marcescence, which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and 8 tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomic community, which will expedite comparative genomics and biological studies in Quercus species.
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Affiliation(s)
- Beant Kapoor
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Tatyana Zhebentyayeva
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40506, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Kuelheim
- College of Forest Resources and Environmental Science, Michigan Tech University, Houghton, MI 49931, USA
| | - Mark Coggeshall
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Chris Heim
- Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Leites
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, USDA-FS, SRS-4160, Department of Ecology & Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Victoria L DeLeo
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Lucas
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Desanka Lazic
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - John Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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2
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Couée I. Interplay of Methodology and Conceptualization in Plant Abiotic Stress Signaling. Methods Mol Biol 2023; 2642:3-22. [PMID: 36944870 DOI: 10.1007/978-1-0716-3044-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Characterizing the mechanisms of plant sensitivity and reactivity to physicochemical cues related to abiotic stresses is of utmost importance for understanding plant-environment interactions, adaptations of the sessile lifestyle, and the evolutionary dynamics of plant species and populations. Moreover, plant communities are confronted with an environmental context of global change, involving climate changes, planetary pollutions of soils, waters and atmosphere, and additional anthropogenic changes. The mechanisms through which plants perceive abiotic stress stimuli and transduce stress perception into physiological responses constitute the primary line of interaction between the plant and the environment, and therefore between the plant and global changes. Understanding how plants perceive complex combinations of abiotic stress signals and transduce the resulting information into coordinated responses of abiotic stress tolerance is therefore essential for devising genetic, agricultural, and agroecological strategies that can ensure climate change resilience, global food security, and environmental protection. Discovery and characterization of sensing and signaling mechanisms of plant cells are usually carried out within the general framework of eukaryotic sensing and signal transduction. However, further progress depends on a close relationship between the conceptualization of sensing and signaling processes with adequate methodologies and techniques that encompass biochemical and biophysical approaches, cell biology, molecular biology, and genetics. The integration of subcellular and cellular analyses as well as the integration of in vitro and in vivo analyses are particularly important to evaluate the efficiency of sensing and signaling mechanisms in planta. Major progress has been made in the last 10-20 years with the caveat that cell-specific processes and in vivo processes still remain difficult to analyze and with the additional caveat that the range of plant models under study remains rather limited relatively to plant biodiversity and to the diversity of stress situations.
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Affiliation(s)
- Ivan Couée
- UMR 6553 ECOBIO (Ecosystems-Biodiversity-Evolution), Centre National de la Recherche Scientifique (CNRS), University of Rennes, Rennes, France.
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3
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Rauschendorfer J, Rooney R, Külheim C. Strategies to mitigate shifts in red oak (Quercus sect. Lobatae) distribution under a changing climate. TREE PHYSIOLOGY 2022; 42:2383-2400. [PMID: 35867476 DOI: 10.1093/treephys/tpac090] [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: 11/24/2021] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Red oaks (Quercus sect. Lobatae) are a taxonomic group of hardwood trees, which occur in swamp forests, subtropical chaparral and savannahs from Columbia to Canada. They cover a wide range of ecological niches, and many species are thought to be able to cope with current trends in climate change. Genus Quercus encompasses ca. 500 species, of which ca. 80 make up sect. Lobatae. Species diversity is greatest within the southeastern USA and within the northern and eastern regions of Mexico. This review discusses the weak reproductive barriers between species of red oaks and the effects this has on speciation and niche range. Distribution and diversity have been shaped by drought adaptations common to the species of sect. Lobatae, which enable them to fill various xeric niches across the continent. Drought adaptive traits of this taxonomic group include deciduousness, deep tap roots, ring-porous xylem, regenerative stump sprouting, greater leaf thickness and smaller stomata. The complex interplay between these anatomical and morphological traits has given red oaks features of drought tolerance and avoidance. Here, we discuss physiological and genetic components of these adaptations to address how many species of sect. Lobatae reside within xeric sites and/or sustain normal metabolic function during drought. Although extensive drought adaptation appears to give sect. Lobatae a resilience to climate change, aging tree stands, oak life history traits and the current genetic structures place many red oak species at risk. Furthermore, oak decline, a complex interaction between abiotic and biotic agents, has severe effects on red oaks and is likely to accelerate species decline and fragmentation. We suggest that assisted migration can be used to avoid species fragmentation and increase climate change resilience of sect. Lobatae.
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Affiliation(s)
- James Rauschendorfer
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rebecca Rooney
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Carsten Külheim
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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4
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Malec M, Kurban H, Dalkilic M. ccImpute: an accurate and scalable consensus clustering based algorithm to impute dropout events in the single-cell RNA-seq data. BMC Bioinformatics 2022; 23:291. [PMID: 35869420 PMCID: PMC9306045 DOI: 10.1186/s12859-022-04814-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/27/2022] [Indexed: 12/13/2022] Open
Abstract
Background In recent years, the introduction of single-cell RNA sequencing (scRNA-seq) has enabled the analysis of a cell’s transcriptome at an unprecedented granularity and processing speed. The experimental outcome of applying this technology is a \documentclass[12pt]{minimal}
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\begin{document}$$M \times N$$\end{document}M×N matrix containing aggregated mRNA expression counts of M genes and N cell samples. From this matrix, scientists can study how cell protein synthesis changes in response to various factors, for example, disease versus non-disease states in response to a treatment protocol. This technology’s critical challenge is detecting and accurately recording lowly expressed genes. As a result, low expression levels tend to be missed and recorded as zero - an event known as dropout. This makes the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. Results To address this problem, we propose an approach to measure cell similarity using consensus clustering and demonstrate an effective and efficient algorithm that takes advantage of this new similarity measure to impute the most probable dropout events in the scRNA-seq datasets. We demonstrate that our approach exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities. Conclusions ccImpute is an effective algorithm to correct for dropout events and thus improve downstream analysis of scRNA-seq data. ccImpute is implemented in R and is available at https://github.com/khazum/ccImpute.
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5
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Gan C, Liu Z, Pang B, Zuo D, Hou Y, Zhou L, Yu J, Chen L, Wang H, Gu L, Du X, Zhu B, Yi Y. Integrative physiological and transcriptome analyses provide insights into the Cadmium (Cd) tolerance of a Cd accumulator: Erigeron canadensis. BMC Genomics 2022; 23:778. [PMID: 36443662 PMCID: PMC9703714 DOI: 10.1186/s12864-022-09022-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022] Open
Abstract
Cadmium (Cd) is a highly toxic pollutant in soil and water that severely hampers the growth and reproduction of plants. Phytoremediation has been presented as a cost-effective and eco-friendly method for addressing heavy metal pollution. However, phytoremediation is restricted by the limited number of accumulators and the unknown mechanisms underlying heavy metal tolerance. In this study, we demonstrated that Erigeron canadensis (Asteraceae), with its strong adaptability, is tolerant to intense Cd stress (2 mmol/L CdCl2 solution). Moreover, E. canadensis exhibited a strong ability to accumulate Cd2+ when treated with CdCl2 solution. The activity of some antioxidant enzymes, as well as the malondialdehyde (MDA) level, was significantly increased when E. canadensis was treated with different CdCl2 solutions (0.5, 1, 2 mmol/L CdCl2). We found high levels of superoxide dismutase (SOD) and ascorbate peroxidase (APX) activities under 1 mmol/L CdCl2 treatment. Comparative transcriptomic analysis identified 5,284 differentially expressed genes (DEGs) in the roots and 3,815 DEGs in the shoots after E. canadensis plants were exposed to 0.5 mM Cd. Functional annotation of key DEGs indicated that signal transduction, hormone response, and reactive oxygen species (ROS) metabolism responded significantly to Cd. In particular, the DEGs involved in auxin (IAA) and ethylene (ETH) signal transduction were overrepresented in shoots, indicating that these genes are mainly involved in regulating plant growth and thus likely responsible for the Cd tolerance. Overall, these results not only determined that E. canadensis can be used as a potential accumulator of Cd but also provided some clues regarding the mechanisms underlying heavy metal tolerance.
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Affiliation(s)
- Chenchen Gan
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Zhaochao Liu
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Biao Pang
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Dan Zuo
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Yunyan Hou
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Lizhou Zhou
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Jie Yu
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Li Chen
- grid.449845.00000 0004 1757 5011School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100 People’s Republic of China
| | - Hongcheng Wang
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Lei Gu
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Xuye Du
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Bin Zhu
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Yin Yi
- grid.443395.c0000 0000 9546 5345School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
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6
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Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How. Int J Mol Sci 2022; 23:ijms23179980. [PMID: 36077370 PMCID: PMC9456323 DOI: 10.3390/ijms23179980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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7
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Dias MC, Santos C, Araújo M, Barros PM, Oliveira M, de Oliveira JMPF. Quercus suber Roots Activate Antioxidant and Membrane Protective Processes in Response to High Salinity. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040557. [PMID: 35214887 PMCID: PMC8875824 DOI: 10.3390/plants11040557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 05/27/2023]
Abstract
Cork oak (Quercus suber) is a species native to Mediterranean areas and its adaptation to the increasingly prevalent abiotic stresses, such as soil salinization, remain unknown. In sequence with recent studies on salt stress response in the leaf, it is fundamental to uncover the plasticity of roots directly exposed to high salinity to better understand how Q. suber copes with salt stress. In the present study we aimed to unveil the antioxidants and key-genes involved in the stress-responses (early vs. later responses) of Q. suber roots exposed to high salinity. Two-month-old Q. suber plants were watered with 300 mM NaCl solution and enzymatic and non-enzymatic antioxidants, lipid peroxidation and the relative expression of genes related to stress response were analysed 8 h and 6 days after salt treatment. After an 8 h of exposure, roots activated the expression of QsLTI30 and QsFAD7 genes involved in stress membrane protection, and QsRAV1 and QsCZF1 genes involved in tolerance and adaptation. As a result of the continued salinity stress (6 days), lipid peroxidation increased, which was associated with an upregulation of QsLTI30 gene. Moreover, other protective mechanisms were activated, such as the upregulation of genes related to antioxidant status, QsCSD1 and QsAPX2, and the increase of the antioxidant enzyme activities of superoxide dismutase, catalase, and ascorbate peroxidase, concomitantly with total antioxidant activity and phenols. These data suggest a response dependent on the time of salinity exposure, leading Q. suber roots to adopt protective complementary strategies to deal with salt stress.
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Affiliation(s)
- Maria Celeste Dias
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (M.C.D.); (M.A.)
| | - Conceição Santos
- LAQV, REQUIMTE, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal;
- IB2 Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Márcia Araújo
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (M.C.D.); (M.A.)
- IB2 Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro M. Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress, Av. da República, 2780-157 Oeiras, Portugal; (P.M.B.); (M.O.)
| | - Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress, Av. da República, 2780-157 Oeiras, Portugal; (P.M.B.); (M.O.)
| | - José Miguel P. Ferreira de Oliveira
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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8
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Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis. FORESTS 2021. [DOI: 10.3390/f12030364] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.
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9
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Arias-Baldrich C, Silva MC, Bergeretti F, Chaves I, Miguel C, Saibo NJM, Sobral D, Faria D, Barros PM. CorkOakDB-The Cork Oak Genome Database Portal. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6056470. [PMID: 33382885 PMCID: PMC7774466 DOI: 10.1093/database/baaa114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/04/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022]
Abstract
Quercus suber (cork oak) is an evergreen tree native to the Mediterranean basin, which plays a key role in the ecology and economy of this area. Over the last decades, this species has gone through an observable decline, mostly due to environmental factors. Deciphering the mechanisms of cork oak's response to the environment and getting a deep insight into its biology are crucial to counteract biotic and abiotic stresses compromising the stability of a unique ecosystem. In the light of these setbacks, the publication of the genome in 2018 was a major step towards understanding the genetic make-up of this species. In an effort to integrate this information in a comprehensive, accessible and intuitive format, we have developed The Cork Oak Genome Database Portal (CorkOakDB). The CorkOakDB is supported by the BioData.pt e-infrastructure, the Portuguese ELIXIR node for biological data. The portal gives public access to search and explore the curated genomic and transcriptomic data on this species. Moreover, CorkOakDB provides a user-friendly interface and functional tools to help the research community take advantage of the increased accessibility to genomic information. A study case is provided to highlight the functionalities of the portal. CorkOakDB guarantees the update, curation and data collection, aiming to collect data besides the genetic/genomic information, in order to become the main repository in cork oak research. Database URL: http://corkoakdb.org/.
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Affiliation(s)
- Cirenia Arias-Baldrich
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras 2780-156, Lisboa, Portugal.,Department of Biological and Medical Sciences, Oxford Brookes University, Headington Campus, Oxford OX3 0BP, UK
| | - Marta Contreiras Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Lisboa, Portugal
| | - Filippo Bergeretti
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Lisboa, Portugal
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Lisboa, Portugal.,Instituto de Biologia Experimental Tecnológica (iBET), Av. da República, 2780-157 Oeiras, Lisboa, Portugal
| | - Célia Miguel
- Instituto de Biologia Experimental Tecnológica (iBET), Av. da República, 2780-157 Oeiras, Lisboa, Portugal.,Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Lisboa, Portugal
| | - Daniel Sobral
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras 2780-156, Lisboa, Portugal.,UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, Caparica 2825-149, Setúbal, Portugal
| | - Daniel Faria
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras 2780-156, Lisboa, Portugal.,INESC-ID- Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento, Rua Alves Redol, Lisboa 1000-029, Portugal
| | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Lisboa, Portugal
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10
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Genes, pathways and networks responding to drought stress in oil palm roots. Sci Rep 2020; 10:21303. [PMID: 33277563 PMCID: PMC7719161 DOI: 10.1038/s41598-020-78297-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/18/2020] [Indexed: 12/28/2022] Open
Abstract
Oil palm is the most productive oilseed crop and its oil yield is seriously affected by frequent drought stress. However, little is known about the molecular responses of oil palm to drought stress. We studied the root transcriptomic responses of oil palm seedlings under 14-day drought stress. We identified 1293 differentially expressed genes (DEGs), involved in several molecular processes, including cell wall biogenesis and functions, phenylpropanoid biosynthesis and metabolisms, ion transport and homeostasis and cellular ketone metabolic process, as well as small molecule biosynthetic process. DEGs were significantly enriched into two categories: hormone regulation and metabolism, as well as ABC transporters. In addition, three protein–protein interaction networks: ion transport, reactive nitrogen species metabolic process and nitrate assimilation, were identified to be involved in drought stress responses. Finally, 96 differentially expressed transcription factors were detected to be associated with drought stress responses, which were classified into 28 families. These results provide not only novel insights into drought stress responses, but also valuable genomic resources to improve drought tolerance of oil palm by both genetic modification and selective breeding.
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11
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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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Genome-Wide Identification of Epigenetic Regulators in Quercus suber L. Int J Mol Sci 2020; 21:ijms21113783. [PMID: 32471127 PMCID: PMC7313042 DOI: 10.3390/ijms21113783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
Modifications of DNA and histones, including methylation and acetylation, are critical for the epigenetic regulation of gene expression during plant development, particularly during environmental adaptation processes. However, information on the enzymes catalyzing all these modifications in trees, such as Quercus suber L., is still not available. In this study, eight DNA methyltransferases (DNA Mtases) and three DNA demethylases (DDMEs) were identified in Q. suber. Histone modifiers involved in methylation (35), demethylation (26), acetylation (8), and deacetylation (22) were also identified in Q. suber. In silico analysis showed that some Q. suber DNA Mtases, DDMEs and histone modifiers have the typical domains found in the plant model Arabidopsis, which might suggest a conserved functional role. Additional phylogenetic analyses of the DNA and histone modifier proteins were performed using several plant species homologs, enabling the classification of the Q. suber proteins. A link between the expression levels of each gene in different Q. suber tissues (buds, flowers, acorns, embryos, cork, and roots) with the functions already known for their closest homologs in other species was also established. Therefore, the data generated here will be important for future studies exploring the role of epigenetic regulators in this economically important species.
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Ghafari H, Hassanpour H, Jafari M, Besharat S. Physiological, biochemical and gene-expressional responses to water deficit in apple subjected to partial root-zone drying (PRD). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:333-346. [PMID: 32004917 DOI: 10.1016/j.plaphy.2020.01.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/07/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Water scarcity is one of the major factors limiting apple production. Partial root-zone drying (PRD) is a water-saving irrigation technique necessary to improve the efficiency of irrigation techniques to optimize the amount of fruit produced with the volume of water used. The apple trees cv. Red Delicious were exposed to four treatments, including (1) control with 100% of the crop evapotranspiration (ETc) needs; (2) alternate partial root-zone drying with 75% of the ETc needs (APRD75); (3) fixed partial root-zone drying with 75% of the ETc needs (FPRD75); (4) fixed partial root-zone irrigation with 50% of the ETc needs (FPRD50) in a semiarid region of Iran. Results showed that leaf water potential (Ψ leaf), and chlorophyll were significantly decreased in FPRD50 compared to control and other PRD treatments. APRD75 and FPRD75 treatments significantly enhanced (+) -catechin (+C), epicatechin (EC), chlorogenic acid (CGA), caffeic acid (CA) as well as increased water use efficiency (WUE) (by 30-40% compared to control) without significant reduction of yield. PRD reduced gibberellic acid (GA3) and kinetin, while, increased the abscisic acid (ABA) and salicylic acid (SA) levels. The abiotic stress-responsive transcription factors (TFs) MdoMYB121, MdoMYB155, MdbZIP2, and MdbZIP48 were highly expressed in all PRD treatments. Our results demonstrated that APRD75 and FPRD75 have the potential to stimulate antioxidant defense mechanisms, hormonal signaling pathways, and expression of drought-tolerance TFs to improve WUE while maintaining crop yield. Therefore, APRD75andFPRD75 with water savings as compared to full irrigation might be a suitable strategy for irrigation apple trees under water scarcity.
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Affiliation(s)
- Hajar Ghafari
- Department of Horticultural Sciences, Faculty of Agricultural Sciences, Urmia University, Urmia, Iran
| | - Hamid Hassanpour
- Department of Horticultural Sciences, Faculty of Agricultural Sciences, Urmia University, Urmia, Iran.
| | - Morad Jafari
- Department of Plant Breeding and Biotechnology, Faculty of Agricultural Sciences, Urmia University, Urmia, Iran
| | - Sina Besharat
- Department of Water Engineering, Faculty of Agricultural Sciences, Urmia University, Urmia, Iran
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14
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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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Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species Transcriptomics. G3-GENES GENOMES GENETICS 2019; 9:3181-3199. [PMID: 31395652 PMCID: PMC6778798 DOI: 10.1534/g3.119.400456] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The impact of climate change that comes with a dramatic increase of long periods of extreme summer drought associated with heat is a fundamental challenge for European forests. As a result, forests are expected to shift their distribution patterns toward north-east, which may lead to a dramatic loss in value of European forest land. Consequently, unraveling key processes that underlie drought stress tolerance is not only of great scientific but also of utmost economic importance for forests to withstand future heat and drought wave scenarios. To reveal drought stress-related molecular patterns we applied cross-species comparative transcriptomics of three major European oak species: the less tolerant deciduous pedunculate oak (Quercus robur), the deciduous but quite tolerant pubescent oak (Q. pubescens), and the very tolerant evergreen holm oak (Q. ilex). We found 415, 79, and 222 differentially expressed genes during drought stress in Q. robur, Q. pubescens, and Q. ilex, respectively, indicating species-specific response mechanisms. Further, by comparative orthologous gene family analysis, 517 orthologous genes could be characterized that may play an important role in drought stress adaptation on the genus level. New regulatory candidate pathways and genes in the context of drought stress response were identified, highlighting the importance of the antioxidant capacity, the mitochondrial respiration machinery, the lignification of the water transport system, and the suppression of drought-induced senescence - providing a valuable knowledge base that could be integrated in breeding programs in the face of climate change.
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Transcriptome profiling of faba bean (Vicia faba L.) drought-tolerant variety hassawi-2 under drought stress using RNA sequencing. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Zhao D, Shi Y, Senthilkumar HA, Qiao Q, Wang Q, Shen Y, Hu G. Enriched networks 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' potentially conferred to drought adaptation of the epiphytic orchid Dendrobium wangliangii. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:31-45. [PMID: 30804628 PMCID: PMC6352522 DOI: 10.1007/s12298-018-0607-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 08/12/2018] [Accepted: 09/24/2018] [Indexed: 05/17/2023]
Abstract
Dendrobium wangliangii is an endangered and epiphytic orchid with tolerance to seasonally extreme arid conditions and occurs exclusively in the hot-dry valley area of southwestern China. To reveal its molecular basis responsible for ecological adaptation, large-scale transcriptome sequencing was performed using Illumina sequencing with pooled mRNA extracted from whole plants and pseudobulbs during drought and rainy seasons. Based on the target transcript selection, the differentially expressed genes were related to 8 well-known drought-tolerant categories, and to morphological traits in resistance to water stress including pseudobulbs and roots. Further gene ontology enrichment analysis revealed that 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' were the two most important aspects in resistance to drought stress with respect to the whole plant. In addition, the difference in the number and category of differentially expressed genes in whole plant and stem suggested the involvement of genes specifically localized in the stem, such as GTP-binding protein, lipases, signaling related transcripts and those involved in the ATP metabolic process. The comprehensive analysis of the epiphytic orchid in response to water deprivation indicates that integral tactics lead to active adaptation as a basal defense response to drought stress by the endangered epiphyte, including the collaboration of metabolic processes, responses to a various stimulus and other candidate genes contribute to its extreme drought tolerance. Insights from this study can be further utilized to understand stress-responsive genes in other medicinally important species and to improve the drought tolerance of food crops.
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Affiliation(s)
- Dake Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, China
| | - Yana Shi
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, China
| | | | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, China
| | - Qiuxia Wang
- Key Laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan Province, Kunming University, Kunming, China
| | - Yong Shen
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guangwan Hu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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18
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Alghamdi SS, Khan MA, Ammar MH, Sun Q, Huang L, Migdadi HM, El-Harty EH, Al-Faifi SA. Characterization of drought stress-responsive root transcriptome of faba bean ( Vicia faba L.) using RNA sequencing. 3 Biotech 2018; 8:502. [PMID: 30498675 PMCID: PMC6258570 DOI: 10.1007/s13205-018-1518-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/14/2018] [Indexed: 11/29/2022] Open
Abstract
Drought and salinity are the major factors that limit the faba bean (Vicia faba L.) production worldwide. The aim of this study is to identify the water stress differentially expressed genes (DEGs) through the root transcriptome analyses of the drought-tolerant Hassawi 2 genotype at vegetative and flowering stages. A total of 624.8 M high-quality Illumina reads were generated and assembled into 198,155 all-unigenes with a mean length of 738 bp and an N50 length of 1347 bp. Among all-unigenes, 78,262 were assigned to non-redundant (Nr), 66,254 to nucleotide (Nt), 54,034 to KEGG, and 43,913 to gene ontology (GO) annotations. A total of 36,834 and 35,510 unigenes were differentially expressed at the vegetative and flowering stages of Hassawi 2 under drought stress, respectively. The majority of unigenes were down-regulated at both developmental stages. However, the number of genes up-regulated (15,366) at the flowering stage exceeded the number of those up-regulated (14,097) at the vegetative stage, and the number of genes down-regulated (20,144) at the flowering stage was smaller than the number of those down-regulated (22,737) at the vegetative stage. The drought stress-responsive differentially expressed unigenes coded for various regulatory proteins, including protein kinases and phosphatases, transcription factors and plant hormones and functional proteins including enzymes for osmoprotectant, detoxification and transporters were differentially expressed, most of which were largely up-regulated. Moreover, a substantial proportion of the DEGs identified in this study were novel, most exhibited a significant change in their expression levels under water stress, making them an unexploited resource that might control specific responses to drought stress in the faba bean. Finally, qRT-PCR results were found almost consistent with the results of next-generation sequencing. Our data will help in understanding the drought tolerance mechanisms in plants and will provide resources for functional genomics.
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Affiliation(s)
- Salem S. Alghamdi
- Legume Research Group, Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad A. Khan
- Legume Research Group, Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | | | - Qiwei Sun
- International Bioinformatics Center, BGI Genomics, Co., Ltd, Shenzhen, Guangdong China
| | - Lihua Huang
- International Bioinformatics Center, BGI Genomics, Co., Ltd, Shenzhen, Guangdong China
| | - Hussein M. Migdadi
- Legume Research Group, Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ehab H. El-Harty
- Legume Research Group, Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Sulieman A. Al-Faifi
- Legume Research Group, Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
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De Dato G, Teani A, Mattioni C, Marchi M, Monteverdi MC, Ducci F. Delineation of seed collection zones based on environmental and genetic characteristics for Quercus suber L. in Sardinia, Italy. IFOREST - BIOGEOSCIENCES AND FORESTRY 2018. [PMID: 0 DOI: 10.3832/ifor2572-011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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20
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Bielsa B, Hewitt S, Reyes-Chin-Wo S, Dhingra A, Rubio-Cabetas MJ. Identification of water use efficiency related genes in 'Garnem' almond-peach rootstock using time-course transcriptome analysis. PLoS One 2018; 13:e0205493. [PMID: 30308016 PMCID: PMC6181374 DOI: 10.1371/journal.pone.0205493] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/26/2018] [Indexed: 11/19/2022] Open
Abstract
Drought is one of the main abiotic stresses with far-reaching ecological and socioeconomic impacts, especially in perennial food crops such as Prunus. There is an urgent need to identify drought resilient rootstocks that can adapt to changes in water availability. In this study, we tested the hypothesis that PEG-induced water limitation stress will simulate drought conditions and drought-related genes, including transcription factors (TFs), will be differentially expressed in response to this stress. 'Garnem' genotype, an almond × peach hybrid [P. amygdalus Batsch, syn P. dulcis (Mill.) x P. persica (L.) Batsch] was exposed to PEG-6000 solution, and a time-course transcriptome analysis of drought-stressed roots was performed at 0, 2 and 24 h time points post-stress. Transcriptome analysis resulted in the identification of 12,693 unique differentially expressed contigs (DECs) at the 2 h time point, and 7,705 unique DECs at the 24 h time point after initiation of the drought treatment. Interestingly, three drought-induced genes, directly related to water use efficiency (WUE) namely, ERF023 TF; LRR receptor-like serine/threonine-kinase ERECTA; and NF-YB3 TF, were found induced under stress. The RNAseq results were validated with quantitative RT-PCR analysis of eighteen randomly selected differentially expressed contigs (DECs). Pathway analysis in the present study provides valuable information regarding metabolic events that occur during stress-induced signalling in 'Garnem' roots. This information is expected to be useful in understanding the potential mechanisms underlying drought stress responses and drought adaptation strategies in Prunus species.
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Affiliation(s)
- Beatriz Bielsa
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
| | - Seanna Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | | | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - María José Rubio-Cabetas
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
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21
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Ramos AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I, Simões F, Abreu I, Carrasquinho I, Faro C, Guimarães JB, Mendonça D, Nóbrega F, Rodrigues L, Saibo NJM, Varela MC, Egas C, Matos J, Miguel CM, Oliveira MM, Ricardo CP, Gonçalves S. The draft genome sequence of cork oak. Sci Data 2018; 5:180069. [PMID: 29786699 PMCID: PMC5963338 DOI: 10.1038/sdata.2018.69] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/26/2018] [Indexed: 12/21/2022] Open
Abstract
Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.
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Affiliation(s)
- António Marcos Ramos
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja 7801-908, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora 7006-554, Portugal
| | - Ana Usié
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja 7801-908, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora 7006-554, Portugal
| | - Pedro Barbosa
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja 7801-908, Portugal
| | - Pedro M. Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras 2780-157, Portugal
| | - Tiago Capote
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja 7801-908, Portugal
| | - Inês Chaves
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras 2780-157, Portugal
| | - Fernanda Simões
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Oeiras 2780-157, Portugal
| | - Isabl Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras 2780-157, Portugal
| | - Isabel Carrasquinho
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Oeiras 2780-157, Portugal
| | - Carlos Faro
- Biocant – Associação de Transferência de Biotecnologia, Cantanhede 3060-197, Portugal
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Coimbra 3004-504, Portugal
| | - Joana B. Guimarães
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Oeiras 2780-157, Portugal
| | - Diogo Mendonça
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Oeiras 2780-157, Portugal
| | - Filomena Nóbrega
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Oeiras 2780-157, Portugal
| | - Leandra Rodrigues
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja 7801-908, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora 7006-554, Portugal
| | - Nelson J. M. Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras 2780-157, Portugal
| | - Maria Carolina Varela
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Oeiras 2780-157, Portugal
| | - Conceição Egas
- Biocant – Associação de Transferência de Biotecnologia, Cantanhede 3060-197, Portugal
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Coimbra 3004-504, Portugal
| | - José Matos
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Oeiras 2780-157, Portugal
- Centre for Ecology, Evolution and Environmental Changes - cE3c, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Célia M. Miguel
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras 2780-157, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa (FCUL), Lisboa 1749-016, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras 2780-157, Portugal
| | - Cândido P. Ricardo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras 2780-157, Portugal
| | - Sónia Gonçalves
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja 7801-908, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora 7006-554, Portugal
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Jia J, Zhou J, Shi W, Cao X, Luo J, Polle A, Luo ZB. Comparative transcriptomic analysis reveals the roles of overlapping heat-/drought-responsive genes in poplars exposed to high temperature and drought. Sci Rep 2017; 7:43215. [PMID: 28233854 PMCID: PMC5324098 DOI: 10.1038/srep43215] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 01/20/2017] [Indexed: 02/03/2023] Open
Abstract
High temperature (HT) and drought are both critical factors that constrain tree growth and survival under global climate change, but it is surprising that the transcriptomic reprogramming and physiological relays involved in the response to HT and/or drought remain unknown in woody plants. Thus, Populus simonii saplings were exposed to either ambient temperature or HT combined with sufficient watering or drought. RNA-sequencing analysis showed that a large number of genes were differentially expressed in poplar roots and leaves in response to HT and/or desiccation, but only a small number of these genes were identified as overlapping heat-/drought-responsive genes that are mainly involved in RNA regulation, transport, hormone metabolism, and stress. Furthermore, the overlapping heat-/drought-responsive genes were co-expressed and formed hierarchical genetic regulatory networks under each condition compared. HT-/drought-induced transcriptomic reprogramming is linked to physiological relays in poplar roots and leaves. For instance, HT- and/or drought-induced abscisic acid accumulation and decreases in auxin and other phytohormones corresponded well with the differential expression of a few genes involved in hormone metabolism. These results suggest that overlapping heat-/drought-responsive genes will play key roles in the transcriptional and physiological reconfiguration of poplars to HT and/or drought under future climatic scenarios.
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Affiliation(s)
- Jingbo Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Jing Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenguang Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xu Cao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Jie Luo
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Andrea Polle
- Büsgen-Institute, Department of Forest Botany and Tree Physiology, Georg-August University, Büsgenweg 2, 37077 Göttingen, Germany
| | - Zhi-Bin Luo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Carvalho LC, Silva M, Coito JL, Rocheta MP, Amâncio S. Design of a Custom RT-qPCR Array for Assignment of Abiotic Stress Tolerance in Traditional Portuguese Grapevine Varieties. FRONTIERS IN PLANT SCIENCE 2017; 8:1835. [PMID: 29118776 PMCID: PMC5660995 DOI: 10.3389/fpls.2017.01835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/10/2017] [Indexed: 05/21/2023]
Abstract
Widespread agricultural losses attributed to drought, often combined with high temperatures, frequently occur in the field, namely in Mediterranean climate areas, where the existing scenarios for climate change indicate an increase in the frequency of heat waves and severe drought events in summer. Grapevine (Vitis vinifera L.) is the most cultivated fruit species in the world and the most valuable one and is a traditional Mediterranean species. Currently, viticulture must adjust to impending climate changes that are already pushing vine-growers toward the use of ancient and resilient varieties. Portugal is very rich in grapevine biodiversity, however, currently, 90% of the total producing area is planted with only 16 varieties. There is a pressing need to understand the existing genetic diversity and the physiological potential of the varieties/genotypes available to be able to respond to climate changes. With the above scenario in mind, an assembly of 65 differentially expresses genes (DEGs) previously identified as responsive to abiotic stresses in two well studied genotypes, 'Touriga Nacional' and 'Trincadeira,' was designed to scan the gene expression of leaf samples from 10 traditional Portuguese varieties growing in two regions with distinct environmental conditions. Forty-five of those DEGs proved to be associated to "abiotic stress" and were chosen to build a custom qPCR array to identify uncharacterized genotypes as sensitive or tolerant to abiotic stress. According to the experimental set-up behind the array design these DEGs can also be used as indicators of the main abiotic stress that the plant is subjected and responding to (drought, heat, or excess light).
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Ksouri N, Jiménez S, Wells CE, Contreras-Moreira B, Gogorcena Y. Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1715. [PMID: 27933070 PMCID: PMC5120087 DOI: 10.3389/fpls.2016.01715] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/31/2016] [Indexed: 05/02/2023]
Abstract
Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear. Hence, in this study, high-throughput sequencing (RNA-seq) was performed to assess the transcriptomic changes and the key genes involved in the response to drought in root tissues (GF677 rootstock) and leaf tissues (graft, var. Catherina) subjected to 16 days of drought stress. In total, 12 RNA libraries were constructed and sequenced. This generated a total of 315 M raw reads from both tissues, which allowed the assembly of 22,079 and 17,854 genes associated with the root and leaf tissues, respectively. Subsets of 500 differentially expressed genes (DEGs) in roots and 236 in leaves were identified and functionally annotated with 56 gene ontology (GO) terms and 99 metabolic pathways, which were mostly associated with aminobenzoate degradation and phenylpropanoid biosynthesis. The GO analysis highlighted the biological functions that were exclusive to the root tissue, such as "locomotion," "hormone metabolic process," and "detection of stimulus," indicating the stress-buffering role of the GF677 rootstock. Furthermore, the complex regulatory network involved in the drought response was revealed, involving proteins that are associated with signaling transduction, transcription and hormone regulation, redox homeostasis, and frontline barriers. We identified two poorly characterized genes in P. persica: growth-regulating factor 5 (GRF5), which may be involved in cellular expansion, and AtHB12, which may be involved in root elongation. The reliability of the RNA-seq experiment was validated by analyzing the expression patterns of 34 DEGs potentially involved in drought tolerance using quantitative reverse transcription polymerase chain reaction. The transcriptomic resources generated in this study provide a broad characterization of the acclimation of P. persica to drought, shedding light on the major molecular responses to the most important environmental stressor.
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Affiliation(s)
- Najla Ksouri
- Department of Pomology, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Sergio Jiménez
- Department of Pomology, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | | | - Bruno Contreras-Moreira
- Laboratory of Computational and Structural Biology, Department of Genetics and Plant Production, Estación Experimental de Aula Dei – Consejo Superior de Investigaciones CientíficasZaragoza, Spain
- Fundación ARAIDZaragoza, Spain
- *Correspondence: Yolanda Gogorcena, Bruno Contreras-Moreira,
| | - Yolanda Gogorcena
- Department of Pomology, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones CientíficasZaragoza, Spain
- *Correspondence: Yolanda Gogorcena, Bruno Contreras-Moreira,
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