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Florez-Rueda AM, Miguel CM, Figueiredo DD. Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1134-1157. [PMID: 38709819 DOI: 10.1111/tpj.16786] [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: 10/13/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.
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Affiliation(s)
- Ana Marcela Florez-Rueda
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Karl-Liebknechts-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Célia M Miguel
- Faculty of Sciences, Biosystems and Integrative Sciences Institute (BioISI), University of Lisbon, Lisboa, Portugal
| | - Duarte D Figueiredo
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
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2
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Cheng A, Sadali NM, Rejab NA, Uludag A. Piece and parcel of gymnosperm organellar genomes. PLANTA 2024; 260:14. [PMID: 38829418 DOI: 10.1007/s00425-024-04449-4] [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: 03/07/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
MAIN CONCLUSION Significant past, present, and potential future research into the organellar (plastid and mitochondrial) genomes of gymnosperms that can provide insight into the unknown origin and evolution of plants is highlighted. Gymnosperms are vascular seed plants that predominated the ancient world before their sister clade, angiosperms, took over during the Late Cretaceous. The divergence of gymnosperms and angiosperms took place around 300 Mya, with the latter evolving into the diverse group of flowering plants that dominate the plant kingdom today. Although gymnosperms have reportedly made some evolutionary innovations, the literature on their genome advances, particularly their organellar (plastid and mitochondrial) genomes, is relatively scattered and fragmented. While organellar genomes can shed light on plant origin and evolution, they are frequently overlooked, due in part to their limited contribution to gene expression and lack of evolutionary dynamics when compared to nuclear genomes. A better understanding of gymnosperm organellar genomes is critical because they reveal genetic changes that have contributed to their unique adaptations and ecological success, potentially aiding in plant survival, enhancement, and biodiversity conservation in the face of climate change. This review reveals significant information and gaps in the existing knowledge base of organellar genomes in gymnosperms, as well as the challenges and research needed to unravel their complexity.
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Affiliation(s)
- Acga Cheng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Najiah Mohd Sadali
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ahmet Uludag
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Faculty of Agriculture, Canakkale Onsekiz Mart University, 17100, Canakkale, Türkiye
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3
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Li HZ, Wu H, Song KK, Zhao HH, Tang XY, Zhang XH, Wang D, Dong SL, Liu F, Wang J, Li ZC, Yang L, Xiang QZ. Transcriptome analysis revealed enrichment pathways and regulation of gene expression associated with somatic embryogenesis in Camellia sinensis. Sci Rep 2023; 13:15946. [PMID: 37743377 PMCID: PMC10518320 DOI: 10.1038/s41598-023-43355-9] [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: 06/02/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023] Open
Abstract
The high frequency, stable somatic embryo system of tea has still not been established due to the limitations of its own characteristics and therefore severely restricts the genetic research and breeding process of tea plants. In this study, the transcriptome was used to illustrate the mechanisms of gene expression regulation in the somatic embryogenesis of tea plants. The number of DEGs for the (IS intermediate stage)_PS (preliminary stage), ES (embryoid stage)_IS and ES_PS stages were 109, 2848 and 1697, respectively. The enrichment analysis showed that carbohydrate metabolic processes were considerably enriched at the ES_IS stage and performed a key role in somatic embryogenesis, while enhanced light capture in photosystem I could provide the material basis for carbohydrates. The pathway analysis showed that the enriched pathways in IS_PS process were far less than those in ES_IS or ES_PS, and the photosynthesis and photosynthetic antenna protein pathway of DEGs in ES_IS or ES_PS stage were notably enriched and up-regulated. The key photosynthesis and photosynthesis antenna protein pathways and the Lhcb1 gene were discovered in tea plants somatic embryogenesis. These results were of great significance to clarify the mechanism of somatic embryogenesis and the breeding research of tea plants.
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Affiliation(s)
- Hao-Zhen Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Hui Wu
- AgricultureIsLife, Gembloux Agro-Bio Tech, Liege University, 5030, Gembloux 2, Belgium
| | - Kang-Kang Song
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Hui-Hui Zhao
- Ri Zhao Cha Cang Tea Co. Ltd, Ri'zhao, 276800, China
| | - Xiao-Yan Tang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, He'fei, 230036, China
| | - Xiao-Hua Zhang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Di Wang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Shao-Lin Dong
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Feng Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Jun Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhong-Cong Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China.
| | - Qin-Zeng Xiang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
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4
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Ávila C, Llebrés MT, Castro-Rodríguez V, Lobato-Fernández C, Reymond I, Harvengt L, Trontin JF, Cánovas FM. Identification of Metabolic Pathways Differentially Regulated in Somatic and Zygotic Embryos of Maritime Pine. FRONTIERS IN PLANT SCIENCE 2022; 13:877960. [PMID: 35665168 PMCID: PMC9159154 DOI: 10.3389/fpls.2022.877960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Embryogenesis is a complex phase of conifer development involving hundreds of genes, and a proper understanding of this process is critical not only to produce embryos with different applied purposes but also for comparative studies with angiosperms. A global view of transcriptome dynamics during pine somatic and zygotic embryogenesis is currently missing. Here, we present a genome-wide transcriptome analysis of somatic and zygotic embryos at three developmental stages to identify conserved biological processes and gene functions during late embryogenesis. Most of the differences became more significant as the developmental process progressed from early to cotyledonary stages, and a higher number of genes were differentially expressed in somatic than in zygotic embryos. Metabolic pathways substantially affected included those involved in amino acid biosynthesis and utilization, and this difference was already observable at early developmental stages. Overall, this effect was found to be independent of the line (genotype) used to produce the somatic embryos. Additionally, transcription factors differentially expressed in somatic versus zygotic embryos were analyzed. Some potential hub regulatory genes were identified that can provide clues as to what transcription factors are controlling the process and to how the observed differences between somatic and zygotic embryogenesis in conifers could be regulated.
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Affiliation(s)
- Concepción Ávila
- Grupo de Biología Molecular y Biotecnología (BIO-114), Universidad de Málaga, Málaga, Spain
| | - María Teresa Llebrés
- Grupo de Biología Molecular y Biotecnología (BIO-114), Universidad de Málaga, Málaga, Spain
| | | | - César Lobato-Fernández
- Grupo de Biología Molecular y Biotecnología (BIO-114), Universidad de Málaga, Málaga, Spain
| | - Isabelle Reymond
- BioForBois, Pôle Industrie Bois Construction, Institut Technologique FCBA, Cestas, France
| | - Luc Harvengt
- BioForBois Laboratory, Pôle Industrie Bois Construction, Institut Technologique FCBA, Bordeaux, France
| | - Jean-François Trontin
- BioForBois, Pôle Industrie Bois Construction, Institut Technologique FCBA, Cestas, France
| | - Francisco M Cánovas
- Grupo de Biología Molecular y Biotecnología (BIO-114), Universidad de Málaga, Málaga, Spain
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5
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Yan J, Buer H, Wang YP, Zhula G, Bai YE. Transcriptomic Time-Series Analyses of Gene Expression Profile During Zygotic Embryo Development in Picea mongolica. Front Genet 2021; 12:738649. [PMID: 34659359 PMCID: PMC8513737 DOI: 10.3389/fgene.2021.738649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Zygotic embryogenesis is a critical process during seed development in gymnosperms. However, knowledge on the genome-wide transcriptional activation that guides this process in conifers is limited, especially in Picea mongolica. This tree species is endemic to semiarid habitats of Inner Mongolia in China. To extend what is known about the molecular events underpinning its zygotic embryogenesis, comparative transcriptomic analyses of gene expression in zygotic embryos were performed by RNA sequencing in P. mongolica. Our results showed that most changes in transcript levels occurred in the early embryonic pattering determination and formation of mature embryos. Transcripts related to embryogenic competence, cell division pattern, hormones, and stress response genes were identified during embryogenesis. Auxin is essential for early embryo patterning and pre-cotyledon embryonic formation. However, ABA is a major regulator of embryo maturation. Moreover, we found that methylation-related gene expression is associated with activation of early-stage embryos, late embryogenesis abundant proteins, and storage/energy-related genes with late and mature embryos. Furthermore, network analysis revealed stage-specific and multistage gene expression clusters during embryogenesis. WOX, MYB, AP2, and HLH transcription factors seem more relevant to embryogenesis in different stages. Our results provide large-scale and comprehensive transcriptome data for embryo development in P. mongolica. These data will lay a foundation for the protection and utilization of P. mongolica resources.
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Affiliation(s)
- Jia Yan
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China.,Life Science of College, Inner Mongolia University, Hohhot, China
| | - Ha Buer
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China
| | - Ya Ping Wang
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China
| | - Gegen Zhula
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu E Bai
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China
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6
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Bueno N, Cuesta C, Centeno ML, Ordás RJ, Alvarez JM. In Vitro Plant Regeneration in Conifers: The Role of WOX and KNOX Gene Families. Genes (Basel) 2021; 12:genes12030438. [PMID: 33808690 PMCID: PMC8003479 DOI: 10.3390/genes12030438] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Conifers are a group of woody plants with an enormous economic and ecological importance. Breeding programs are necessary to select superior varieties for planting, but they have many limitations due to the biological characteristics of conifers. Somatic embryogenesis (SE) and de novo organogenesis (DNO) from in vitro cultured tissues are two ways of plant mass propagation that help to overcome this problem. Although both processes are difficult to achieve in conifers, they offer advantages like a great efficiency, the possibilities to cryopreserve the embryogenic lines, and the ability of multiplying adult trees (the main bottleneck in conifer cloning) through DNO. Moreover, SE and DNO represent appropriate experimental systems to study the molecular bases of developmental processes in conifers such as embryogenesis and shoot apical meristem (SAM) establishment. Some of the key genes regulating these processes belong to the WOX and KNOX homeobox gene families, whose function has been widely described in Arabidopsis thaliana. The sequences and roles of these genes in conifers are similar to those found in angiosperms, but some particularities exist, like the presence of WOXX, a gene that putatively participates in the establishment of SAM in somatic embryos and plantlets of Pinus pinaster.
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Affiliation(s)
- Natalia Bueno
- Plant Physiology, Biotechnology Institute of Asturias (IUBA), Department of Organisms and Systems Biology, University of Oviedo, ES-33071 Oviedo, Spain; (N.B.); (C.C.); (R.J.O.)
| | - Candela Cuesta
- Plant Physiology, Biotechnology Institute of Asturias (IUBA), Department of Organisms and Systems Biology, University of Oviedo, ES-33071 Oviedo, Spain; (N.B.); (C.C.); (R.J.O.)
| | - María Luz Centeno
- Plant Physiology, Department of Engineering and Agricultural Sciences, University of León, ES-24071 León, Spain;
| | - Ricardo J. Ordás
- Plant Physiology, Biotechnology Institute of Asturias (IUBA), Department of Organisms and Systems Biology, University of Oviedo, ES-33071 Oviedo, Spain; (N.B.); (C.C.); (R.J.O.)
| | - José M. Alvarez
- Plant Physiology, Biotechnology Institute of Asturias (IUBA), Department of Organisms and Systems Biology, University of Oviedo, ES-33071 Oviedo, Spain; (N.B.); (C.C.); (R.J.O.)
- Correspondence:
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7
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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8
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Pérez-Oliver MA, Haro JG, Pavlović I, Novák O, Segura J, Sales E, Arrillaga I. Priming Maritime Pine Megagametophytes during Somatic Embryogenesis Improved Plant Adaptation to Heat Stress. PLANTS 2021; 10:plants10030446. [PMID: 33652929 PMCID: PMC7996847 DOI: 10.3390/plants10030446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]
Abstract
In the context of global climate change, forest tree research should be addressed to provide genotypes with increased resilience to high temperature events. These improved plants can be obtained by heat priming during somatic embryogenesis (SE), which would produce an epigenetic-mediated transgenerational memory. Thereby, we applied 37 °C or 50 °C to maritime pine (Pinus pinaster) megagametophytes and the obtained embryogenic masses went through the subsequent SE phases to produce plants that were further subjected to heat stress conditions. A putative transcription factor WRKY11 was upregulated in priming-derived embryonal masses, and also in the regenerated P37 and P50 plants, suggesting its role in establishing an epigenetic memory in this plant species. In vitro-grown P50 plants also showed higher cytokinin content and SOD upregulation, which points to a better responsiveness to heat stress. Heat exposure of two-year-old maritime pine plants induced upregulation of HSP70 in those derived from primed embryogenic masses, that also showed better osmotic adjustment and higher increases in chlorophyll, soluble sugars and starch contents. Moreover, ϕPSII of P50 plants was less affected by heat exposure. Thus, our results suggest that priming at 50 °C at the SE induction phase is a promising strategy to improve heat resilience in maritime pine.
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Affiliation(s)
- María Amparo Pérez-Oliver
- Plant Biology Department, Faculty of Pharmacy, Biotechnology and Biomedicine (BiotecMed) Institute, Universidad de Valencia, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain; (M.A.P.-O.); (J.G.H.); (J.S.)
| | - Juan Gregorio Haro
- Plant Biology Department, Faculty of Pharmacy, Biotechnology and Biomedicine (BiotecMed) Institute, Universidad de Valencia, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain; (M.A.P.-O.); (J.G.H.); (J.S.)
| | - Iva Pavlović
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (I.P.); (O.N.)
- Laboratory for Chemical Biology, Division of MoLecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (I.P.); (O.N.)
| | - Juan Segura
- Plant Biology Department, Faculty of Pharmacy, Biotechnology and Biomedicine (BiotecMed) Institute, Universidad de Valencia, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain; (M.A.P.-O.); (J.G.H.); (J.S.)
| | - Ester Sales
- Agrarian and Environmental Sciences Department, Institute of Environmental Sciences (IUCA), University of Zaragoza, High Polytechnic School, Ctra. Cuarte s/n, 22071 Huesca, Spain;
| | - Isabel Arrillaga
- Plant Biology Department, Faculty of Pharmacy, Biotechnology and Biomedicine (BiotecMed) Institute, Universidad de Valencia, Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain; (M.A.P.-O.); (J.G.H.); (J.S.)
- Correspondence:
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Xiao Y, Li J, Zhang Y, Zhang X, Liu H, Qin Z, Chen B. Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus. BMC Genomics 2020; 21:803. [PMID: 33208105 PMCID: PMC7672952 DOI: 10.1186/s12864-020-07214-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/08/2020] [Indexed: 01/11/2023] Open
Abstract
Background Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE. Results We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9229 and 8989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2687 up-regulated and 2581 down-regulated genes shared. Next, we identified 2003 up-regulated and 1958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07214-5.
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Affiliation(s)
- Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Xiaoning Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Hailong Liu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Zihai Qin
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China.
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10
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Song S, Wang Z, Ren Y, Sun H. Full-Length Transcriptome Analysis of the ABCB, PIN/PIN-LIKES, and AUX/LAX Families Involved in Somatic Embryogenesis of Lilium pumilum DC. Fisch. Int J Mol Sci 2020; 21:E453. [PMID: 31936841 PMCID: PMC7014436 DOI: 10.3390/ijms21020453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022] Open
Abstract
Plant cell totipotency is one of the 25 major topics in current scientific research, and somatic embryos are good experimental material for studying cell totipotency. Polar auxin transport plays an important regulatory role in somatic embryogenesis (SE). However, little is known about the auxin transport genes and their regulatory mechanisms in Lilium SE. In this study, we applied single-molecule real-time (SMRT) sequencing to Lilium pumilum DC. Fisch. for the first time and obtained a total of 119,649 transcripts, of which 14 encoded auxin transport genes. Correlation analyses between somatic embryo induction and gene expression under different treatments revealed that auxin transport genes, especially ATP-binding cassette (ABC) transporter B family member 21 (ABCB21) and PIN-FORMED (PIN) LIKES 7 (PILS7), may be key players in SE, and the necessary duration of picloram (PIC) treatment to induce SE is as short as 3 days. Our research provides valuable genetic information on Lilium pumilum, elucidating the candidate auxin transport genes involved in SE and their influencing factors. This study lays a foundation for elucidating the regulatory mechanism of auxin transport in SE.
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Affiliation(s)
- Shengli Song
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (Z.W.); (Y.R.)
| | - Zhiping Wang
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (Z.W.); (Y.R.)
| | - Yamin Ren
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (Z.W.); (Y.R.)
| | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (Z.W.); (Y.R.)
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Horticulture Department, Shenyang Agricultural University, Shenyang 110866, China
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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