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Elbl PM, de Souza DT, Rosado D, de Oliveira LF, Navarro BV, Matioli SR, Floh EIS. Building an embryo: An auxin gene toolkit for zygotic and somatic embryogenesis in Brazilian pine. Gene 2022; 817:146168. [PMID: 34995731 DOI: 10.1016/j.gene.2021.146168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/04/2022]
Abstract
Many studies in the model species Arabidopsis thaliana characterized genes involved in embryo formation. However, much remains to be learned about the portfolio of genes that are involved in signal transduction and transcriptional regulation during plant embryo development in other species, particularly in an evolutionary context, especially considering that some genes involved in embryo patterning are not exclusive of land plants. This study, used a combination of domain architecture phylostratigraphy and phylogenetic reconstruction to investigate the evolutionary history of embryo patterning and auxin metabolism (EPAM) genes in Viridiplantae. This approach shed light on the co-optation of auxin metabolism and other molecular mechanisms that contributed to the radiation of land plants, and specifically to embryo formation. These results have potential to assist conservation programs, by directing the development of tools for obtaining somatic embryos. In this context, we employed this methodology with critically endangered and non-model species Araucaria angustifolia, the Brazilian pine, which is current focus of conservation efforts using somatic embryogenesis. So far, this approach had little success since somatic embryos fail to completely develop. By profiling the expression of genes that we identified as necessary for the emergence of land-plant embryos, we found striking differences between zygotic and somatic embryos that might explain the developmental arrest and be used to improve A. angustifolia somatic culture.
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Affiliation(s)
- Paula M Elbl
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil.
| | - Diego T de Souza
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil; Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, SP, Brazil
| | - Daniele Rosado
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States
| | - Leandro F de Oliveira
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil
| | - Bruno V Navarro
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil; Laboratory of Plant Physiological Ecology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Sergio R Matioli
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Eny I S Floh
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil
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Navarro BV, Elbl P, De Souza AP, Jardim V, de Oliveira LF, Macedo AF, dos Santos ALW, Buckeridge MS, Floh EIS. Carbohydrate-mediated responses during zygotic and early somatic embryogenesis in the endangered conifer, Araucaria angustifolia. PLoS One 2017; 12:e0180051. [PMID: 28678868 PMCID: PMC5497979 DOI: 10.1371/journal.pone.0180051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022] Open
Abstract
Three zygotic developmental stages and two somatic Araucaria angustifolia cell lines with contrasting embryogenic potential were analyzed to identify the carbohydrate-mediated responses associated with embryo formation. Using a comparison between zygotic and somatic embryogenesis systems, the non-structural carbohydrate content, cell wall sugar composition and expression of genes involved in sugar sensing were analyzed, and a network analysis was used to identify coordinated features during embryogenesis. We observed that carbohydrate-mediated responses occur mainly during the early stages of zygotic embryo formation, and that during seed development there are coordinated changes that affect the development of the different structures (embryo and megagametophyte). Furthermore, sucrose and starch accumulation were associated with the responsiveness of the cell lines. This study sheds light on how carbohydrate metabolism is influenced during zygotic and somatic embryogenesis in the endangered conifer species, A. angustifolia.
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Affiliation(s)
- Bruno V. Navarro
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
| | - Paula Elbl
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
| | - Amanda P. De Souza
- Laboratory of Plant Physiological Ecology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
| | - Vinicius Jardim
- Laboratory of Plant Physiological Ecology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
| | - Leandro F. de Oliveira
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
| | - Amanda F. Macedo
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
| | - André L. W. dos Santos
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
| | - Marcos S. Buckeridge
- Laboratory of Plant Physiological Ecology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
| | - Eny I. S. Floh
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo-SP, Brazil
- * E-mail:
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de Oliveira LF, Elbl P, Navarro BV, Macedo AF, Dos Santos ALW, Floh EIS, Cooke J. Elucidation of the polyamine biosynthesis pathway during Brazilian pine (Araucaria angustifolia) seed development. Tree Physiol 2017; 37:116-130. [PMID: 28175909 DOI: 10.1093/treephys/tpw107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/28/2016] [Accepted: 10/21/2016] [Indexed: 05/25/2023]
Abstract
Polyamines (PAs), such as spermidine and spermine, as well as amino acids that are substrates for their biosynthesis, are known to be essential for plant development. However, little is known about the gene expression and metabolic switches associated with the ornithine/arginine and PA biosynthetic pathway during seed development in conifers. To understand these metabolic switches, the enzyme activity of arginine decarboxylase and ornithine decarboxylase, as well as the contents of PAs and amino acids were evaluated in three Araucaria angustifolia (Bertol. Kuntze) seed developmental stages in combination with expression profile analyses of genes associated with the ornithine/arginine and PA biosynthetic pathway. Twelve genes were selected for further analysis and it was shown that the expression profiles of AaADC and AaSAMDC were up-regulated during zygotic embryo development. Polyamines and amino acids were found to accumulate differently in embryos and megagametophytes, and the transition from the globular to the cotyledonary stage was marked by an increase in free and conjugated spermidine and spermine contents. Putrescine is made from arginine, which was present at low content at the late embryogenesis stage, when high content of citrulline was observed. Differences in amino acids, PAs and gene expression profiles of biosynthetic genes at specific seed stages and at each seed transition stage were investigated, providing insights into molecular and physiological aspects of conifer embryogenesis for use in future both basic and applied studies.
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Affiliation(s)
- Leandro F de Oliveira
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, São Paulo, Brazil
| | - Paula Elbl
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, São Paulo, Brazil
| | - Bruno V Navarro
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, São Paulo, Brazil
| | - Amanda F Macedo
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, São Paulo, Brazil
| | - André L W Dos Santos
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, São Paulo, Brazil
| | - Eny I S Floh
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, São Paulo, Brazil
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Elbl P, Navarro BV, de Oliveira LF, Almeida J, Mosini AC, dos Santos ALW, Rossi M, Floh EIS. Identification and Evaluation of Reference Genes for Quantitative Analysis of Brazilian Pine (Araucaria angustifolia Bertol. Kuntze) Gene Expression. PLoS One 2015; 10:e0136714. [PMID: 26313945 PMCID: PMC4552031 DOI: 10.1371/journal.pone.0136714] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/07/2015] [Indexed: 11/29/2022] Open
Abstract
Quantitative analysis of gene expression is a fundamental experimental approach in many fields of plant biology, but it requires the use of internal controls representing constitutively expressed genes for reliable transcript quantification. In this study, we identified fifteen putative reference genes from an A. angustifolia transcriptome database. Variation in transcript levels was first evaluated in silico by comparing read counts and then by quantitative real-time PCR (qRT-PCR), resulting in the identification of six candidate genes. The consistency of transcript abundance was also calculated applying geNorm and NormFinder software packages followed by a validation approach using four target genes. The results presented here indicate that a diverse set of samples should ideally be used in order to identify constitutively expressed genes, and that the use of any two reference genes in combination, of the six tested genes, is sufficient for effective expression normalization. Finally, in agreement with the in silico prediction, a comprehensive analysis of the qRT-PCR data combined with validation analysis revealed that AaEIF4B-L and AaPP2A are the most suitable reference genes for comparative studies of A. angustifolia gene expression.
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Affiliation(s)
- Paula Elbl
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Bruno V. Navarro
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Leandro F. de Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Juliana Almeida
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Amanda C. Mosini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - André L. W. dos Santos
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Eny I. S. Floh
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
- * E-mail:
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