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Laosuntisuk K, Vennapusa A, Somayanda IM, Leman AR, Jagadish SK, Doherty CJ. A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1241-1257. [PMID: 38289828 DOI: 10.1111/tpj.16654] [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: 10/27/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/01/2024]
Abstract
RNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike-ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike-ins with 3' RNA-Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.
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Affiliation(s)
- Kanjana Laosuntisuk
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Amaranatha Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, Delaware, USA
| | - Impa M Somayanda
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79410, USA
| | - Adam R Leman
- Department of Science and Technology, The Good Food Institute, Washington, District of Columbia, 20090, USA
| | - Sv Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79410, USA
- Department of Agronomy, Kansas State University, Manhattan, Kansas, 66506, USA
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
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2
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Yin R, Xia K, Xu X. Spatial transcriptomics drives a new era in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1571-1581. [PMID: 37651723 DOI: 10.1111/tpj.16437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/25/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
SUMMARYThe plant community lags far behind the animal and human fields concerning the application of single‐cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single‐cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell‐fate lineages, and reveal cell‐to‐cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple‐omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology.
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Affiliation(s)
- Ruilian Yin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- BGI Research, Shenzhen, 518083, China
| | - Keke Xia
- BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518120, China
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3
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Povilus RA, Friedman WE. Transcriptomes across fertilization and seed development in the water lily Nymphaea thermarum (Nymphaeales): evidence for epigenetic patterning during reproduction. PLANT REPRODUCTION 2022; 35:161-178. [PMID: 35184212 DOI: 10.1007/s00497-022-00438-3] [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: 05/19/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The first record of gene expression during seed development within the Nymphaeales provides evidence for a variety of biological processes, including dynamic epigenetic patterning during sexual reproduction in the water lily Nymphaea thermarum. Studies of gene expression during seed development have been performed for a growing collection of species from a phylogenetically broad sampling of flowering plants (angiosperms). However, angiosperm lineages whose origins predate the divergence of monocots and eudicots have been largely overlooked. In order to provide a new resource for understanding the early evolution of seed development in flowering plants, we sequenced transcriptomes of whole ovules and seeds from three key stages of reproductive development in the waterlily Nymphaea thermarum, an experimentally tractable member of the Nymphaeales. We first explore patterns of gene expression, beginning with mature ovules and continuing through fertilization into early- and mid-stages of seed development. We find patterns of gene expression that corroborate histological/morphological observations of seed development in this species, such as expression of genes involved in starch synthesis and transcription factors that have been associated with embryo and endosperm development in other species. We also find evidence for processes that were previously not known to be occurring during seed development in this species, such as epigenetic modification. We then examine the expression of genes associated with patterning DNA and histone methylation-processes that are essential for seed development in distantly related and structurally diverse monocots and eudicots. Around 89% of transcripts putatively homologous to DNA and histone methylation modifiers are expressed during seed development in N. thermarum, including homologs of genes known to pattern imprinting-related epigenetic modifications. Our results suggest that dynamic epigenetic patterning is a deeply conserved aspect of angiosperm seed development.
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Affiliation(s)
- Rebecca A Povilus
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - William E Friedman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA, 02131, USA.
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4
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Liu X, Yang Z, Wang Y, Shen Y, Jia Q, Zhao C, Zhang M. Multiple caleosins have overlapping functions in oil accumulation and embryo development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3946-3962. [PMID: 35419601 DOI: 10.1093/jxb/erac153] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Caleosins are lipid droplet- and endoplasmic reticulum-associated proteins. To investigate their functions in oil accumulation, expression levels of caleosins in developing seeds of Arabidopsis thaliana were examined and four seed-expressed caleosins (CLO1, CLO2, CLO4, and CLO6) were identified. The four single mutants showed similar minor changes of fatty acid composition in seeds. Two double mutants (clo1 clo2 and clo1×clo2) demonstrated distinct changes of fatty acid composition, a 16-23% decrease of oil content, and a 10-13% decrease of seed weight. Moreover, a 40% decrease of oil content, further fatty acid changes, and misshapen membranes of smaller lipid droplets were found in seeds of quadruple CLO RNAi lines. Notably, ~40% of quadruple CLO RNAi T1 seeds failed to germinate, and deformed embryos and seedlings were also observed. Complementation experiments showed that CLO1 rescued the phenotype of clo1 clo2. Overexpression of CLO1 in seedlings and BY2 cells increased triacylglycerol content up to 73.6%. Transcriptome analysis of clo1 clo2 developing seeds showed that expression levels of some genes related to lipid, embryo development, calcium signaling, and stress responses were affected. Together, these results suggest that the major seed-expressed caleosins have overlapping functions in oil accumulation and show pleiotropic effects on embryo development.
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Affiliation(s)
- Xiangling Liu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | | | - Yun Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | | | - Qingli Jia
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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5
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Ibarra-Laclette E, Venancio-Rodríguez CA, Vásquez-Aguilar AA, Alonso-Sánchez AG, Pérez-Torres CA, Villafán E, Ramírez-Barahona S, Galicia S, Sosa V, Rebollar EA, Lara C, González-Rodríguez A, Díaz-Fleisher F, Ornelas JF. Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes. Front Genet 2022; 13:929490. [PMID: 35769994 PMCID: PMC9235361 DOI: 10.3389/fgene.2022.929490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
The mistletoe Psittacanthus schiedeanus, a keystone species in interaction networks between plants, pollinators, and seed dispersers, infects a wide range of native and non-native tree species of commercial interest. Here, using RNA-seq methodology we assembled the whole circularized quadripartite structure of P. schiedeanus chloroplast genome and described changes in the gene expression of the nuclear genomes across time of experimentally inoculated seeds. Of the 140,467 assembled and annotated uniGenes, 2,000 were identified as differentially expressed (DEGs) and were classified in six distinct clusters according to their expression profiles. DEGs were also classified in enriched functional categories related to synthesis, signaling, homoeostasis, and response to auxin and jasmonic acid. Since many orthologs are involved in lateral or adventitious root formation in other plant species, we propose that in P. schiedeanus (and perhaps in other rootless mistletoe species), these genes participate in haustorium formation by complex regulatory networks here described. Lastly, and according to the structural similarities of P. schiedeanus enzymes with those that are involved in host cell wall degradation in fungi, we suggest that a similar enzymatic arsenal is secreted extracellularly and used by mistletoes species to easily parasitize and break through tissues of the host.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- *Correspondence: Enrique Ibarra-Laclette, ; Juan Francisco Ornelas,
| | | | | | | | - Claudia-Anahí Pérez-Torres
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- Investigador por Mexico-CONACyT en el Instituto de Ecología A.C. (INECOL), Xalapa, Mexico
| | - Emanuel Villafán
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico, Mexico
| | - Sonia Galicia
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
| | - Victoria Sosa
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
| | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Carlos Lara
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Antonio González-Rodríguez
- Laboratorio de Genética de la Conservación, Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Morelia, Mexico
| | | | - Juan Francisco Ornelas
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
- *Correspondence: Enrique Ibarra-Laclette, ; Juan Francisco Ornelas,
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6
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Sánchez R, González-Thuillier I, Venegas-Calerón M, Garcés R, Salas JJ, Martínez-Force E. The Sunflower WRINKLED1 Transcription Factor Regulates Fatty Acid Biosynthesis Genes through an AW Box Binding Sequence with a Particular Base Bias. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070972. [PMID: 35406952 PMCID: PMC9002759 DOI: 10.3390/plants11070972] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 06/12/2023]
Abstract
Sunflower is an important oilseed crop in which the biochemical pathways leading to seed oil synthesis and accumulation have been widely studied. However, how these pathways are regulated is less well understood. The WRINKLED1 (WRI1) transcription factor is considered a key regulator in the control of triacylglycerol biosynthesis, acting through the AW box binding element (CNTNG(N)7CG). Here, we identified the sunflower WRI1 gene and characterized its activity in electrophoretic mobility shift assays. We studied its role as a co-regulator of sunflower genes involved in plastidial fatty acid synthesis. Sunflower WRI1-targets included genes encoding the pyruvate dehydrogenase complex, the α-CT and BCCP genes, genes encoding ACPs and the fatty acid synthase complex, together with the FATA1 gene. As such, sunflower WRI1 regulates genes involved in seed plastidial fatty acid biosynthesis in a coordinated manner, establishing a WRI1 push and pull strategy that drives oleic acid synthesis for its export into the cytosol. We also determined the base bias at the N positions in the active sunflower AW box motif. The sunflower AW box is sequence-sensitive at the non-conserved positions, enabling WRI1-binding. Moreover, sunflower WRI1 could bind to a non-canonical AW-box motif, opening the possibility of searching for new target genes.
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Affiliation(s)
- Rosario Sánchez
- Instituto de la Grasa (CSIC), Pablo de Olavide University Campus, Building 46, Carretera de Utrera km 1, 41013 Seville, Spain; (R.S.); (I.G.-T.); (M.V.-C.); (R.G.); (J.J.S.)
| | - Irene González-Thuillier
- Instituto de la Grasa (CSIC), Pablo de Olavide University Campus, Building 46, Carretera de Utrera km 1, 41013 Seville, Spain; (R.S.); (I.G.-T.); (M.V.-C.); (R.G.); (J.J.S.)
- Jealotts Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Mónica Venegas-Calerón
- Instituto de la Grasa (CSIC), Pablo de Olavide University Campus, Building 46, Carretera de Utrera km 1, 41013 Seville, Spain; (R.S.); (I.G.-T.); (M.V.-C.); (R.G.); (J.J.S.)
| | - Rafael Garcés
- Instituto de la Grasa (CSIC), Pablo de Olavide University Campus, Building 46, Carretera de Utrera km 1, 41013 Seville, Spain; (R.S.); (I.G.-T.); (M.V.-C.); (R.G.); (J.J.S.)
| | - Joaquín J. Salas
- Instituto de la Grasa (CSIC), Pablo de Olavide University Campus, Building 46, Carretera de Utrera km 1, 41013 Seville, Spain; (R.S.); (I.G.-T.); (M.V.-C.); (R.G.); (J.J.S.)
| | - Enrique Martínez-Force
- Instituto de la Grasa (CSIC), Pablo de Olavide University Campus, Building 46, Carretera de Utrera km 1, 41013 Seville, Spain; (R.S.); (I.G.-T.); (M.V.-C.); (R.G.); (J.J.S.)
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7
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da Fonseca-Pereira P, Pham PA, Cavalcanti JHF, Omena-Garcia RP, Barros JAS, Rosado-Souza L, Vallarino JG, Mutwil M, Avin-Wittenberg T, Nunes-Nesi A, Fernie AR, Araújo WL. The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:196-214. [PMID: 34741366 DOI: 10.1111/tpj.15566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
The importance of the alternative donation of electrons to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) complex has been demonstrated. However, the functional significance of this pathway during seed development and germination remains to be elucidated. To assess the function of this pathway, we performed a detailed metabolic and transcriptomic analysis of Arabidopsis mutants to test the molecular consequences of a dysfunctional ETF/ETFQO pathway. We demonstrate that the disruption of this pathway compromises seed germination in the absence of an external carbon source and also impacts seed size and yield. Total protein and storage protein content is reduced in dry seeds, whilst sucrose levels remain invariant. Seeds of ETFQO and related mutants were also characterized by an altered fatty acid composition. During seed development, lower levels of fatty acids and proteins accumulated in the etfqo-1 mutant as well as in mutants in the alternative electron donors isovaleryl-CoA dehydrogenase (ivdh-1) and d-2-hydroxyglutarate dehydrogenase (d2hgdh1-2). Furthermore, the content of several amino acids was increased in etfqo-1 mutants during seed development, indicating that these mutants are not using such amino acids as alternative energy source for respiration. Transcriptome analysis revealed alterations in the expression levels of several genes involved in energy and hormonal metabolism. Our findings demonstrated that the alternative pathway of respiration mediated by the ETF/ETFQO complex affects seed germination and development by directly adjusting carbon storage during seed filling. These results indicate a role for the pathway in the normal plant life cycle to complement its previously defined roles in the response to abiotic stress.
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Affiliation(s)
- Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Phuong Anh Pham
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - João Henrique F Cavalcanti
- Instituto de Educação, Agricultura e Ambiente, Universidade Federal do Amazonas, Humaitá, Amazonas, Brazil
| | - Rebeca P Omena-Garcia
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Jessica A S Barros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Laise Rosado-Souza
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - José G Vallarino
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Tamar Avin-Wittenberg
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, 9190401, Israel
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
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8
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Bajrai LH, Sohrab SS, Alandijany TA, Mobashir M, Reyaz M, Kamal MA, Firoz A, Parveen S, Azhar EI. Gene Expression Profiling of Early Acute Febrile Stage of Dengue Infection and Its Comparative Analysis With Streptococcus pneumoniae Infection. Front Cell Infect Microbiol 2021; 11:707905. [PMID: 34778101 PMCID: PMC8581568 DOI: 10.3389/fcimb.2021.707905] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/30/2021] [Indexed: 02/05/2023] Open
Abstract
Infectious diseases are the disorders caused by organisms such as bacteria, viruses, fungi, or parasites. Although many of them are permentantly hazardous, a number of them live in and on our bodies and they are normally harmless or even helpful. Under certain circumstances, some organisms may cause diseases and these infectious diseases may be passed directly from person to person or via intermediate vectors including insects and other animals. Dengue virus and Streptococcus pneumoniae are the critical and common sources of infectious diseases. So, it is critical to understand the gene expression profiling and their inferred functions in comparison to the normal and virus infected conditions. Here, we have analyzed the gene expression profiling for dengue hemorrhagic fever, dengue fever, and normal human dataset. Similar to it, streptococcus pneumoniae infectious data were analyzed and both the outcomes were compared. Our study leads to the conclusion that the dengue hemorrhagic fever arises in result to potential change in the gene expression pattern, and the inferred functions obviously belong to the immune system, but also there are some additional potential pathways which are critical signaling pathways. In the case of pneumoniae infection, 19 pathways were enriched, almost all these pathways are associated with the immune system and 17 of the enriched pathways were common with dengue infection except platelet activation and antigen processing and presentation. In terms of the comparative study between dengue virus and Streptococcus pneumoniae infection, we conclude that cell adhesion molecules (CAMs), MAPK signaling pathway, natural killer cell mediated cytotoxicity, regulation of actin cytoskeleton, and cytokine-cytokine receptor interaction are commonly enriched in all the three cases of dengue infection and Streptococcus pneumoniae infection, focal adhesion was enriched between classical dengue fever — dengue hemorrhagic fever, dengue hemorrhagic fever—normal samples, and SP, and antigen processing and presentation and Leukocyte transendothelial migration were enriched in classical dengue fever —normal samples, dengue hemorrhagic fever—normal samples, and Streptococcus pneumoniae infection.
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Affiliation(s)
- Leena H Bajrai
- Special Infectious Agents Unit - BSL-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed S Sohrab
- Special Infectious Agents Unit - BSL-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamir A Alandijany
- Special Infectious Agents Unit - BSL-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Mobashir
- SciLifeLab, Department of Oncology and Pathology Karolinska Institutet, Stockholm, Sweden
| | - Muddassir Reyaz
- Department of Healthcare Management, Jamia Hamdard Hamdard Nagar, New Delhi, India
| | - Mohammad A Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Ahmad Firoz
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Shabana Parveen
- Department of Bioscience, Jamia Millia Islamia, New Delhi, India
| | - Esam I Azhar
- Special Infectious Agents Unit - BSL-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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9
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Zhang S, Ghatak A, Bazargani MM, Bajaj P, Varshney RK, Chaturvedi P, Jiang D, Weckwerth W. Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:669-687. [PMID: 34227164 PMCID: PMC9291999 DOI: 10.1111/tpj.15410] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Grain filling and grain development are essential biological processes in the plant's life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In-gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule-bound and soluble starch synthase, pyruvate phosphate dikinase, 14-3-3 proteins as well as sugar precursors undergo a major tissue-dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue-specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.
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Affiliation(s)
- Shuang Zhang
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Arindam Ghatak
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | | | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationMurdoch UniversityMurdochWA6150Australia
| | - Palak Chaturvedi
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjing210095China
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Vienna Metabolomics Center (VIME)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
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10
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Li JS, Suzui N, Nakai Y, Yin YG, Ishii S, Fujimaki S, Kawachi N, Rai H, Matsumoto T, Sato-Izawa K, Ohkama-Ohtsu N, Nakamura SI. Shoot base responds to root-applied glutathione and functions as a critical region to inhibit cadmium translocation from the roots to shoots in oilseed rape (Brassica napus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110822. [PMID: 33691958 DOI: 10.1016/j.plantsci.2021.110822] [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: 09/07/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
Glutathione (GSH) is a tripeptide involved in controlling heavy metal movement in plants. Our previous study showed that GSH, when site-specifically applied to plant roots, inhibits Cd translocation from the roots to shoots in hydroponically cultured oilseed rape (Brassica napus) plants. A factor that led to this inhibitory effect was the activation of Cd efflux from root cells. To further investigate the molecular mechanism triggered by root-applied GSH, Cd movement was non-invasively monitored using a positron-emitting tracer imaging system. The Cd absorption and efflux process in the roots were visualized successfully. The effects of GSH on Cd efflux from root cells were estimated by analyzing imaging data. Reanalysis of image data suggested that GSH applied to roots, at the shoot base, activated Cd return. Cutting the shoot base significantly inhibited Cd efflux from root cells. These experimental results demonstrate that the shoot base plays an important role in distributing Cd throughout the plant body. Furthermore, microarray analysis revealed that about 400 genes in the roots responded to root-applied GSH. Among these, there were genes for transporter proteins related to heavy metal movement in plants and proteins involved in the structure modification of cell walls.
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Affiliation(s)
- Jun-Song Li
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8, Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Nobuo Suzui
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 1233 Watanuki-cho, Takasaki-shi, Gunma, 370-1207, Japan
| | - Yuji Nakai
- Institute of Regional Innovation, Hirosaki University, 2-2-1 Yanagawa, Aomori-shi, Aomori, 038-0012, Japan
| | - Yon-Gen Yin
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 1233 Watanuki-cho, Takasaki-shi, Gunma, 370-1207, Japan
| | - Satomi Ishii
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 1233 Watanuki-cho, Takasaki-shi, Gunma, 370-1207, Japan
| | - Shu Fujimaki
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 1233 Watanuki-cho, Takasaki-shi, Gunma, 370-1207, Japan; Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Naoki Kawachi
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 1233 Watanuki-cho, Takasaki-shi, Gunma, 370-1207, Japan
| | - Hiroki Rai
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita-shi, Akita, 010-0195, Japan
| | - Takashi Matsumoto
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka Setagaya-ku, Tokyo, 156-8502, Japan
| | - Kanna Sato-Izawa
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka Setagaya-ku, Tokyo, 156-8502, Japan
| | - Naoko Ohkama-Ohtsu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8, Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8, Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Shin-Ichi Nakamura
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita-shi, Akita, 010-0195, Japan; Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka Setagaya-ku, Tokyo, 156-8502, Japan.
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11
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Harnvanichvech Y, Gorelova V, Sprakel J, Weijers D. The Arabidopsis embryo as a quantifiable model for studying pattern formation. QUANTITATIVE PLANT BIOLOGY 2021; 2:e3. [PMID: 37077211 PMCID: PMC10095805 DOI: 10.1017/qpb.2021.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 05/03/2023]
Abstract
Phenotypic diversity of flowering plants stems from common basic features of the plant body pattern with well-defined body axes, organs and tissue organisation. Cell division and cell specification are the two processes that underlie the formation of a body pattern. As plant cells are encased into their cellulosic walls, directional cell division through precise positioning of division plane is crucial for shaping plant morphology. Since many plant cells are pluripotent, their fate establishment is influenced by their cellular environment through cell-to-cell signaling. Recent studies show that apart from biochemical regulation, these two processes are also influenced by cell and tissue morphology and operate under mechanical control. Finding a proper model system that allows dissecting the relationship between these aspects is the key to our understanding of pattern establishment. In this review, we present the Arabidopsis embryo as a simple, yet comprehensive model of pattern formation compatible with high-throughput quantitative assays.
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Affiliation(s)
- Yosapol Harnvanichvech
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Vera Gorelova
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Author for correspondence: Dolf Weijers, E-mail:
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12
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To A, Joubès J, Thueux J, Kazaz S, Lepiniec L, Baud S. AtMYB92 enhances fatty acid synthesis and suberin deposition in leaves of Nicotiana benthamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:660-676. [PMID: 32246506 DOI: 10.1111/tpj.14759] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/02/2020] [Accepted: 03/18/2020] [Indexed: 05/11/2023]
Abstract
Acyl lipids are important constituents of the plant cell. Depending on the cell type, requirements in acyl lipids vary greatly, implying a tight regulation of fatty acid and lipid metabolism. The discovery of the WRINKLED1 (WRI1) transcription factors, members of the AP2-EREBP (APETALA2-ethylene-responsive element binding protein) family, has emphasized the importance of transcriptional regulation for adapting the rate of acyl chain production to cell requirements. Here, we describe the identification of another activator of the fatty acid biosynthetic pathway, the Arabidopsis MYB92 transcription factor. This MYB and all the members of the subgroups S10 and S24 of MYB transcription factors can directly activate the promoter of BCCP2 that encodes a component of the fatty acid biosynthetic pathway. Two adjacent MYB cis-regulatory elements are essential for the binding and activation of the BCCP2 promoter by MYB92. Overexpression of MYB92 or WRI1 in Nicotiana benthamiana induces the expression of fatty acid biosynthetic genes but results in the accumulation of different types of acyl lipids. In the presence of WRI1, triacylglycerol biosynthetic enzymes coded by constitutively expressed genes efficiently channel the excess fatty acids toward reserve lipid accumulation. By contrast, MYB92 activates both fatty acid and suberin biosynthetic genes; hence, the remarkable increase in suberin monomers measured in leaves expressing MYB92. These results provide additional insight into the molecular mechanisms that control the biosynthesis of an important cell wall-associated acylglycerol polymer playing critical roles in plants.
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Affiliation(s)
- Alexandra To
- Institut Jean-Pierre Bourgin, INRAE, CNRS, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Jérôme Joubès
- Laboratoire de Biogenèse Membranaire, UMR 5200, Université de Bordeaux, 33882, Villenave d'Ornon, France
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, 33882, Villenave d'Ornon, France
| | - Jean Thueux
- Institut Jean-Pierre Bourgin, INRAE, CNRS, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Sami Kazaz
- Institut Jean-Pierre Bourgin, INRAE, CNRS, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
- Université Paris-Sud, Université Paris-Saclay, 91400, Orsay, France
| | - Loïc Lepiniec
- Institut Jean-Pierre Bourgin, INRAE, CNRS, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Sébastien Baud
- Institut Jean-Pierre Bourgin, INRAE, CNRS, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
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13
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Hwang JH, Yu SI, Lee BH, Lee DH. Modulation of Energy Metabolism Is Important for Low-Oxygen Stress Adaptation in Brassicaceae Species. Int J Mol Sci 2020; 21:E1787. [PMID: 32150906 PMCID: PMC7084654 DOI: 10.3390/ijms21051787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 01/16/2023] Open
Abstract
Low-oxygen stress, mainly caused by soil flooding, is a serious abiotic stress affecting crop productivity worldwide. To understand the mechanisms of low-oxygen stress responses and adaptation of plants, we characterized and compared low-oxygen responses in six species with different accessions of the Brassicaceae family. Based on the growth and survival responses to submergence or low-oxygen condition, these accessions could be divided into three groups: (i) Highly tolerant species (Rorippa islandica and Arabis stelleri); (ii) moderately tolerant species (Arabidopsis thaliana [esk-1, Ler, Ws and Col-0 ecotype]); and (iii) intolerant species (Thlaspi arvense, Thellungiella salsuginea [Shandong and Yukon ecotype], and Thellungiella parvula). Gene expression profiling using Operon Arabidopsis microarray was carried out with RNA from roots of A. thaliana (Col-0), A. stelleri, R. islandica, and T. salsuginea (Shandong) treated with low-oxygen stress (0.1% O2/99.9% N2) for 0, 1, 3, 8, 24, and 72 h. We performed a comparative analysis of the gene expression profiles using the gene set enrichment analysis (GSEA) method. Our comparative analysis suggested that under low-oxygen stress each species distinctively reconfigures the energy metabolic pathways including sucrose-starch metabolism, glycolysis, fermentation and nitrogen metabolism, tricarboxylic acid flow, and fatty acid degradation via beta oxidation and glyoxylate cycle. In A. thaliana, a moderately tolerant species, the dynamical reconfiguration of energy metabolisms occurred in the early time points of low-oxygen treatment, but the energy reconfiguration in the late time points was not as dynamic as in the early time points. Highly tolerant A. stelleri appeared to have high photosynthesis capacity that could produce more O2 and in turn additional ATP energy to cope with energy depletion caused by low-oxygen stress. R. islandica seemed to retain some ATP energy produced by anaerobic energy metabolism during a prolonged period of low-oxygen conditions. Intolerant T. salsuginea did not show significant changes in the expression of genes involved in anaerobic energy metabolisms. These results indicate that plants developed different energy metabolisms to cope with the energy crisis caused by low-oxygen stress.
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Affiliation(s)
- Ji-Hye Hwang
- Graduate Department of Life and Pharmaceutical Sciences and the Center for Cell Signaling & Drug Discovery Research, Ewha Womans University, Seoul 03760, Korea;
| | - Si-in Yu
- Department of Life Science, Sogang University, Seoul 04107, Korea;
| | - Byeong-ha Lee
- Department of Life Science, Sogang University, Seoul 04107, Korea;
| | - Dong-Hee Lee
- Graduate Department of Life and Pharmaceutical Sciences and the Center for Cell Signaling & Drug Discovery Research, Ewha Womans University, Seoul 03760, Korea;
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14
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Qu C, Zhao H, Chen J, Zuo Z, Sun X, Huang J, Yang C, Zhang X, Zhang P, Quan X, Xu Z, Liu G. The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination. BMC Genomics 2019; 20:801. [PMID: 31684868 PMCID: PMC6829952 DOI: 10.1186/s12864-019-6180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background Seed germination, the foundation of plant propagation, involves a series of changes at the molecular level. Poplar is a model woody plant, but the molecular events occurring during seed germination in this species are unclear. Results In this study, we investigated changes in gene transcriptional levels during different germination periods in poplar by high-throughput sequencing technology. Analysis of genes expressed at specific germination stages indicated that these genes are distributed in many metabolic pathways. Enrichment analysis of significantly differentially expressed genes based on hypergeometric testing revealed that multiple pathways, such as pathways related to glycolysis, lipid, amino acid, protein and ATP synthesis metabolism, changed significantly at the transcriptional level during seed germination. A comparison of ΣZ values uncovered a series of transcriptional changes in biological processes related to primary metabolism during poplar seed germination. Among these changes, genes related to CHO metabolism were the first to be activated, with subsequent expression of genes involved in lipid metabolism and then those associated with protein metabolism. The pattern of metabolomic and physiological index changes further verified the sequence of some biological events. Conclusions Our study revealed molecular events occurring at the transcriptional level during seed germination and determined their order. These events were further verified by patterns of changes of metabolites and physiological indexes. Our findings lay a foundation for the elucidation of the molecular mechanisms responsible for poplar seed germination.
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Affiliation(s)
- Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Hancheng Zhao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jinyuan Chen
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiuli Zhang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Peng Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiankui Quan
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China. .,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
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15
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Tayade R, Kulkarni KP, Jo H, Song JT, Lee JD. Insight Into the Prospects for the Improvement of Seed Starch in Legume-A Review. FRONTIERS IN PLANT SCIENCE 2019; 10:1213. [PMID: 31736985 PMCID: PMC6836628 DOI: 10.3389/fpls.2019.01213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/03/2019] [Indexed: 05/18/2023]
Abstract
In addition to proteins and/or oils, mature seeds of most legume crops contain important carbohydrate components, including starches and sugars. Starch is also an essential nutritional component of human and animal diets and has various food and non-food industrial applications. Starch is a primary insoluble polymeric carbohydrate produced by higher plants and consists of amylose and amylopectin as a major fraction. Legume seeds are an affordable source of not only protein but also the starch, which has an advantage of being resistant starch compared with cereal, root, and tuber starch. For these reasons, legume seeds form a good source of resistant starch-rich healthy food with a high protein content and can be utilized in various food applications. The genetics and molecular details of starch and other carbohydrate components are well studied in cereal crops but have received little attention in legumes. In order to improve legume starch content, quality, and quantity, it is necessary to understand the genetic and molecular factors regulating carbohydrate metabolism in legume crops. In this review, we assessed the current literature reporting the genetic and molecular basis of legume carbohydrate components, primarily focused on seed starch content. We provided an overview of starch biosynthesis in the heterotrophic organs, the chemical composition of major consumable legumes, the factors influencing starch digestibility, and advances in the genetic, transcriptomic, and metabolomic studies in important legume crops. Further, we discussed breeding and biotechnological approaches for the improvement of the starch composition in major legume crops. The information reviewed in this study will be helpful in facilitating the food and non-food applications of legume starch and provide economic benefits to farmers and industries.
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Affiliation(s)
| | | | | | | | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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16
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A Weighted Mean Value Analysis to Identify Biological Pathway Activity Changes during Poplar Seed Germination. FORESTS 2019. [DOI: 10.3390/f10080664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Poplar (Populus × xiaohei T. S. Hwang et Liang) is an excellent model plant, with a known genome sequence, for studying woody plant developmental processes, such as seed germination. Here, we report the transcriptional profiling of poplar seeds at five germination stages using RNA-Seq technology. We focused on identifying biological pathway activity changes during seed germination and transcription factors that play important roles in different stages. Among the 16 significantly changing clusters obtained using the STEM method, transcription was significantly enriched in five different clusters, 8, 21, 25, 27, and 35. The oxidative phosphorylation-related genes were only enriched in cluster 9, and expression patterns decreased in 6 and 24 HAI, while ubiquitin-dependent protein catabolic processes were only enriched in cluster 16, and expression patterns increased in 6 HAI. A weighted mean method analysis determined that most primary metabolism-associated categories, such as major carbohydrate metabolism, glycolysis, oxidative pentose phosphate, tricarboxylic acid cycle, lipid metabolism, nucleotide metabolism, amino acid metabolism, and protein metabolism, were elevated between 6 and 48 h after imbibition (HAI). ATP synthesis and C1 metabolism had highly active expression patterns between 0.75 and 48 HAI. The photosynthesis category-associated genes that were identified appeared highly active at 144 HAI. The homogenization of transcription factors in each cluster revealed that the HAP2, C3H zinc finger family, and C2C2(Zn) GATA transcription factors were present in relatively high numbers in cluster 8, while HAP5, Zn-finger (CCHC), FHA, and E2F/DP transcription factor families, as well as SNF7, were present in high numbers in cluster 25. Thus, we identified a series of biological pathway activity changes that occur, and transcription factors that are active, during poplar seed germination. Moreover, this study provides an integrated view of transcriptional regulation that can reveal the molecular events occurring during seed germination.
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17
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Qu C, Zuo Z, Cao L, Huang J, Sun X, Zhang P, Yang C, Li L, Xu Z, Liu G. Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar. BMC PLANT BIOLOGY 2019; 19:279. [PMID: 31242858 PMCID: PMC6595626 DOI: 10.1186/s12870-019-1862-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/31/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Seed germination, a complex, physiological-morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant. RESULTS In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites. CONCLUSIONS Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.
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Affiliation(s)
- Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Lina Cao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Peng Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Lixin Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China.
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
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18
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Nakamura SI, Wongkaew A, Nakai Y, Rai H, Ohkama-Ohtsu N. Foliar-applied glutathione activates zinc transport from roots to shoots in oilseed rape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:424-434. [PMID: 31128714 DOI: 10.1016/j.plantsci.2018.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/24/2018] [Accepted: 10/21/2018] [Indexed: 05/28/2023]
Abstract
Glutathione is a tripeptide involved in diverse aspects of plant metabolism. We investigated how the reduced form of glutathione, GSH, applied site-specifically to plants, affects zinc (Zn) distribution and behavior in oilseed rape plants (Brassica napus) cultured hydroponically. Foliar-applied GSH significantly increased the Zn content in shoots and the root-to-shoot Zn translocation ratio; furthermore, this treatment raised the Zn concentration in the cytosol of root cells and substantially enhanced Zn xylem loading. Notably, microarray analysis revealed that the gene encoding pectin methylesterase was upregulated in roots following foliar GSH treatment. We conclude that certain physiological signals triggered in response to foliar-applied GSH were transported via sieve tubes and functioned in root cells, which, in turn, increased Zn availability in roots by releasing Zn from their cell wall. Consequently, root-to-shoot translocation of Zn was activated and Zn accumulation in the shoot was markedly increased.
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Affiliation(s)
- Shin-Ichi Nakamura
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka Setagaya-ku, Tokyo, 156-8502, Japan; Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita-shi, Akita, 010-0195, Japan.
| | - Arunee Wongkaew
- United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Yuji Nakai
- Institute for Food Sciences, Hirosaki University, 2-1-1 Yanagawa, Aomori-shi, Aomori, 038-0012, Japan
| | - Hiroki Rai
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita-shi, Akita, 010-0195, Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
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19
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Mouzo D, Bernal J, López-Pedrouso M, Franco D, Zapata C. Advances in the Biology of Seed and Vegetative Storage Proteins Based on Two-Dimensional Electrophoresis Coupled to Mass Spectrometry. Molecules 2018; 23:E2462. [PMID: 30261600 PMCID: PMC6222612 DOI: 10.3390/molecules23102462] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/18/2018] [Accepted: 09/21/2018] [Indexed: 12/24/2022] Open
Abstract
Seed storage proteins play a fundamental role in plant reproduction and human nutrition. They accumulate during seed development as reserve material for germination and seedling growth and are a major source of dietary protein for human consumption. Storage proteins encompass multiple isoforms encoded by multi-gene families that undergo abundant glycosylations and phosphorylations. Two-dimensional electrophoresis (2-DE) is a proteomic tool especially suitable for the characterization of storage proteins because of their peculiar characteristics. In particular, storage proteins are soluble multimeric proteins highly represented in the seed proteome that contain polypeptides of molecular mass between 10 and 130 kDa. In addition, high-resolution profiles can be achieved by applying targeted 2-DE protocols. 2-DE coupled with mass spectrometry (MS) has traditionally been the methodology of choice in numerous studies on the biology of storage proteins in a wide diversity of plants. 2-DE-based reference maps have decisively contributed to the current state of our knowledge about storage proteins in multiple key aspects, including identification of isoforms and quantification of their relative abundance, identification of phosphorylated isoforms and assessment of their phosphorylation status, and dynamic changes of isoforms during seed development and germination both qualitatively and quantitatively. These advances have translated into relevant information about meaningful traits in seed breeding such as protein quality, longevity, gluten and allergen content, stress response and antifungal, antibacterial, and insect susceptibility. This review addresses progress on the biology of storage proteins and application areas in seed breeding using 2-DE-based maps.
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Affiliation(s)
- Daniel Mouzo
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Javier Bernal
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Daniel Franco
- Meat Technology Center of Galicia, 32900 San Cibrao das Viñas, Ourense, Spain.
| | - Carlos Zapata
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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20
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Bahaji A, Almagro G, Ezquer I, Gámez-Arcas S, Sánchez-López ÁM, Muñoz FJ, Barrio RJ, Sampedro MC, De Diego N, Spíchal L, Doležal K, Tarkowská D, Caporali E, Mendes MA, Baroja-Fernández E, Pozueta-Romero J. Plastidial Phosphoglucose Isomerase Is an Important Determinant of Seed Yield through Its Involvement in Gibberellin-Mediated Reproductive Development and Storage Reserve Biosynthesis in Arabidopsis. THE PLANT CELL 2018; 30:2082-2098. [PMID: 30099384 PMCID: PMC6181017 DOI: 10.1105/tpc.18.00312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/18/2018] [Accepted: 08/06/2018] [Indexed: 05/04/2023]
Abstract
The plastid-localized phosphoglucose isomerase isoform PGI1 is an important determinant of growth in Arabidopsis thaliana, likely due to its involvement in the biosynthesis of plastidial isoprenoid-derived hormones. Here, we investigated whether PGI1 also influences seed yields. PGI1 is strongly expressed in maturing seed embryos and vascular tissues. PGI1-null pgi1-2 plants had ∼60% lower seed yields than wild-type plants, with reduced numbers of inflorescences and thus fewer siliques and seeds per plant. These traits were associated with low bioactive gibberellin (GA) contents. Accordingly, wild-type phenotypes were restored by exogenous GA application. pgi1-2 seeds were lighter and accumulated ∼50% less fatty acids (FAs) and ∼35% less protein than wild-type seeds. Seeds of cytokinin-deficient plants overexpressing CYTOKININ OXIDASE/DEHYDROGENASE1 (35S:AtCKX1) and GA-deficient ga20ox1 ga20ox2 mutants did not accumulate low levels of FAs, and exogenous application of the cytokinin 6-benzylaminopurine and GAs did not rescue the reduced weight and FA content of pgi1-2 seeds. Seeds from reciprocal crosses between pgi1-2 and wild-type plants accumulated wild-type levels of FAs and proteins. Therefore, PGI1 is an important determinant of Arabidopsis seed yield due to its involvement in two processes: GA-mediated reproductive development and the metabolic conversion of plastidial glucose-6-phosphate to storage reserves in the embryo.
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Affiliation(s)
- Abdellatif Bahaji
- Instituto de Agrobiotecnología (CSIC/UPNA/Gobierno de Navarra), 31192 Mutiloabeti, Nafarroa, Spain
| | - Goizeder Almagro
- Instituto de Agrobiotecnología (CSIC/UPNA/Gobierno de Navarra), 31192 Mutiloabeti, Nafarroa, Spain
| | - Ignacio Ezquer
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Samuel Gámez-Arcas
- Instituto de Agrobiotecnología (CSIC/UPNA/Gobierno de Navarra), 31192 Mutiloabeti, Nafarroa, Spain
| | | | - Francisco José Muñoz
- Instituto de Agrobiotecnología (CSIC/UPNA/Gobierno de Navarra), 31192 Mutiloabeti, Nafarroa, Spain
| | - Ramón José Barrio
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country, UPV/EHU, E-01006 Vitoria-Gasteiz, Spain
| | - M Carmen Sampedro
- Central Service of Analysis of Alava, SGIker, University of the Basque Country, UPV/EHU, E-01006 Vitoria-Gasteiz, Spain
| | - Nuria De Diego
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Lukáš Spíchal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Karel Doležal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, CZ-78371 Olomouc, Czech Republic
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR and Faculty of Science, Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR and Faculty of Science, Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Elisabetta Caporali
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Marta Adelina Mendes
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (CSIC/UPNA/Gobierno de Navarra), 31192 Mutiloabeti, Nafarroa, Spain
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC/UPNA/Gobierno de Navarra), 31192 Mutiloabeti, Nafarroa, Spain
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Rahman F, Hassan M, Rosli R, Almousally I, Hanano A, Murphy DJ. Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae. PLoS One 2018; 13:e0196669. [PMID: 29771926 PMCID: PMC5957377 DOI: 10.1371/journal.pone.0196669] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 03/06/2018] [Indexed: 12/04/2022] Open
Abstract
Bioinformatics analyses of caleosin/peroxygenases (CLO/PXG) demonstrated that these genes are present in the vast majority of Viridiplantae taxa for which sequence data are available. Functionally active CLO/PXG proteins with roles in abiotic stress tolerance and lipid droplet storage are present in some Trebouxiophycean and Chlorophycean green algae but are absent from the small number of sequenced Prasinophyceaen genomes. CLO/PXG-like genes are expressed during dehydration stress in Charophyte algae, a sister clade of the land plants (Embryophyta). CLO/PXG-like sequences are also present in all of the >300 sequenced Embryophyte genomes, where some species contain as many as 10–12 genes that have arisen via selective gene duplication. Angiosperm genomes harbour at least one copy each of two distinct CLO/PX isoforms, termed H (high) and L (low), where H-forms contain an additional C-terminal motif of about 30–50 residues that is absent from L-forms. In contrast, species in other Viridiplantae taxa, including green algae, non-vascular plants, ferns and gymnosperms, contain only one (or occasionally both) of these isoforms per genome. Transcriptome and biochemical data show that CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression. CLO/PXG proteins can associate with cytosolic lipid droplets and/or bilayer membranes. Many of the analysed isoforms also have peroxygenase activity and are involved in oxylipin metabolism. The distribution of CLO/PXG-like genes is consistent with an origin >1 billion years ago in at least two of the earliest diverging groups of the Viridiplantae, namely the Chlorophyta and the Streptophyta, after the Viridiplantae had already diverged from other Archaeplastidal groups such as the Rhodophyta and Glaucophyta. While algal CLO/PXGs have roles in lipid packaging and stress responses, the Embryophyte proteins have a much wider spectrum of roles and may have been instrumental in the colonisation of terrestrial habitats and the subsequent diversification as the major land flora.
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Affiliation(s)
- Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
| | - Mehedi Hassan
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
| | - Rozana Rosli
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kuala Lumpur, Malaysia
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- * E-mail:
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Marmon S, Sturtevant D, Herrfurth C, Chapman K, Stymne S, Feussner I. Two Acyltransferases Contribute Differently to Linolenic Acid Levels in Seed Oil. PLANT PHYSIOLOGY 2017; 173:2081-2095. [PMID: 28235891 PMCID: PMC5373062 DOI: 10.1104/pp.16.01865] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/22/2017] [Indexed: 05/19/2023]
Abstract
Acyltransferases are key contributors to triacylglycerol (TAG) synthesis and, thus, are of great importance for seed oil quality. The effects of increased or decreased expression of ACYL-COENZYME A:DIACYLGLYCEROL ACYLTRANSFERASE1 (DGAT1) or PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) on seed lipid composition were assessed in several Camelina sativa lines. Furthermore, in vitro assays of acyltransferases in microsomal fractions prepared from developing seeds of some of these lines were performed. Decreased expression of DGAT1 led to an increased percentage of 18:3n-3 without any change in total lipid content of the seed. The tri-18:3 TAG increase occurred predominantly in the cotyledon, as determined with matrix-assisted laser desorption/ionization-mass spectrometry, whereas species with two 18:3n-3 acyl groups were elevated in both cotyledon and embryonal axis. PDAT overexpression led to a relative increase of 18:2n-6 at the expense of 18:3n-3, also without affecting the total lipid content. Differential distributions of TAG species also were observed in different parts of the seed. The microsomal assays revealed that C.sativa seeds have very high activity of diacylglycerol-phosphatidylcholine interconversion. The combination of analytical and biochemical data suggests that the higher 18:2n-6 content in the seed oil of the PDAT overexpressors is due to the channeling of fatty acids from phosphatidylcholine into TAG before being desaturated to 18:3n-3, caused by the high activity of PDAT in general and by PDAT specificity for 18:2n-6. The higher levels of 18:3n-3 in DGAT1-silencing lines are likely due to the compensatory activity of a TAG-synthesizing enzyme with specificity for this acyl group and more desaturation of acyl groups occurring on phosphatidylcholine.
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Affiliation(s)
- Sofia Marmon
- Albrecht-von-Haller Institute for Plant Sciences (S.M., C.H., I.F.) and Göttingen Center for Molecular Biosciences (I.F.), Department of Plant Biochemistry, Georg-August-University, 37077 Goettingen, Germany;
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden (S.M., S.S.); and
- Center for Plant Lipid Research and BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017 (D.S., K.C.)
| | - Drew Sturtevant
- Albrecht-von-Haller Institute for Plant Sciences (S.M., C.H., I.F.) and Göttingen Center for Molecular Biosciences (I.F.), Department of Plant Biochemistry, Georg-August-University, 37077 Goettingen, Germany
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden (S.M., S.S.); and
- Center for Plant Lipid Research and BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017 (D.S., K.C.)
| | - Cornelia Herrfurth
- Albrecht-von-Haller Institute for Plant Sciences (S.M., C.H., I.F.) and Göttingen Center for Molecular Biosciences (I.F.), Department of Plant Biochemistry, Georg-August-University, 37077 Goettingen, Germany
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden (S.M., S.S.); and
- Center for Plant Lipid Research and BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017 (D.S., K.C.)
| | - Kent Chapman
- Albrecht-von-Haller Institute for Plant Sciences (S.M., C.H., I.F.) and Göttingen Center for Molecular Biosciences (I.F.), Department of Plant Biochemistry, Georg-August-University, 37077 Goettingen, Germany
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden (S.M., S.S.); and
- Center for Plant Lipid Research and BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017 (D.S., K.C.)
| | - Sten Stymne
- Albrecht-von-Haller Institute for Plant Sciences (S.M., C.H., I.F.) and Göttingen Center for Molecular Biosciences (I.F.), Department of Plant Biochemistry, Georg-August-University, 37077 Goettingen, Germany
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden (S.M., S.S.); and
- Center for Plant Lipid Research and BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017 (D.S., K.C.)
| | - Ivo Feussner
- Albrecht-von-Haller Institute for Plant Sciences (S.M., C.H., I.F.) and Göttingen Center for Molecular Biosciences (I.F.), Department of Plant Biochemistry, Georg-August-University, 37077 Goettingen, Germany
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden (S.M., S.S.); and
- Center for Plant Lipid Research and BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017 (D.S., K.C.)
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Lin Z, An J, Wang J, Niu J, Ma C, Wang L, Yuan G, Shi L, Liu L, Zhang J, Zhang Z, Qi J, Lin S. Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:134. [PMID: 28559925 PMCID: PMC5445305 DOI: 10.1186/s13068-017-0820-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/15/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Lindera glauca fruit with high quality and quantity of oil has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of carbon flux and energy source for oil biosynthesis in developing fruits is still unknown. To better develop fruit oils of L. glauca as woody biodiesel, a combination of two different sequencing platforms (454 and Illumina) and qRT-PCR analysis was used to define a minimal reference transcriptome of developing L. glauca fruits, and to construct carbon and energy metabolic model for regulation of carbon partitioning and energy supply for FA biosynthesis and oil accumulation. RESULTS We first analyzed the dynamic patterns of growth tendency, oil content, FA compositions, biodiesel properties, and the contents of ATP and pyridine nucleotide of L. glauca fruits from seven different developing stages. Comprehensive characterization of transcriptome of the developing L. glauca fruit was performed using a combination of two different next-generation sequencing platforms, of which three representative fruit samples (50, 125, and 150 DAF) and one mixed sample from seven developing stages were selected for Illumina and 454 sequencing, respectively. The unigenes separately obtained from long and short reads (201, and 259, respectively, in total) were reconciled using TGICL software, resulting in a total of 60,031 unigenes (mean length = 1061.95 bp) to describe a transcriptome for developing L. glauca fruits. Notably, 198 genes were annotated for photosynthesis, sucrose cleavage, carbon allocation, metabolite transport, acetyl-CoA formation, oil synthesis, and energy metabolism, among which some specific transporters, transcription factors, and enzymes were identified to be implicated in carbon partitioning and energy source for oil synthesis by an integrated analysis of transcriptomic sequencing and qRT-PCR. Importantly, the carbon and energy metabolic model was well established for oil biosynthesis of developing L. glauca fruits, which could help to reveal the molecular regulatory mechanism of the increased oil production in developing fruits. CONCLUSIONS This study presents for the first time the application of an integrated two different sequencing analyses (Illumina and 454) and qRT-PCR detection to define a minimal reference transcriptome for developing L. glauca fruits, and to elucidate the molecular regulatory mechanism of carbon flux control and energy provision for oil synthesis. Our results will provide a valuable resource for future fundamental and applied research on the woody biodiesel plants.
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Affiliation(s)
- Zixin Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Jiyong An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Jia Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Jun Niu
- College of Horticulture and Landscape Architecture, Key Laboratory of Protection and Development Utilization of Tropical Crop Germplasm Resources, Ministry of Education, Hainan University, Haikou, 570228 China
| | - Chao Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Libing Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China
| | - Guanshen Yuan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Lingling Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Lili Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Jinsong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Zhixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Ji Qi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Shanzhi Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
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Zhang L, Wang SB, Li QG, Song J, Hao YQ, Zhou L, Zheng HQ, Dunwell JM, Zhang YM. An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants. PLoS One 2016; 11:e0154882. [PMID: 27159078 PMCID: PMC4861283 DOI: 10.1371/journal.pone.0154882] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/20/2016] [Indexed: 11/19/2022] Open
Abstract
Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes and pathways for acyl-lipid metabolism have been identified, little is known about whether there is a specific mechanism for high-oil content in high-oil plants. Based on the distinct differences in seed oil content between four high-oil dicots (20~50%) and three low-oil grasses (<3%), comparative genome, transcriptome and differential expression analyses were used to investigate this mechanism. Among 4,051 dicot-specific soybean genes identified from 252,443 genes in the seven species, 54 genes were shown to directly participate in acyl-lipid metabolism, and 93 genes were found to be associated with acyl-lipid metabolism. Among the 93 dicot-specific genes, 42 and 27 genes, including CBM20-like SBDs and GPT2, participate in carbohydrate degradation and transport, respectively. 40 genes highly up-regulated during seed oil rapid accumulation period are mainly involved in initial fatty acid synthesis, triacylglyceride assembly and oil-body formation, for example, ACCase, PP, DGAT1, PDAT1, OLEs and STEROs, which were also found to be differentially expressed between high- and low-oil soybean accessions. Phylogenetic analysis revealed distinct differences of oleosin in patterns of gene duplication and loss between high-oil dicots and low-oil grasses. In addition, seed-specific GmGRF5, ABI5 and GmTZF4 were predicted to be candidate regulators in seed oil accumulation. This study facilitates future research on lipid biosynthesis and potential genetic improvement of seed oil content.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Shi-Bo Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Statistical Genomics Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Qi-Gang Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People’s Republic of China
| | - Jian Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Yu-Qi Hao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Ling Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Institute of Biotechnology, Jiangsu Academy of Agricultural Science, Nanjing 210014, People’s Republic of China
| | - Huan-Quan Zheng
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AS, United Kingdom
| | - Yuan-Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Statistical Genomics Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
- * E-mail: ;
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Oneal E, Willis JH, Franks RG. Disruption of endosperm development is a major cause of hybrid seed inviability between Mimulus guttatus and Mimulus nudatus. THE NEW PHYTOLOGIST 2016; 210:1107-20. [PMID: 26824345 PMCID: PMC4833662 DOI: 10.1111/nph.13842] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 11/30/2015] [Indexed: 05/06/2023]
Abstract
Divergence of developmental mechanisms within populations could lead to hybrid developmental failure, and might be a factor driving speciation in angiosperms. We investigate patterns of endosperm and embryo development in Mimulus guttatus and the closely related, serpentine endemic Mimulus nudatus, and compare them to those of reciprocal hybrid seed. We address whether disruption in hybrid seed development is the primary source of reproductive isolation between these sympatric taxa. M. guttatus and M. nudatus differ in the pattern and timing of endosperm and embryo development. Some hybrid seeds exhibit early disruption of endosperm development and are completely inviable, while others develop relatively normally at first, but later exhibit impaired endosperm proliferation and low germination success. These developmental patterns are reflected in mature hybrid seeds, which are either small and flat (indicating little to no endosperm) or shriveled (indicating reduced endosperm volume). Hybrid seed inviability forms a potent reproductive barrier between M. guttatus and M. nudatus. We shed light on the extent of developmental variation between closely related species within the M. guttatus species complex, an important ecological model system, and provide a partial mechanism for the hybrid barrier between M. guttatus and M. nudatus.
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Affiliation(s)
- Elen Oneal
- Department of Biology, Duke University, 3319 French Family Science Center, 125 Science Drive, Durham, NC 27705, USA
| | - John H. Willis
- Department of Biology, Duke University, 3319 French Family Science Center, 125 Science Drive, Durham, NC 27705, USA
| | - Robert G. Franks
- Department of Genetics, North Carolina State University, 2548 Thomas Hall, Raleigh, NC 27695, USA
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Jiawang F, Xiaoyan H, Xiaojie H, Xiaoyu W, Shiming T, Xiaoshan K, Danlin L, Xiaowei C. Study on rapid detection of seven common foodborne pathogens by gene chip. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajmr2015.7495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Han R, Rai A, Nakamura M, Suzuki H, Takahashi H, Yamazaki M, Saito K. De Novo Deep Transcriptome Analysis of Medicinal Plants for Gene Discovery in Biosynthesis of Plant Natural Products. Methods Enzymol 2016; 576:19-45. [DOI: 10.1016/bs.mie.2016.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Fernie AR, Pichersky E. Focus Issue on Metabolism: Metabolites, Metabolites Everywhere. PLANT PHYSIOLOGY 2015; 169:1421-3. [PMID: 26531677 PMCID: PMC4634105 DOI: 10.1104/pp.15.01499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institute of MolecularPlant Physiology14476 Potsdam-GolmGermany
| | - Eran Pichersky
- Department of Molecular, Cellular, andDevelopmental BiologyUniversity of MichiganAnn Arbor, MI 48109
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Pollard M, Martin TM, Shachar-Hill Y. Lipid analysis of developing Camelina sativa seeds and cultured embryos. PHYTOCHEMISTRY 2015; 118:23-32. [PMID: 26262674 DOI: 10.1016/j.phytochem.2015.07.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/17/2015] [Accepted: 07/27/2015] [Indexed: 05/20/2023]
Abstract
Camelina sativa is a cultivated oilseed rich in triacylglycerols containing oleic, linoleic, α-linolenic and eicosenoic acids. As it holds promise as a model species, its lipid synthesis was characterized in vivo and in culture. Lipid accumulates at a maximum rate of about 26 μg/day/seed (11.5 mg lipid/day/g fresh seed weight), a rate comparable with other oilseeds. Noteworthy is a late stage surge in α-linolenic acid accumulation. Small amounts of unusual epoxy and hydroxy fatty acids are also present in the triacylglycerols. These include 15,16-epoxy- and 15-hydroxy-octadecadienoic acids and homologous series of ω7-hydroxy-alk-ω9-enoic and ω9/10-hydroxy-alkanoic acids. Mid-maturation embryos cultured in vitro have growth and lipid deposition rates and fatty acid compositions that closely match that of seeds, but extended culture periods allow these rates to rise and surpass those observed in planta. Optimized thin layer chromatography systems for characterization of labeled products from acetate or glycerol labeling are described. Glycerol label is only found in acylglycerols, largely as the intact glyceryl backbone, but acetate can label acyl groups and sterols, the latter to a much higher relative specific activity. This presumably occurs because mevalonic acid precursor is derived from the non-plastid pool of acetyl-CoA that is also the source for malonyl-CoA to drive FAE1-dependent chain elongation. Particular attention has been paid to the separation of sterols and diacylglycerols, and to hydrogenation of triacylglycerols to simplify their analysis. These improved methods will allow more accurate analyses of the fluxes of lipid metabolism in cultured plant embryos.
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Affiliation(s)
- Mike Pollard
- Department of Plant Biology, Michigan State University, 612 Wilson Rd., East Lansing, MI 48824, United States.
| | - Tina M Martin
- Department of Plant Biology, Michigan State University, 612 Wilson Rd., East Lansing, MI 48824, United States
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, 612 Wilson Rd., East Lansing, MI 48824, United States
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He M, Zhu C, Dong K, Zhang T, Cheng Z, Li J, Yan Y. Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination. BMC PLANT BIOLOGY 2015; 15:97. [PMID: 25888100 PMCID: PMC4407426 DOI: 10.1186/s12870-015-0471-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/16/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Wheat seeds provide a staple food and an important protein source for the world's population. Seed germination is vital to wheat growth and development and directly affects grain yield and quality. In this study, we performed the first comparative proteomic analysis of wheat embryo and endosperm during seed germination. RESULTS The proteomic changes in embryo and endosperm during the four different seed germination stages of elite Chinese bread wheat cultivar Zhengmai 9023 were first investigated. In total, 74 and 34 differentially expressed protein (DEP) spots representing 63 and 26 unique proteins were identified in embryo and endosperm, respectively. Eight common DEP were present in both tissues, and 55 and 18 DEP were specific to embryo and endosperm, respectively. These identified DEP spots could be sorted into 13 functional groups, in which the main group was involved in different metabolism pathways, particularly in the reserves necessary for mobilization in preparation for seed germination. The DEPs from the embryo were mainly related to carbohydrate metabolism, proteometabolism, amino acid metabolism, nucleic acid metabolism, and stress-related proteins, whereas those from the endosperm were mainly involved in protein storage, carbohydrate metabolism, inhibitors, stress response, and protein synthesis. During seed germination, both embryo and endosperm had a basic pattern of oxygen consumption, so the proteins related to respiration and energy metabolism were up-regulated or down-regulated along with respiration of wheat seeds. When germination was complete, most storage proteins from the endosperm began to be mobilized, but only a small amount was degraded during germination. Transcription expression of six representative DEP genes at the mRNA level was consistent with their protein expression changes. CONCLUSION Wheat seed germination is a complex process with imbibition, stirring, and germination stages, which involve a series of physiological, morphological, and proteomic changes. The first process is a rapid water uptake, in which the seed coat becomes softer and the physical state of storage materials change gradually. Then the germinated seed enters the second process (a plateau phase) and the third process (the embryonic axes elongation). Seed embryo and endosperm display distinct differentially expressed proteins, and their synergistic expression mechanisms provide a basis for the normal germination of wheat seeds.
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Affiliation(s)
- Miao He
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Chong Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Kun Dong
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Ting Zhang
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Zhiwei Cheng
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Jiarui Li
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, 100048, China.
- Hubei Collaborative Innovation Center for Grain Industry, 434025, Jingzhou, China.
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Liu H, Yang Q, Fan C, Zhao X, Wang X, Zhou Y. Transcriptomic basis of functional difference and coordination between seeds and the silique wall of Brassica napus during the seed-filling stage. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 233:186-199. [PMID: 25711826 DOI: 10.1016/j.plantsci.2015.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 06/04/2023]
Abstract
The silique of oilseed rape (Brassica napus) is a composite organ including seeds and the silique wall (SW) that possesses distinctly physiological, biochemical and functional differentiations. Yet, the molecular events controlling such differences between the SW and seeds, as well as their coordination during silique development at transcriptional level are largely unknown. Here, we identified large sets of differentially expressed genes in the SW and seeds of siliques at 21-22 days after flowering with a Brassica 95K EST microarray. At this particular stage, there were 3278 SW preferentially expressed genes and 2425 seed preferentially expressed genes. Using the MapMan visualization software, genes differentially regulated in various metabolic pathways and sub-pathways between the SW and seeds were revealed. Photosynthesis and transport-related genes were more actively transcripted in the SW, while those involved in lipid metabolism were more active in seeds during the seed filling stage. On the other hand, genes involved in secondary metabolisms were selectively regulated in the SW and seeds. Large numbers of transcription factors were identified to be differentially expressed between the SW and seeds, suggesting a complex pattern of transcriptional control in these two organs. Furthermore, most genes discussed in categories or pathways showed a similar expression pattern through 21 DAF to 42 DAF. Our results thus provide insights into the coordination of seeds and the SW in the developing silique at the transcriptional levels, which will facilitate the functional studies of important genes for improving B. napus seed productivity and quality.
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Affiliation(s)
- Han Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaoqin Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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Ke T, Yu J, Dong C, Mao H, Hua W, Liu S. ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. BMC PLANT BIOLOGY 2015; 15:19. [PMID: 25604238 PMCID: PMC4312456 DOI: 10.1186/s12870-014-0399-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 12/22/2014] [Indexed: 05/29/2023]
Abstract
BACKGROUND Oil crop seeds are important sources of fatty acids (FAs) for human and animal nutrition. Despite their importance, there is a lack of an essential bioinformatics resource on gene transcription of oil crops from a comparative perspective. In this study, we developed ocsESTdb, the first database of expressed sequence tag (EST) information on seeds of four large-scale oil crops with an emphasis on global metabolic networks and oil accumulation metabolism that target the involved unigenes. DESCRIPTION A total of 248,522 ESTs and 106,835 unigenes were collected from the cDNA libraries of rapeseed (Brassica napus), soybean (Glycine max), sesame (Sesamum indicum) and peanut (Arachis hypogaea). These unigenes were annotated by a sequence similarity search against databases including TAIR, NR protein database, Gene Ontology, COG, Swiss-Prot, TrEMBL and Kyoto Encyclopedia of Genes and Genomes (KEGG). Five genome-scale metabolic networks that contain different numbers of metabolites and gene-enzyme reaction-association entries were analysed and constructed using Cytoscape and yEd programs. Details of unigene entries, deduced amino acid sequences and putative annotation are available from our database to browse, search and download. Intuitive and graphical representations of EST/unigene sequences, functional annotations, metabolic pathways and metabolic networks are also available. ocsESTdb will be updated regularly and can be freely accessed at http://ocri-genomics.org/ocsESTdb/ . CONCLUSION ocsESTdb may serve as a valuable and unique resource for comparative analysis of acyl lipid synthesis and metabolism in oilseed plants. It also may provide vital insights into improving oil content in seeds of oil crop species by transcriptional reconstruction of the metabolic network.
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Affiliation(s)
- Tao Ke
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
- Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang, 473061, China.
| | - Jingyin Yu
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
| | - Caihua Dong
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
| | - Han Mao
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
| | - Wei Hua
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
| | - Shengyi Liu
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
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Nayidu NK, Tan Y, Taheri A, Li X, Bjorndahl TC, Nowak J, Wishart DS, Hegedus D, Gruber MY. Brassica villosa, a system for studying non-glandular trichomes and genes in the Brassicas. PLANT MOLECULAR BIOLOGY 2014; 85:519-39. [PMID: 24831512 DOI: 10.1007/s11103-014-0201-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 05/11/2014] [Indexed: 05/18/2023]
Abstract
Brassica villosa is a wild Brassica C genome species with very dense trichome coverage and strong resistance to many insect pests of Brassica oilseeds and vegetables. Transcriptome analysis of hairy B. villosa leaves indicated higher expression of several important trichome initiation genes compared with glabrous B. napus leaves and consistent with the Arabidopsis model of trichome development. However, transcripts of the TRY inhibitory gene in hairy B. villosa were surprisingly high relative to B. napus and relative transcript levels of SAD2, EGL3, and several XIX genes were low, suggesting potential ancillary or less important trichome-related roles for these genes in Brassica species compared with Arabidopsis. Several antioxidant, calcium, non-calcium metal and secondary metabolite genes also showed differential expression between these two species. These coincided with accumulation of two alkaloid-like compounds, high levels of calcium, and other metals in B. villosa trichomes that are correlated with the known tolerance of B. villosa to high salt and the calcium-rich natural habitat of this wild species. This first time report on the isolation of large amounts of pure B. villosa trichomes, on trichome content, and on relative gene expression differences in an exceptionally hairy Brassica species compared with a glabrous species opens doors for the scientific community to understand trichome gene function in the Brassicas and highlights the potential of B. villosa as a trichome research platform.
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Affiliation(s)
- Naghabushana K Nayidu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N0X2, Canada,
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Pradhan S, Bandhiwal N, Shah N, Kant C, Gaur R, Bhatia S. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds. FRONTIERS IN PLANT SCIENCE 2014; 5:698. [PMID: 25566273 PMCID: PMC4267183 DOI: 10.3389/fpls.2014.00698] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/24/2014] [Indexed: 05/20/2023]
Abstract
Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.
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Affiliation(s)
| | | | | | | | | | - Sabhyata Bhatia
- *Correspondence: Sabhyata Bhatia, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India e-mail:
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Feeney M, Frigerio L, Kohalmi SE, Cui Y, Menassa R. Reprogramming cells to study vacuolar development. FRONTIERS IN PLANT SCIENCE 2013; 4:493. [PMID: 24348496 PMCID: PMC3848493 DOI: 10.3389/fpls.2013.00493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 11/15/2013] [Indexed: 05/29/2023]
Abstract
During vegetative and embryonic developmental transitions, plant cells are massively reorganized to support the activities that will take place during the subsequent developmental phase. Studying cellular and subcellular changes that occur during these short transitional periods can sometimes present challenges, especially when dealing with Arabidopsis thaliana embryo and seed tissues. As a complementary approach, cellular reprogramming can be used as a tool to study these cellular changes in another, more easily accessible, tissue type. To reprogram cells, genetic manipulation of particular regulatory factors that play critical roles in establishing or repressing the seed developmental program can be used to bring about a change of cell fate. During different developmental phases, vacuoles assume different functions and morphologies to respond to the changing needs of the cell. Lytic vacuoles (LVs) and protein storage vacuoles (PSVs) are the two main vacuole types found in flowering plants such as Arabidopsis. Although both are morphologically distinct and carry out unique functions, they also share some similar activities. As the co-existence of the two vacuole types is short-lived in plant cells, how they replace each other has been a long-standing curiosity. To study the LV to PSV transition, LEAFY COTYLEDON2, a key transcriptional regulator of seed development, was overexpressed in vegetative cells to activate the seed developmental program. At the cellular level, Arabidopsis leaf LVs were observed to convert to PSV-like organelles. This presents the opportunity for further research to elucidate the mechanism of LV to PSV transitions. Overall, this example demonstrates the potential usefulness of cellular reprogramming as a method to study cellular processes that occur during developmental transitions.
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Affiliation(s)
- Mistianne Feeney
- Department of Biology, University of Western OntarioLondon, ON, Canada
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
- School of Life Sciences, University of WarwickCoventry, UK
| | | | | | - Yuhai Cui
- Department of Biology, University of Western OntarioLondon, ON, Canada
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
| | - Rima Menassa
- Department of Biology, University of Western OntarioLondon, ON, Canada
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
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Kim SH, Hwang SG, Hwang JE, Jang CS, Velusamy V, Kim JB, Kim SH, Ha BK, Kang SY, Kim DS. The identification of candidate radio marker genes using a coexpression network analysis in gamma-irradiated rice. PHYSIOLOGIA PLANTARUM 2013; 149:554-570. [PMID: 23617399 DOI: 10.1111/ppl.12058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 02/28/2013] [Accepted: 03/25/2013] [Indexed: 06/02/2023]
Abstract
Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma-ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma-irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up- and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root-induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT-PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root-induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.
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Affiliation(s)
- Sun-Hee Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Sun-Goo Hwang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Jung Eun Hwang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Vijayanand Velusamy
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Bo-Keun Ha
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Dong Sub Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
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Basnet RK, Moreno-Pachon N, Lin K, Bucher J, Visser RGF, Maliepaard C, Bonnema G. Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes. BMC Genomics 2013; 14:840. [PMID: 24289287 PMCID: PMC4046715 DOI: 10.1186/1471-2164-14-840] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/13/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed. RESULTS Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 "gene modules", of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways. CONCLUSIONS This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa. The identification of key physiological events, major expression patterns, and putative cis-regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of seed quality traits.
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Affiliation(s)
| | | | | | | | | | | | - Guusje Bonnema
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
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Osaka M, Matsuda T, Sakazono S, Masuko-Suzuki H, Maeda S, Sewaki M, Sone M, Takahashi H, Nakazono M, Iwano M, Takayama S, Shimizu KK, Yano K, Lim YP, Suzuki G, Suwabe K, Watanabe M. Cell type-specific transcriptome of Brassicaceae stigmatic papilla cells from a combination of laser microdissection and RNA sequencing. PLANT & CELL PHYSIOLOGY 2013; 54:1894-906. [PMID: 24058146 PMCID: PMC3814185 DOI: 10.1093/pcp/pct133] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pollination is an early and critical step in plant reproduction, leading to successful fertilization. It consists of many sequential processes, including adhesion of pollen grains onto the surface of stigmatic papilla cells, foot formation to strengthen pollen-stigma interaction, pollen hydration and germination, and pollen tube elongation and penetration. We have focused on an examination of the expressed genes in papilla cells, to increase understanding of the molecular systems of pollination. From three representative species of Brassicaceae (Arabidopsis thaliana, A. halleri and Brassica rapa), stigmatic papilla cells were isolated precisely by laser microdissection, and cell type-specific gene expression in papilla cells was determined by RNA sequencing. As a result, 17,240, 19,260 and 21,026 unigenes were defined in papilla cells of A. thaliana, A. halleri and B. rapa, respectively, and, among these, 12,311 genes were common to all three species. Among the17,240 genes predicted in A. thaliana, one-third were papilla specific while approximately half of the genes were detected in all tissues examined. Bioinformatics analysis revealed that genes related to a wide range of reproduction and development functions are expressed in papilla cells, particularly metabolism, transcription and membrane-mediated information exchange. These results reflect the conserved features of general cellular function and also the specific reproductive role of papilla cells, highlighting a complex cellular system regulated by a diverse range of molecules in these cells. This study provides fundamental biological knowledge to dissect the molecular mechanisms of pollination in papilla cells and will shed light on our understanding of plant reproduction mechanisms.
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Affiliation(s)
- Masaaki Osaka
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
- These authors contributed equally to this work
| | - Tomoki Matsuda
- Graduate School of Bioresources, Mie University, Tsu, 514-8507 Japan
- These authors contributed equally to this work
| | - Satomi Sakazono
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | | | - Shunsuke Maeda
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Misato Sewaki
- Graduate School of Bioresources, Mie University, Tsu, 514-8507 Japan
| | - Mikako Sone
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Hirokazu Takahashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Mikio Nakazono
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Megumi Iwano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Seiji Takayama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Kentaro Yano
- Faculty of Agriculture, Meiji University, Kawasaki, 214-8571 Japan
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Kashiwara 582-8582, Japan
| | - Keita Suwabe
- Graduate School of Bioresources, Mie University, Tsu, 514-8507 Japan
- *Corresponding authors: Masao Watanabe, E-mail, ; Fax, +81-22-217-5683; Keita Suwabe, E-mail, ; Fax, +81-59-231-9540
| | - Masao Watanabe
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
- *Corresponding authors: Masao Watanabe, E-mail, ; Fax, +81-22-217-5683; Keita Suwabe, E-mail, ; Fax, +81-59-231-9540
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Palovaara J, Saiga S, Weijers D. Transcriptomics approaches in the early Arabidopsis embryo. TRENDS IN PLANT SCIENCE 2013; 18:514-21. [PMID: 23726727 DOI: 10.1016/j.tplants.2013.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/24/2013] [Accepted: 04/30/2013] [Indexed: 05/20/2023]
Abstract
Early plant embryogenesis condenses the fundamental processes underlying plant development into a short sequence of predictable steps. The main tissues, as well as stem cells for their post-embryonic maintenance, are specified through genetic control networks. A key question is how cell fates are instructed by unique cellular transcriptomes, and important insights have recently been gained through cell type-specific transcriptomics during post-embryonic development. However, the poor accessibility and small size of Arabidopsis (Arabidopsis thaliana) embryos have obstructed similar progress during embryogenesis. Here, we review the current situation in plant embryo transcriptomics, and discuss how the recent development of novel cell-specific analysis technologies will enable the identification of cellular transcriptomes in the early Arabidopsis embryo.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, The Netherlands
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Gao Y, Xu H, Shen Y, Wang J. Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique. PLANT MOLECULAR BIOLOGY 2013; 81:363-78. [PMID: 23322175 DOI: 10.1007/s11103-013-0009-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 12/31/2012] [Indexed: 05/11/2023]
Abstract
The endosperm plays an important role in seed formation and germination, especially in rice (Oryza sativa). We used a high-throughput sequencing technique (RNA-Seq) to reveal the molecular mechanisms involved in rice endosperm development. Three cDNA libraries were taken from rice endosperm at 3, 6 and 10 days after pollination (DAP), which resulted in the detection of 21,596, 20,910 and 19,459 expressed gens, respectively. By ERANGE, we identified 10,371 differentially expressed genes (log(2)Ratio ≥1, FDR ≤0.001). The results were compared against three public databases (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and MapMan) in order to annotate the gene descriptions, associate them with gene ontology terms and to assign each to pathways. A large number of genes related to ribosomes, the spliceosome and oxidative phosphorylation were found to be expressed in the early and middle stages. Plant hormone, galactose metabolism and carbon fixation related genes showed a significant increase in expression at the middle stage, whereas genes for defense against disease or response to stress as well as genes for starch/sucrose metabolism were strongly expressed during the later stages of endosperm development. Interestingly, most metabolic pathways were down-regulated between 3 and 10 DAP except for those involved in the accumulation of material, such as starch/sucrose and protein metabolism. We also identified the expression of 1,118 putative transcription factor genes in endosperm development. The RNA-Seq results provide further systematic understanding of rice endosperm development at a fine scale and a foundation for future studies.
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Affiliation(s)
- Yi Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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41
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Teoh KT, Requesens DV, Devaiah SP, Johnson D, Huang X, Howard JA, Hood EE. Transcriptome analysis of embryo maturation in maize. BMC PLANT BIOLOGY 2013; 13:19. [PMID: 23379350 PMCID: PMC3621147 DOI: 10.1186/1471-2229-13-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/28/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Maize is one of the most important crops in the world. With the exponentially increasing population and the need for ever increased food and feed production, an increased yield of maize grain (as well as rice, wheat and other grains) will be critical. Maize grain development is understood from the perspective of morphology, hormone responses, and storage reserve accumulation. This includes various studies on gene expression during embryo development and maturation but a global study of gene expression of the embryo has not been possible until recently. Transcriptome analysis is a powerful new tool that can be used to understand the genetic basis of embryo maturation. RESULTS We undertook a transcriptomic analysis of normal maturing embryos at 15, 21 and 27 days after pollination (DAP), of one elite maize germplasm line that was utilized in crosses to transgenic plants. More than 19,000 genes were analyzed by this method and the challenge was to select subsets of genes that are vitally important to embryo development and maturation for the initial analysis. We describe the changes in expression for genes relating to primary metabolic pathways, DNA synthesis, late embryogenesis proteins and embryo storage proteins, shown through transcriptome analysis and confirmed levels of transcription for some genes in the transcriptome using qRT-PCR. CONCLUSIONS Numerous genes involved in embryo maturation have been identified, many of which show changes in expression level during the progression from 15 to 27 DAP. An expected array of genes involved in primary metabolism was identified. Moreover, more than 30% of transcripts represented un-annotated genes, leaving many functions to be discovered. Of particular interest are the storage protein genes, globulin-1, globulin-2 and an unidentified cupin family gene. When expressing foreign proteins in maize, the globulin-1 promoter is most often used, but this cupin family gene has much higher expression and may be a better candidate for foreign gene expression in maize embryos. Results such as these allow identification of candidate genes and promoters that may not otherwise be available for use. mRNA seq data archived in NCBI SRA; Accession number: ACC=SRA060791 subid=108584.
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Affiliation(s)
- Keat Thomas Teoh
- Arkansas State University Biosciences Institute, PO Box 639, 72467, State University, AR, USA
| | | | - Shivakumar P Devaiah
- Arkansas State University Biosciences Institute, PO Box 639, 72467, State University, AR, USA
| | - Daniel Johnson
- Arkansas State University Biosciences Institute, PO Box 639, 72467, State University, AR, USA
| | - Xiuzhen Huang
- Arkansas State University Biosciences Institute, PO Box 639, 72467, State University, AR, USA
| | - John A Howard
- Applied Biotechnology Institute, San Luis Obispo, CA, USA
| | - Elizabeth E Hood
- Arkansas State University Biosciences Institute, PO Box 639, 72467, State University, AR, USA
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Pallara G, Todeschini V, Lingua G, Camussi A, Racchi ML. Transcript analysis of stress defence genes in a white poplar clone inoculated with the arbuscular mycorrhizal fungus Glomus mosseae and grown on a polluted soil. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 63:131-9. [PMID: 23257078 DOI: 10.1016/j.plaphy.2012.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/09/2012] [Indexed: 05/06/2023]
Abstract
In this study we investigated if the symbiosis with the arbuscular mycorrhizal fungus Glomus mosseae, which contributes to alleviate heavy metal stress in plants, may affect the transcription of genes involved in the stress defence in the white poplar clone 'AL35' grown on a multimetal (Cu and Zn) contaminated soil. The results obtained showed that the symbiosis with G. mosseae reduced transcript abundance of genes involved in antioxidant defence in leaves and roots of 'AL35' plants grown on the heavy metal-polluted soil. Moreover, the interaction between this poplar clone and the arbuscular mycorrhizal fungus induced the gene coding for phytochelatin synthase in leaves, whereas the expression of genes involved in heavy metal homeostasis did not change in roots. The present results suggest that, in presence of high levels of heavy metals, inoculation with G. mosseae may confer to 'AL35' a more efficient control of the oxidant level. Moreover, in mycorrhizal plants heavy metal chelation pathways appear involved in the defence strategies in leaves, whereas in roots they do not seem to contribute to increase the plant tolerance of heavy metals.
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Affiliation(s)
- G Pallara
- Dipartimento di Biotecnologie Agrarie, Sezione di Genetica, Università di Firenze, Via Maragliano 77, 50144 Firenze, Italy
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De Wilde K, De Buck S, Vanneste K, Depicker A. Recombinant antibody production in Arabidopsis seeds triggers an unfolded protein response. PLANT PHYSIOLOGY 2013; 161:1021-33. [PMID: 23188806 PMCID: PMC3561000 DOI: 10.1104/pp.112.209718] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 11/26/2012] [Indexed: 05/07/2023]
Abstract
Among the many plant-based production systems that are being tested for molecular farming, seeds are very attractive, as they provide a stable environment in which the accumulating recombinant proteins can be stored. However, it is not known exactly how high production levels of recombinant antibodies influence the endogenous transcriptome and proteome of the developing seed. To address this question, we studied the transcriptomic status in developing Arabidopsis (Arabidopsis thaliana) seeds 13 d post anthesis of three transgenic lines, producing varying levels of recombinant VHH or single-chain Fv antibody fragments fused to the human immunoglobulin G1-derived Fc fragment under the control of the β-PHASEOLIN seed-specific promoter. Using genome-wide Tiling arrays, we demonstrated that only a small proportion of the transcriptome was significantly changed in each of the lines compared with the wild type. Strikingly, in all three lines, we found a large overlap of up-regulated genes corresponding to protein folding, glycosylation/modification, translocation, vesicle transport, and protein degradation, suggestive of a state of cellular stress called the unfolded protein response. Moreover, the gene up-regulation amplitude was similar in all three lines. We hypothesize that the production of recombinant antibodies in the endoplasmic reticulum triggers endoplasmic reticulum stress, causing a disturbance of the normal cellular homeostasis.
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Affiliation(s)
- Kirsten De Wilde
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Sylvie De Buck
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Kevin Vanneste
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Ann Depicker
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
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Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD, Baud S, Bird D, DeBono A, Durrett TP, Franke RB, Graham IA, Katayama K, Kelly AA, Larson T, Markham JE, Miquel M, Molina I, Nishida I, Rowland O, Samuels L, Schmid KM, Wada H, Welti R, Xu C, Zallot R, Ohlrogge J. Acyl-lipid metabolism. THE ARABIDOPSIS BOOK 2013; 11:e0161. [PMID: 23505340 PMCID: PMC3563272 DOI: 10.1199/tab.0161] [Citation(s) in RCA: 699] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Acyl lipids in Arabidopsis and all other plants have a myriad of diverse functions. These include providing the core diffusion barrier of the membranes that separates cells and subcellular organelles. This function alone involves more than 10 membrane lipid classes, including the phospholipids, galactolipids, and sphingolipids, and within each class the variations in acyl chain composition expand the number of structures to several hundred possible molecular species. Acyl lipids in the form of triacylglycerol account for 35% of the weight of Arabidopsis seeds and represent their major form of carbon and energy storage. A layer of cutin and cuticular waxes that restricts the loss of water and provides protection from invasions by pathogens and other stresses covers the entire aerial surface of Arabidopsis. Similar functions are provided by suberin and its associated waxes that are localized in roots, seed coats, and abscission zones and are produced in response to wounding. This chapter focuses on the metabolic pathways that are associated with the biosynthesis and degradation of the acyl lipids mentioned above. These pathways, enzymes, and genes are also presented in detail in an associated website (ARALIP: http://aralip.plantbiology.msu.edu/). Protocols and methods used for analysis of Arabidopsis lipids are provided. Finally, a detailed summary of the composition of Arabidopsis lipids is provided in three figures and 15 tables.
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Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD, Baud S, Bird D, Debono A, Durrett TP, Franke RB, Graham IA, Katayama K, Kelly AA, Larson T, Markham JE, Miquel M, Molina I, Nishida I, Rowland O, Samuels L, Schmid KM, Wada H, Welti R, Xu C, Zallot R, Ohlrogge J. Acyl-lipid metabolism. THE ARABIDOPSIS BOOK 2013. [PMID: 23505340 DOI: 10.1199/tab.0161m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Acyl lipids in Arabidopsis and all other plants have a myriad of diverse functions. These include providing the core diffusion barrier of the membranes that separates cells and subcellular organelles. This function alone involves more than 10 membrane lipid classes, including the phospholipids, galactolipids, and sphingolipids, and within each class the variations in acyl chain composition expand the number of structures to several hundred possible molecular species. Acyl lipids in the form of triacylglycerol account for 35% of the weight of Arabidopsis seeds and represent their major form of carbon and energy storage. A layer of cutin and cuticular waxes that restricts the loss of water and provides protection from invasions by pathogens and other stresses covers the entire aerial surface of Arabidopsis. Similar functions are provided by suberin and its associated waxes that are localized in roots, seed coats, and abscission zones and are produced in response to wounding. This chapter focuses on the metabolic pathways that are associated with the biosynthesis and degradation of the acyl lipids mentioned above. These pathways, enzymes, and genes are also presented in detail in an associated website (ARALIP: http://aralip.plantbiology.msu.edu/). Protocols and methods used for analysis of Arabidopsis lipids are provided. Finally, a detailed summary of the composition of Arabidopsis lipids is provided in three figures and 15 tables.
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Roh KH, Park JS, Kim JB, Kim HU, Lee KR, Kim SH. Gene Expression Profiling of Oilseed Rape Embryos Using Microarray Analysis. ACTA ACUST UNITED AC 2012. [DOI: 10.3839/jabc.2012.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
To gain insights into the protein dynamics during seed development, a proteomic study on the developing Brassica campestri L. seeds with embryos in different embryogenesis stages was carried out. The seed proteins at 10, 16, 20, 25 and 35 DAP (days after pollination), respectively, were separated using two-dimensional gel electrophoresis and identities of 209 spots with altered abundance were determined by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS). These proteins were classified into 16 groups according to their functions. The most abundant proteins were related to primary metabolism, indicating the heavy demand of materials for rapid embryo growth. Besides, the high amount of proteins involved in protein processing and destination indicated importance of protein renewal during seed development. The remaining were those participated in oxidation/detoxification, energy, defense, transcription, protein synthesis, transporter, cell structure, signal transduction, secondary metabolism, transposition, DNA repair, storage and so on. Protein abundance profiles of each functional class were generated and hierarchical cluster analysis established 8 groups of dynamic patterns. Our results revealed novel characters of protein dynamics in seed development in Brassica campestri L. and provided valuable information about the complex process of seed development in plants.
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Affiliation(s)
- Wenlan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Yi Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hong Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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Kim DS, Lee KJ, Yim WC, Kim JB, Ha BK, Kim SH, Kang SY. Transcriptional network analysis of the tryptophan-accumulating rice mutant during grain filling. Mol Genet Genomics 2012; 287:699-709. [PMID: 22836167 DOI: 10.1007/s00438-012-0712-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 07/14/2012] [Indexed: 01/03/2023]
Abstract
In a previous study, we selected a high tryptophan (Trp)-accumulating rice (Oryza sativa L.) mutant line by in vitro mutagenesis using gamma rays. To obtain detailed information about the Trp biosynthetic pathway during the grain-filling in rice, we investigated the gene expression profiles in the wild-type (cv. Dongan) and the high-level Trp-accumulating mutant line (MRVII-33) at five different grain-filling stages using microarray analysis. The mutant line showed approximately 6.3-fold higher Trp content and 2.3-fold higher amino acids compared with the original cultivar at the final stage (stage V). The intensity of gene expression was analyzed and compared between the wild-type and mutant line at each of the five grain-filling stages using the Rice 4 × 44K oligo DNA microarray. Among the five stages, stage III showed the highest gene expression changes for both up- and down-regulated genes. Among the Trp biosynthesis-related genes, trpG showed high expression in the mutant line during stages I to IV and trpE showed higher at stage III. Gene clustering was performed based on the genes of KEGG's amino acid metabolism, and a total of 276 genes related to amino acid metabolism were placed into three clusters. The functional annotation enrichment analysis of the genes classified into the three clusters was also conducted using ClueGO. It was found that cluster 3 uniquely included biological processes related to aromatic amino acid metabolism. These results suggest that gene analysis based on microarray data is useful for elucidating the biological mechanisms of Trp accumulation in high Trp-accumulating mutants at each of the grain-filling stages.
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Affiliation(s)
- Dong Sub Kim
- Radiation Research Center for Bio-technology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk 580-185, Korea.
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Guan M, Li X, Guan C. Microarray analysis of differentially expressed genes between Brassica napus strains with high- and low-oleic acid contents. PLANT CELL REPORTS 2012; 31:929-43. [PMID: 22203212 DOI: 10.1007/s00299-011-1213-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 12/02/2011] [Accepted: 12/12/2011] [Indexed: 05/03/2023]
Abstract
An increase in oleic acid (C18:1) content is a desirable trait. Despite the critical roles of the two desaturases, FAD2 and FAD3, in the control of fatty acid desaturation, a dispute remains over whether inactivation of their genes alone is sufficient enough to generate the high-oleic trait. To address this question, we employed microarray technology to investigate the difference in gene expression profile between two different Brassica napus strains with high-C18:1 (71.71%) and low-C18:1 (55.6%) contents, respectively. Our study revealed 562 differentially expressed genes, of which 194 genes were up-regulated and 368 down-regulated. Based on the Gene Ontology classification, these genes were classified into 23 functional categories. Three of the up-regulated genes represent B. napus homologs of Arabidopsis genes encoding a cytosolic isoform of pyruvate kinase (AT3G55810), Δ9 acyl-lipid desaturase (AT1G06080, ADS1) and fatty acyl-ACP thioesterase B (AT1G08510), respectively. Conversely, the homologs of two Arabidopsis sequences encoding Δ9 acyl-lipid desaturase (AT2G31360, ADS2) and FAD3 desaturase (AT2G29980) were down-regulated in the high-oleic acid strain. Furthermore, 60 differentially expressed genes were classified as associated with relevant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, our results suggest that expressing the high-oleic acid trait may require a coordinated regulation of diverse regulatory and metabolic gene networks in addition to inactivation of the FAD2 and FAD3 genes in the oilseed. A set of the differentially expressed genes identified in this study will facilitate our efforts to tap the germplasms with the potential to express the high-oleic acid trait.
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Affiliation(s)
- Mei Guan
- The Oilseed Crop Research Institute, National Oilseed Crop Improvement Center, Hunan Agricultural University, Changsha 410128, China
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Sha AH, Li C, Yan XH, Shan ZH, Zhou XA, Jiang ML, Mao H, Chen B, Wan X, Wei WH. Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs. Mol Biol Rep 2012; 39:2867-74. [PMID: 21667246 DOI: 10.1007/s11033-011-1046-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 06/04/2011] [Indexed: 12/15/2022]
Abstract
Although GenBank has now covered over 1,400,000 expressed sequence tags (ESTs) from soybean, most ESTs available to the public have been derived from tissues or environmental conditions rather than developing seeds. It is absolutely necessary for annotating the molecular mechanisms of soybean seed development to analyze completely the gene expression profiles of its immature seed at various stages. Here we have constructed a full-length-enriched cDNA library comprised of a total of 45,408 cDNA clones which cover various stages of soybean seed development. Furthermore, we have sequenced from 5' ends of these clones, 36,656 ESTs were obtained in the present study. These EST sequences could be categorized into 27,982 unigenes, including 22,867 contigs and 5,115 singletons, among which 27,931 could be mapped onto soybean 20 chromosome sequences. Comparative genomic analysis with other plants has revealed that these unigenes include lots of candidate genes specific to dicot, legume and soybean. Approximately 1,789 of these unigenes currently show no homology to known soybean sequences, suggesting that many represent mRNAs specifically expressed in seeds. Novel abundant genes involved in the oil synthesis have been found in this study, may serve as a valuable resource for soybean seed improvement.
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Affiliation(s)
- Ai-Hua Sha
- Institute of Oil Crops, Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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