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Differences in the Abundance of Auxin Homeostasis Proteins Suggest Their Central Roles for In Vitro Tissue Differentiation in Coffea arabica. PLANTS 2021; 10:plants10122607. [PMID: 34961078 PMCID: PMC8708889 DOI: 10.3390/plants10122607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/04/2023]
Abstract
Coffea arabica is one of the most important crops worldwide. In vitro culture is an alternative for achieving Coffea regeneration, propagation, conservation, genetic improvement, and genome editing. The aim of this work was to identify proteins involved in auxin homeostasis by isobaric tandem mass tag (TMT) and the synchronous precursor selection (SPS)-based MS3 technology on the Orbitrap Fusion™ Tribrid mass spectrometer™ in three types of biological materials corresponding to C. arabica: plantlet leaves, calli, and suspension cultures. Proteins included in the β-oxidation of indole butyric acid and in the signaling, transport, and conjugation of indole-3-acetic acid were identified, such as the indole butyric response (IBR), the auxin binding protein (ABP), the ATP-binding cassette transporters (ABC), the Gretchen-Hagen 3 proteins (GH3), and the indole-3-acetic-leucine-resistant proteins (ILR). A more significant accumulation of proteins involved in auxin homeostasis was found in the suspension cultures vs. the plantlet, followed by callus vs. plantlet and suspension culture vs. callus, suggesting important roles of these proteins in the cell differentiation process.
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Marrano A, Britton M, Zaini PA, Zimin AV, Workman RE, Puiu D, Bianco L, Pierro EAD, Allen BJ, Chakraborty S, Troggio M, Leslie CA, Timp W, Dandekar A, Salzberg SL, Neale DB. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. Gigascience 2020; 9:giaa050. [PMID: 32432329 PMCID: PMC7238675 DOI: 10.1093/gigascience/giaa050] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 03/13/2020] [Accepted: 04/20/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. FINDINGS Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. CONCLUSION Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.
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Affiliation(s)
- Annarita Marrano
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Rachael E Workman
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Luca Bianco
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Erica Adele Di Pierro
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Sandeep Chakraborty
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, 3400 North Charles Street Baltimore, MD 21218, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Marrano A, Britton M, Zaini PA, Zimin AV, Workman RE, Puiu D, Bianco L, Pierro EAD, Allen BJ, Chakraborty S, Troggio M, Leslie CA, Timp W, Dandekar A, Salzberg SL, Neale DB. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. Gigascience 2020. [PMID: 32432329 DOI: 10.1101/80979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. FINDINGS Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. CONCLUSION Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.
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Affiliation(s)
- Annarita Marrano
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Rachael E Workman
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Luca Bianco
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Erica Adele Di Pierro
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Sandeep Chakraborty
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, 3400 North Charles Street Baltimore, MD 21218, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Shahrokh S, Mansouri V, Razzaghi M. Assessment of the SRC Inhibition Role in the Efficacy of Breast Cancer Radiotherapy. J Lasers Med Sci 2020; 10:S18-S22. [PMID: 32021668 DOI: 10.15171/jlms.2019.s4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: Radiotherapy (RT) is an effective therapeutic method for preventing the recurrence of breast cancer after surgery. The development and improvement of RT are of interest to scientists. Possible improvement of RT via study of dysregulated proteins of breast cancer cell line MDA-MB-231 which is exposed to 10 Gray (Gy) radiation is aim of this study. Methods: Using protein-protein interaction (PPI) network analysis by means of running Cytoscape software via the STRING database, the up-regulated proteins of MDA-MB-231 breast cancer cells irradiated by a single and fractioned 10 Gy 137Cs γ-radiation were analyzed. The network was analyzed by using the Network analyzer to characterize the central genes. The action map was mapped for the queried genes and the added neighbors via CluePedia-STRING ACTIONS-v10.5- 20.11.2017. Results: The 14 differentially expressed proteins (DEPs) plus 10 neighbors interacted to construct a network. Among the 14 queried DEPs, FN1, CSPG4, LRP1, GSN, RTN4, and CTSD were highlighted as a complex set in the analysis. The analysis revealed that SRC as an added neighbor was activated by the critical DEPs. The activation of other oncogenes like AKT1 was also determined. Conclusion: The results indicate that the inhibition of SRC activity or the inhibition of its activators is a useful function of breast cancer RT.
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Affiliation(s)
- Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Mansouri
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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