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Moazzzam Jazi M, Seyedi SM, Ebrahimie E, Ebrahimi M, De Moro G, Botanga C. A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery. BMC Genomics 2017; 18:627. [PMID: 28814265 PMCID: PMC5559799 DOI: 10.1186/s12864-017-3989-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022] Open
Abstract
Background Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress. Results RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars. Conclusion This study, as the first report on the whole transcriptome survey of P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3989-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maryam Moazzzam Jazi
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Seyed Mahdi Seyedi
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
| | - Esmaeil Ebrahimie
- School of Medicine, The University of Adelaide, Adelaide, Australia.,Institute of Biotechnology, Shiraz University, Shiraz, Iran.,Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia.,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
| | | | - Gianluca De Moro
- Center of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - Christopher Botanga
- Department of Biological Sciences, Chicago State University, Chicago, IL, USA
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Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress. Mol Genet Genomics 2017; 292:1307-1322. [PMID: 28710562 DOI: 10.1007/s00438-017-1348-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/03/2017] [Indexed: 01/09/2023]
Abstract
Drought stress is a major problem around the world and there is still little molecular mechanism about how fruit crops deal with moderate drought stress. Here, the physiological and phosphoproteomic responses of drought-sensitive genotype (M26) and drought-tolerant genotype (MBB) under moderate drought stress were investigated. Our results of the physiology analysis indicated that the MBB genotype could produce more osmosis-regulating substances. Furthermore, phosphoproteins from leaves of both genotypes under moderate drought stress were analyzed using the isobaric tags for relative and absolute quantification technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites, and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Five and thirty-five phosphoproteins with the phosphorylation levels significantly changed (PLSC) were identified in M26 and MBB, respectively. Among these, four PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlap of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins represent a unique combination of metabolism, transcription, translation, and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new and unique homeostasis of major cellular processes. The basic trend was an increase in protein and organic molecules abundance related to drought. These increases were higher in MBB than in M26. Our study is the first to address the phosphoproteome of apple rootstocks in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.
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Li MW, Xin D, Gao Y, Li KP, Fan K, Muñoz NB, Yung WS, Lam HM. Using genomic information to improve soybean adaptability to climate change. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1823-1834. [PMID: 27660480 DOI: 10.1093/jxb/erw348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Climate change has brought severe challenges to agriculture. It is anticipated that there will be a drop in crop yield - including that of soybean - due to climatic stress factors that include drastic fluctuations in temperature, drought, flooding and high salinity. Genomic information on soybean has been accumulating rapidly since initial publication of its reference genome, providing a valuable tool for the improvement of cultivated soybean. Not only are many molecular markers that are associated with important quantitative trait loci now identified, but we also have a more detailed picture of the genomic variations among soybean germplasms, enabling us to utilize these as tools to assist crop breeding. In this review, we will summarize and discuss the currently available soybean genomic approaches, including whole-genome sequencing, sequencing-based genotyping, functional genomics, proteomics, and epigenomics. The information uncovered through these techniques will help further pinpoint important gene candidates and genomic loci associated with adaptive traits, as well as achieving a better understanding of how soybeans cope with the changing climate.
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Affiliation(s)
- Man-Wah Li
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Dawei Xin
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Yishu Gao
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Kwan-Pok Li
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Kejing Fan
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Nacira Belen Muñoz
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias-INTA, Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Wai-Shing Yung
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hon-Ming Lam
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I. Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves. J Proteome Res 2016; 15:4304-4317. [DOI: 10.1021/acs.jproteome.6b00348] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lam Dai Vu
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elisabeth Stes
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Michiel Van Bel
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Davy Maddelein
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Dirk Inzé
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lennart Martens
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Kris Gevaert
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Ive De Smet
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Ji W, Cong R, Li S, Li R, Qin Z, Li Y, Zhou X, Chen S, Li J. Comparative Proteomic Analysis of Soybean Leaves and Roots by iTRAQ Provides Insights into Response Mechanisms to Short-Term Salt Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:573. [PMID: 27200046 PMCID: PMC4850148 DOI: 10.3389/fpls.2016.00573] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/13/2016] [Indexed: 05/21/2023]
Abstract
Salinity severely threatens land use capability and crop yields worldwide. Understanding the mechanisms that protect soybeans from salt stress will help in the development of salt-stress tolerant leguminous plants. Here we initially analyzed the changes in malondialdehyde levels, the activities of superoxide dismutase and peroxidases, chlorophyll content, and Na(+)/K(+) ratios in leaves and roots from soybean seedlings treated with 200 mM NaCl at different time points. We found that the 200 mM NaCl treated for 12 h was optimal for undertaking a proteomic analysis on soybean seedlings. An iTRAQ-based proteomic approach was used to investigate the proteomes of soybean leaves and roots under salt treatment. These data are available via ProteomeXchange with the identifier PXD002851. In total, 278 and 440 proteins with significantly altered abundances were identified in leaves and roots of soybean, respectively. From these data, a total of 50 proteins were identified in the both tissues. These differentially expressed proteins (DEPs) were from 13 biological processes. Moreover, protein-protein interaction analysis revealed that proteins involved in metabolism, carbohydrate and energy metabolism, protein synthesis and redox homeostasis could be assigned to four high salt stress response networks. Furthermore, semi-quantitative RT-PCR analysis revealed that some of the proteins, such as a 14-3-3, MMK2, PP1, TRX-h, were also regulated by salt stress at the level of transcription. These results indicated that effective regulatory protein expression related to signaling, membrane and transport, stress defense and metabolism all played important roles in the short-term salt response of soybean seedlings.
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Affiliation(s)
- Wei Ji
- Department of Plant Biotechnology, College of Life Science, Northeast Agricultural UniversityHarbin, China
| | - Ru Cong
- Department of Plant Biotechnology, College of Life Science, Northeast Agricultural UniversityHarbin, China
| | - Sheng Li
- Department of Plant Biotechnology, College of Life Science, Northeast Agricultural UniversityHarbin, China
| | - Rui Li
- Department of Plant Biotechnology, College of Life Science, Northeast Agricultural UniversityHarbin, China
| | - Zhiwei Qin
- Department of Vegetables, College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Yanjun Li
- Department of Plant Biotechnology, College of Life Science, Northeast Agricultural UniversityHarbin, China
| | - Xiaolin Zhou
- Department of Plant Biotechnology, College of Life Science, Northeast Agricultural UniversityHarbin, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of FloridaGainesville, FL, USA
- Department of Proteomics, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Jing Li
- Department of Plant Biotechnology, College of Life Science, Northeast Agricultural UniversityHarbin, China
- *Correspondence: Jing Li
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