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Macharia TN, Bellieny-Rabelo D, Moleleki LN. Transcriptome Profiling of Potato ( Solanum tuberosum L.) Responses to Root-Knot Nematode ( Meloidogyne javanica) Infestation during A Compatible Interaction. Microorganisms 2020; 8:microorganisms8091443. [PMID: 32967109 PMCID: PMC7563278 DOI: 10.3390/microorganisms8091443] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022] Open
Abstract
Root-knot nematode (RKN) Meloidogyne javanica presents a great challenge to Solanaceae crops, including potato. In this study, we investigated transcriptional responses of potato roots during a compatible interaction with M. javanica. In this respect, differential gene expression of Solanum tuberosum cultivar (cv.) Mondial challenged with M. javanica at 0, 3 and 7 days post-inoculation (dpi) was profiled. In total, 4948 and 4484 genes were detected, respectively, as differentially expressed genes (DEGs) at 3 and 7 dpi. Functional annotation revealed that genes associated with metabolic processes were enriched, suggesting they might have an important role in M. javanica disease development. MapMan analysis revealed down-regulation of genes associated with pathogen perception and signaling suggesting interference with plant immunity system. Notably, delayed activation of pathogenesis-related genes, down-regulation of disease resistance genes, and activation of host antioxidant system contributed to a susceptible response. Nematode infestation suppressed ethylene (ET) and jasmonic acid (JA) signaling pathway hindering JA/ET responsive genes associated with defense. Genes related to cell wall modification were differentially regulated while transport-related genes were up-regulated, facilitating the formation of nematode feeding sites (NFSs). Several families of transcription factors (TFs) were differentially regulated by M. javanica infestation. Suggesting that TFs play an indispensable role in physiological adaptation for successful M. javanica disease development. This genome-wide analysis reveals the molecular regulatory networks in potato roots which are potentially manipulated by M. javanica. Being the first study analyzing transcriptome profiling of M. javanica-diseased potato, it provides unparalleled insight into the mechanism underlying disease development.
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Gao J, Chen Z, Luo M, Peng H, Lin H, Qin C, Yuan G, Shen Y, Ding H, Zhao M, Pan G, Zhang Z. Genome expression profile analysis of the maize sheath in response to inoculation to R. solani. Mol Biol Rep 2014; 41:2471-83. [PMID: 24420865 PMCID: PMC3968446 DOI: 10.1007/s11033-014-3103-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 01/06/2014] [Indexed: 12/27/2022]
Abstract
Currently, the molecular regulation mechanisms of disease-resistant involved in maize leaf sheaths infected by banded leaf and sheath blight (BLSB) are poorly known. To gain insight into the transcriptome dynamics that are associated with their disease-resistant, genome-wide gene expression profiling was conducted by Solexa sequencing. More than four million tags were generated from sheath tissues without any leaf or development leaf, including 193,222 and 204,824 clean tags in the two libraries, respectively. Of these, 82,864 (55.4 %) and 91,678 (51.5 %) tags were matched to the reference genes. The most differentially expressed tags with log2 ratio >2 or <-2 (P < 0.001) were further analyzed, representing 1,476 up-regulated and 1,754 down-regulated genes, except for unknown transcripts, which were classified into 11 functional categories. The most enriched categories were those of metabolism, signal transduction and cellular transport. Next, the expression patterns of 12 genes were assessed by quantitative real-time PCR, and it is showed the results were general agreement with the Solexa analysis, although the degree of change was lower in amplitude. In conclusion, we first reveal the complex changes in the transcriptome during the early development of maize sheath infected by BLSB and provide a comprehensive set of data that are essential for understanding its molecular regulation mechanism.
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Affiliation(s)
- Jian Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Zhe Chen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Mao Luo
- Drug Discovery Research Center of Luzhou Medical College, Luzhou, 646000 Sichuan China
| | - Hua Peng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Haijian Lin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Cheng Qin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Guangsheng Yuan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Haiping Ding
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Maojun Zhao
- Life Science College of Sichuan Agricultural University, Ya’an, 625014 Sichuan China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Zhiming Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
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Lopato S, Borisjuk N, Langridge P, Hrmova M. Endosperm transfer cell-specific genes and proteins: structure, function and applications in biotechnology. FRONTIERS IN PLANT SCIENCE 2014; 5:64. [PMID: 24578704 PMCID: PMC3936200 DOI: 10.3389/fpls.2014.00064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/07/2014] [Indexed: 05/21/2023]
Abstract
Endosperm transfer cells (ETC) are one of four main types of cells in endosperm. A characteristic feature of ETC is the presence of cell wall in-growths that create an enlarged plasma membrane surface area. This specialized cell structure is important for the specific function of ETC, which is to transfer nutrients from maternal vascular tissue to endosperm. ETC-specific genes are of particular interest to plant biotechnologists, who use genetic engineering to improve grain quality and yield characteristics of important field crops. The success of molecular biology-based approaches to manipulating ETC function is dependent on a thorough understanding of the functions of ETC-specific genes and ETC-specific promoters. The aim of this review is to summarize the existing data on structure and function of ETC-specific genes and their products. Potential applications of ETC-specific genes, and in particular their promoters for biotechnology will be discussed.
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Affiliation(s)
- Sergiy Lopato
- *Correspondence: Sergiy Lopato, Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia e-mail:
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Hellmann E, Gruhn N, Heyl A. The more, the merrier: cytokinin signaling beyond Arabidopsis. PLANT SIGNALING & BEHAVIOR 2010; 5:1384-90. [PMID: 21045560 PMCID: PMC3115238 DOI: 10.4161/psb.5.11.13157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The phytohormone cytokinin is a key player in many developmental processes and in the response of plants to biotic and abiotic stress. The cytokinin signal is perceived and transduced via a multistep variant of the bacterial two-component signaling system. Most of the research on cytokinin signaling has been done in the model plant Arabidopsis thaliana. Research on cytokinin signaling has expanded to a much broader range of plants species in recent years. This is due to the natural limitation of Arabidopsis as a model species for the investigation of processes like nodulation or wood formation. The rapidly increasing number of sequenced plant genomes also facilitates the use of other species in this line of research. This review summarizes what is known about the cytokinin signaling in the different organisms and highlights differences to Arabidopsis.
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Affiliation(s)
- Eva Hellmann
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Berlin, Germany
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Wu J, Zhang Y, Zhang H, Huang H, Folta KM, Lu J. Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology. BMC PLANT BIOLOGY 2010; 10:234. [PMID: 21029438 PMCID: PMC3017854 DOI: 10.1186/1471-2229-10-234] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 10/28/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND Downy mildew (DM), caused by pathogen Plasmopara viticola (PV) is the single most damaging disease of grapes (Vitis L.) worldwide. However, the mechanisms of the disease development in grapes are poorly understood. A method for estimating gene expression levels using Solexa sequencing of Type I restriction-endonuclease-generated cDNA fragments was used for deep sequencing the transcriptomes resulting from PV infected leaves of Vitis amurensis Rupr. cv. Zuoshan-1. Our goal is to identify genes that are involved in resistance to grape DM disease. RESULTS Approximately 8.5 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from PV pathogen-infected leaves, and about 7.5 M were sequenced from the cDNA library constructed from the control leaves. When annotated, a total of 15,249 putative genes were identified from the Solexa sequencing tags for the infection (INF) library and 14,549 for the control (CON) library. Comparative analysis between these two cDNA libraries showed about 0.9% of the unique tags increased by at least five-fold, and about 0.6% of the unique tags decreased more than five-fold in infected leaves, while 98.5% of the unique tags showed less than five-fold difference between the two samples. The expression levels of 12 differentially expressed genes were confirmed by Real-time RT-PCR and the trends observed agreed well with the Solexa expression profiles, although the degree of change was lower in amplitude. After pathway enrichment analysis, a set of significantly enriched pathways were identified for the differentially expressed genes (DEGs), which associated with ribosome structure, photosynthesis, amino acid and sugar metabolism. CONCLUSIONS This study presented a series of candidate genes and pathways that may contribute to DM resistance in grapes, and illustrated that the Solexa-based tag-sequencing approach was a powerful tool for gene expression comparison between control and treated samples.
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Affiliation(s)
- Jiao Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Horticultural Sciences Department and the Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Huiqin Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hong Huang
- School of Information, University of South Florida Tampa, FL, 33620, USA
| | - Kevin M Folta
- Horticultural Sciences Department and the Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Center for Viticulture and Small Fruit Research, Florida A&M University, Tallahassee, FL, 32317, USA
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