נגישות
menu      
חיפוש מתקדם
תחביר
חפש...
הספר "אוצר וולקני"
אודות
תנאי שימוש
ניהול
קהילה:
אסיף מאגר המחקר החקלאי
פותח על ידי קלירמאש פתרונות בע"מ -
De novo transcriptome sequencing and development of abscission zone-specific microarray as a new molecular tool for analysis of tomato organ abscission
Year:
2016
Source of publication :
Frontiers in Plant Science
Authors :
מאיר, שמעון
;
.
פילוסוף-הדס, סוניה
;
.
קוכאנק, בטינה
;
.
Volume :
6
Co-Authors:
Sundaresan, S., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
Philosoph-Hadas, S., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel
Riov, J., Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
Mugasimangalam, R., Department of Bioinformatics, QTLomics Technologies Pvt. Ltd, Bangalore, India
Kuravadi, N.A., Department of Bioinformatics, QTLomics Technologies Pvt. Ltd, Bangalore, India
Kochanek, B., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel
Salim, S., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel
Tucker, M.L., Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
Meir, S., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel
Facilitators :
From page:
To page:
(
Total pages:
1
)
Abstract:
Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession. © 2016 Sundaresan, Philosoph-Hadas, Riov, Mugasimangalam, Kuravadi, Kochanek, Salim, Tucker and Meir.
Note:
Related Files :
ethylene
Flower pedicel abscission
Oligonucleotide microarray
RNA-Sequencing
Tomato (Solanum lycopersicum)
transcriptome
עוד תגיות
תוכן קשור
More details
DOI :
10.3389/fpls.2015.01258
Article number:
1258
Affiliations:
Database:
סקופוס
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
18730
Last updated date:
02/03/2022 17:27
Creation date:
16/04/2018 23:23
You may also be interested in
Scientific Publication
De novo transcriptome sequencing and development of abscission zone-specific microarray as a new molecular tool for analysis of tomato organ abscission
6
Sundaresan, S., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
Philosoph-Hadas, S., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel
Riov, J., Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
Mugasimangalam, R., Department of Bioinformatics, QTLomics Technologies Pvt. Ltd, Bangalore, India
Kuravadi, N.A., Department of Bioinformatics, QTLomics Technologies Pvt. Ltd, Bangalore, India
Kochanek, B., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel
Salim, S., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel
Tucker, M.L., Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
Meir, S., Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel
De novo transcriptome sequencing and development of abscission zone-specific microarray as a new molecular tool for analysis of tomato organ abscission
Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession. © 2016 Sundaresan, Philosoph-Hadas, Riov, Mugasimangalam, Kuravadi, Kochanek, Salim, Tucker and Meir.
Scientific Publication
You may also be interested in