The Systemic Response to Fire Damage in Tomato Plants: A Case Study in the Development of Methods for Gene Expression Analysis Using Sequence Data

gene expression;sequencing;tomato;wounding;fire damage

Coker, Jeffrey Scott ; Dr. Judy Thomas, Committee Member,Dr. Eric Davies, Committee Chair,Dr. Jack Wheatley, Committee Member,Dr. Chris Brown, Committee Member,Dr. Dominique Robertson, Committee Member,Coker, Jeffrey Scott ; Dr. Judy Thomas ; Committee Member ; Dr. Eric Davies ; Committee Chair ; Dr. Jack Wheatley ; Committee Member ; Dr. Chris Brown ; Committee Member ; Dr. Dominique Robertson ; Committee Member

University:North Carolina State University

关键词: gene expression;    sequencing;    tomato;    wounding;    fire damage;   

Others  :  https://repository.lib.ncsu.edu/bitstream/handle/1840.16/5702/etd.pdf?sequence=1&isAllowed=y

美国|英语

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【 摘 要 】

Fire is a natural component of most terrestrial ecosystems and can act as a local wound stimulus to plants.The ultimate goal of this work was to characterize the array of transcripts which systemically accumulate in plants after fire damage.Before this could be accomplished, substantial development of methods for gene expression analysis using sequence data was necessary.This involved developing methods for identifying contamination in DNA sequence data (Chapter 2), identifying over 78,000 false sequences in GenBank and several thousand more in the indica rice genome (Chapter 2), developing a novel method for identifying housekeeping controls using sequence data (Chapter 3), performing relative expression analyses for 127 potential housekeeping control transcripts (Chapter 3), and characterizing 23 transcripts which encode all 13 subunits of vacuolar H+-ATPases in tomato plants (Chapter 4).A subtractive cDNA library served as a starting point to identify and characterize 9 novel tomato transcripts systemically up-regulated in leaves in the first hour after a distant leaf is flame wounded (Chapters 5).Real-time RT-PCR using leaf RNA isolated at different times after flaming showed that the most common pattern of transcript accumulation was an increase within 30 to 60 minutes, followed by a return to basal levels within 3 hours.Expression analyses also showed that most up-regulated transcripts were already present in unwounded tissues.A total of 46 different transcripts were identified from the subtractive cDNA library (Chapters 6).Compared with the entire tomato transcriptome, these 46 transcripts are very highly conserved in plants.The vast majority fell into 5 classes: enzymes of general metabolism; protein synthesis, modification, and transport; transcription; membrane transport; and photosynthesis and respiration.At least half of the transcripts have been previously associated with wounding or stress, suggesting that the systemic response to fire damage has components similar to those of other wound and stress responses.On the other hand, 30% of transcripts were associated with photosynthesis and respiration, suggesting that part of the response to fire damage is notably different from other wound and stress responses.Conclusions and future directions are included in Chapter 7.