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| Status |
Public on Apr 11, 2019 |
| Title |
Lasting expression changes in tomato after tomato psyllid (Bactericera cockerelli) infestation |
| Organism |
Solanum lycopersicum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of tomato (Solanum lycopersicum) and potato (S. tuberosum) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’. Plants undergo physiological, transcriptomic, or epigenetic changes in order to mount a stronger, faster response against secondary challenges by previously perceived threats. This is called defense ‘priming’ and it likely has an impact on vectored disease transmission. Currently, it is still unknown whether or not psyllid infestation has any lasting consequences for tomato gene expression or defense. To characterize the genes potentially involved in tomato priming against psyllids, RNA was extracted from psyllid-primed and uninfested tomato (Moneymaker) leaves three weeks after infestation.
Methods: RNA was extracted and sequenced from plants three weeks after psyllid infestation. Plants were either left alone (Control or C) or infested with psyllids (Primed or J1). Libraries were developed using the TruSeq RNA Library Prep Kit v2. Sequencing was performed on the Illumina PE HiSeq 2500 v4 platform. Processed sequences were uploaded to the CyVerse Discovery Environment computational infrastructure where bioinformatic analysis was performed using the Tuxedo Suite 2 workflow.
Results: Illumina HiSeq sequencing of tomato cDNA libraries produced 132,428,443 total reads that met FastQC quality control criteria. 94.6% of all reads mapped to vSL3.0 of the S. lycopersicum genome. CuffDiff2 analysis identified 310 differentially expressed genes (DEGs) between control and psyllid-primed plants (q-value <0.01).
Conclusions: A week-long infestation by a small number of B. cockerelli had lasting consequences for gene expression in tomato plants. Homologs of the DEGs were associated with 1) defense against abiotic and biotic stress, 2) growth and development, and 3) components of plant biology indirectly involved in plant growth and development such as homeostasis, transcription/translation, and molecular transport.
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| Overall design |
FPKM values of control and psyllid-primed tomato leaf transcriptomes were generated by Illumina PE HiSeq 2500 v4 sequencing.
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| Contributor(s) |
Harrison K, Menoza A, Tamborindeguy C, Levy J |
| Citation missing |
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| Submission date |
Apr 10, 2019 |
| Last update date |
Apr 11, 2019 |
| Contact name |
Kyle Harrison |
| E-mail(s) |
kyle.harrison@usda.gov
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| Organization name |
USDA-ARS
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| Department |
Entomology
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| Street address |
1700 E Campus Mall
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| City |
Lincoln |
| State/province |
Nebraska |
| ZIP/Postal code |
68503 |
| Country |
USA |
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| Platforms (1) |
| GPL19694 |
Illumina HiSeq 2500 (Solanum lycopersicum) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA531929 |
| SRA |
SRP191880 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE129610_genes.sorted_by_expression.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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