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| Status |
Public on Jan 01, 2019 |
| Title |
Analysis of Brachypodium miRNA targets: Evidence for diverse control during stress and conservation in bioenergy crops |
| Organisms |
Sorghum bicolor; Brachypodium distachyon; Panicum virgatum |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Background: Since the proposal of Brachypodium distachyon as a model for the grasses over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass, are completely absent from the miRBase database. While a significant number of miRNAs have been identified which are highly conserved across plants, little research has been done with respect to the conservation of miRNA targets. Plant responses to abiotic stresses are regulated by diverse pathways many of which involve miRNAs; however, it can be difficult to identify miRNA guided gene regulation when the miRNA is not the primary regulator of the target mRNA.
Results: To investigate miRNA target conservation and stress response involvement, a set of PARE (Parallel Analysis of RNA Ends) libraries totaling over 2 billion reads was constructed and sequenced from Brachypodium, switchgrass, and sorghum representing the first public release of degradome data from the latter two species. Analysis of this data provided not only PARE evidence for miRNA guided cleavage of over 7,000 predicted target mRNAs in Brachypodium, but also evidence for miRNA guided cleavage of over 1,000 homologous transcripts in sorghum and switchgrass. A pipeline was constructed to compare RNA-seq and PARE data made from Brachypodium plants exposed to various abiotic stress conditions. This resulted in the identification of 44 miRNA targets which exhibit stress regulated cleavage. Time course experiments were performed to reveal the relationship between miR393ab, miR169a, miR394ab, and their respective targets throughout the first 36 hours of the cold stress response in Brachypodium.
Conclusions: Knowledge gained from this study provides considerable insight into the degradomes and the breadth of miRNA target conservation among these three species. Additionally associations of a number of miRNAs and target mRNAs with the stress responses have been revealed which will aid researchers in developing stress tolerant transgenic crops.
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| Overall design |
Libraries were constructed from tissue samples from Brachypodium, sorghum, and switchgrass plants as well as above ground tissue which had been exposed to various stress conditions. Two biological replicates were constructed for each library type. Control libraries were constructed in addition to stress samples. Brachypodium Bd21 seeds were germinated in soil and the plants were grown in a growth chamber at a constant 20°C, under a 20 h light 350 μE⋅m−2⋅s−1, 4 h dark cycle. On day 21, 10 hours after light started, plants were subjected to various stress treatments. For heat stress, plants were placed at 40°C. For drought stress, plants were removed from soil and the roots were dried with paper towels. For submergence stress, plants were submerged completely with at least 5 cm of tap water covering the top of the plants. For cold stress, plants were placed at 4°C. For stress libraries, above ground tissue was sampled after 12 hours of stress; for the cold stress time courses, samples were taken at 0, 1, 2, 3, 6, 12, 24, and 36 hours. Switchgrass (AP13) was grown under greenhouse conditions with an average day temperature of 26°C and an average night temperature of 20°C. Stress treatments were carried out two months after propagation from cuttings and the second and third leaf blades from the top were sampled. After germination, Sorghum bicolor (BTx623) seedlings were transferred to soil in a growth chamber. After 14 days of growth (12 hours light at 28°C, 12 hours dark at 25°C), cold treatments were carried out and the above-ground tissue was harvested. Switchgrass and sorghum cold treatments at 4°C were performed for 24 hours. For switchgrass drought experiments, the drought sample was harvested 11 days after watering was stopped. Plants subjected to recovery were then watered, and on the 12th day they were sampled.
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| Contributor(s) |
Franke KR, Schmidt SA, Park S, Jeong D, Accerbi M, Green PJ |
| Citation(s) |
30029591 |
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| Submission date |
Mar 24, 2018 |
| Last update date |
Apr 16, 2019 |
| Contact name |
Karl Franke |
| Organization name |
University of Delaware
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| Department |
Plant and Soil Sciences
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| Lab |
DBI - Green Lab
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| Street address |
15 Innovation Way
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| City |
Newark |
| State/province |
Delaware |
| ZIP/Postal code |
19711 |
| Country |
USA |
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| Platforms (3) |
| GPL21050 |
Illumina HiSeq 2500 (Brachypodium distachyon) |
| GPL21615 |
Illumina HiSeq 2500 (Sorghum bicolor) |
| GPL24761 |
Illumina HiSeq 2500 (Panicum virgatum) |
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| Samples (44)
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| Relations |
| BioProject |
PRJNA445553 |
| SRA |
SRP136388 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE112296_BDI_miRNA_prominence_level_output.txt.gz |
719.2 Kb |
(ftp)(http) |
TXT |
| GSE112296_RAW.tar |
6.7 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE112296_SBI_miRNA_prominence_level_output.txt.gz |
179.9 Kb |
(ftp)(http) |
TXT |
| GSE112296_SWI_miRNA_prominence_level_output.txt.gz |
81.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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