Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in B. napus
2024-07-12
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Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in B. napus
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2024-07-12
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Ricono, Angela
ricon001@umn.edu
ricon001@umn.edu
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Abstract
Prolonged water limitation is a recurring stress experienced by many crops, yet we have limited understanding of the mechanisms genetically complex (polyploid) crop species use to adjust growth and metabolism under these conditions. Here, we profile 16 diverse Brassica napus accessions under prolonged water limitation and uncover unique, diel homoeolog responses on the subgenome level associated with transcriptome regulation of photosynthesis, carbohydrate and sulfur metabolism, and accumulation of glucosinolate levels.
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Included are the raw ('.raw') files that have not been manipulated in anyway. We provide these files instead of (ex) .mzML files so interested parties may follow the workflow I provide in the methods, and/or create their own preferred workflows with these data. This does mean that the user will have to do a bit of converting to process the raw data. Assuming the user wishes to identify features of interest using mzMine they will first have to convert the raw data to a .mzML format using msConvert (https://mzmine.github.io/mzmine_documentation/data_conversion.html). These data were collected in negative mode and centroided using the CWT algorithm in msConvert. Due to the large size of this dataset (4-5 biological replicates * 3-5 technical replicates * 3 time points * 2 treatments * 2 accessions * 3 positional tissue punches) the files were compressed in chunks so all 7 compressed files must be downloaded for the entire dataset. For the paper we analyzed the 'tip' samples (a hole punch collected at the tip of each leaf); we also provide the raw data for a punch collected at the base of the leaf, to the right of the midvein and tangental to the leaf edge ("tan1" samples), as well as another punch directly above this one ("tan2). For further details see the methods section of the attached paper.
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This project was supported by NSF-IOS (2029540 to K.G. and A.R.; 2025297 to A.H.), NSF-MCB (2225057 to A.H.), NSF-UROL: Epigenetics (1921724 to M.G.), NSF-PGRP (2029959 to P.P.E), DOE-BER (DE-SC0022987 to P.P.E.), NSF-BII (2120153 to M.G.), USDA-DSFAS (2022-67021-36467 to M.G.), USDA-FACT (2019-67021-29926 to M.G.), USDA-NIFA (2020-67034-31901 to A.C.), and the University of Minnesota.
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Ricono, Angela; Ludwig, Ella; Casto, Anna L; Zorich , Stevan; Sumner, Joshua; Bird, Kevin; Edger, Patrick P; Hegeman, Adrian D; Gehan, Malia A; Greenham , Kathleen. (2024). Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in B. napus. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://hdl.handle.net/11299/264077.
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