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Data released on February 28, 2018

Supporting data for "Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum"

Takahagi, K; Inoue, K; Shimizu, M; Uehara-Yamaguchi, Y; Onda, Y; Mochida, K (2018): Supporting data for "Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum" GigaScience Database. http://dx.doi.org/10.5524/100413 RIS BibTeX Text

Allopolyploid plants often show wider environmental tolerances than their ancestors; this is expected to be due to the merger of multiple distinct genomes with a fixed heterozygosity. The complex homoeologous gene expression could have been evolutionarily advantageous for the adaptation of allopolyploid plants. Despite multiple previous studies reporting homoeolog-specific gene expression in allopolyploid species, there are no clear examples of homoeolog-specific function in acclimation to a long-term stress condition.
We found that the allopolyploid grass Brachypodium hybridum and its ancestor Brachypodium stacei show long-term heat stress tolerance, unlike its other ancestor, Brachypodium distachyon. To understand the physiological traits of B. hybridum, we compared the transcriptome of the three Brachypodium species grown under normal and heat stress conditions. We found that the expression patterns of ~26% and ~38% of the homoeolog groups in B. hybridum changed towards non-additive expression and non-ancestral expression, respectively, under normal condition. Moreover, we found that B. distachyon showed similar expression patterns between normal and heat stress conditions, whereas B. hybridum and B. stacei significantly altered their transcriptome in response to heat after 3 days of stress exposure, and homoeologs that were inherited from B. stacei may have contributed to the transcriptional stress response to heat in B. hybridum. After 15 days of heat exposure, B. hybridum and B. stacei maintained transcriptional states similar to those under normal conditions. These results suggested that an earlier response to heat that was specific to homoeologs originating from B. stacei contributed to cellular homeostasis under long-term heat stress in B. hybridum.
Our results provide insights into different regulatory events of the homoeo-transcriptome that are associated with stress acclimation in allopolyploid plants.

Contact Submitter

Protocols.io:

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Accessions (data included in GigaDB):

BioProject: PRJDB5654
BioProject: PRJDB5657

Keywords:

abiotic stress response allopolyploidy brachypodium hybridum heat acclimation homoeolog hybrid species transcriptome 

Transcriptomic, Genomic

http://gigadb.org/images/data/cropped/100413.jpg

Funding:

  • Funding body - Japan Society for the Promotion of Science
  • Award ID - 26712003
  • Comment - Grant-in-Aid for Young Scientists (A)
  • Awardee - Keiichi Mochida
  • Funding body - Japan Science and Technology Agency
  • Award ID - J2013403
  • Comment - Advanced Low Carbon Technology Research and Development Program
  • Awardee - Keiichi Mochida

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Bd21_normal_3days_315368  Brachypodium distachyon Description:RNA extracted from leaf tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048407
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Bd21_leaf_115368  Brachypodium distachyon Description:RNA extracted from leaf tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048387
...
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Bd21_normal_3days_115368  Brachypodium distachyon Description:RNA extracted from leaf tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048405
...
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Bd21_normal_3days_215368  Brachypodium distachyon Description:RNA extracted from leaf tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048406
...
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Bd21_root_315368  Brachypodium distachyon Description:RNA extracted from root tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048392
...
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Bd21_leaf_315368  Brachypodium distachyon Description:RNA extracted from leaf tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048389
...
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Bd21_root_115368  Brachypodium distachyon Description:RNA extracted from root tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048390
...
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Bd21_leaf_215368  Brachypodium distachyon Description:RNA extracted from leaf tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048388
...
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Bd21_heat_stress_3days_115368  Brachypodium distachyon Description:RNA extracted from leaf tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048408
...
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Bd21_root_215368  Brachypodium distachyon Description:RNA extracted from root tissues grown ...
Analyte type:RNA
Alternative accession-SRA Sample:DRS048391
...
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Displaying 1-10 of 58 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
SNPsTEXT129.49 MB2018-02-20
SNPsTEXT860.9 MB2018-02-20
SNPsTEXT141.28 MB2018-02-20
SNPsTEXT747.55 MB2018-02-20
Bd1", ">Bd2", ">Bd3", ">Bd4", and ">Bd5"."> Bdistachyon_314_v3.0.edited.fa
Genome sequenceFASTA261.74 MB2018-02-20
Genome sequenceFASTA261.74 MB2018-02-20
archiveTAR329 MB2018-02-20
scriptUNKNOWN3.24 KB2018-02-20
ReadmeTEXT2.55 KB2018-02-20
Expression dataTEXT11.91 MB2018-02-20
Displaying 1-10 of 12 File(s).

History:

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