Data from: Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns
Data files
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README.md
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SuperSAGE.zip
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Abstract
We have compared the transcriptomic profiles of microdissected live ovules at four developmental stages between a diploid sexual and diploid apomictic Boechera. We sequenced >2 million SuperSAGE tags and identified (1) heterochronic tags (n = 595) that demonstrated significantly different patterns of expression between sexual and apomictic ovules across all developmental stages, (2) stage-specific tags (n = 577) that were found in a single developmental stage and differentially expressed between the sexual and apomictic ovules, and (3) sex-specific (n = 237) and apomixis-specific (n = 1106) tags that were found in all four developmental stages but in only one reproductive mode. Most heterochronic and stage-specific tags were significantly downregulated during early apomictic ovule development, and 110 were associated with reproduction. By contrast, most late stage-specific tags were upregulated in the apomictic ovules, likely the result of increased gene copy number in apomictic (hexaploid) versus sexual (triploid) endosperm or of parthenogenesis. Finally, we show that apomixis-specific gene expression is characterized by a significant overrepresentation of transcription factor activity. We hypothesize that apomeiosis is associated with global downregulation at the megaspore mother cell stage. As the diploid apomict analyzed here is an ancient hybrid, these data are consistent with the postulated link between hybridization and asexuality and provide a hypothesis for multiple evolutionary origins of apomixis in the genus Boechera.
This section describes the overall experiment.
Title
Apomictic and Sexual Ovules of Boechera Display Heterochronic Global Gene Expression Patterns
Summary
“The Plant Cell, Volume 22, Issue 3, March 2010, Pages 655-671, (https://doi.org/10.1105/tpc.109.072223)”
We have compared the transcriptomic profiles of microdissected live ovules at four developmental stages between a diploid sexual and diploid apomictic Boechera.
Overall Design
“We sequenced >2 million SuperSAGE tags and identified (1) heterochronic tags (n = 595) that demonstrated significantly different patterns of expression between sexual and apomictic ovules across all developmental stages, (2) stage-specific tags (n = 577) that were found in a single developmental stage and differentially expressed between the sexual and apomictic ovules, and (3) sex-specific (n = 237) and apomixis-specific (n = 1106) tags that were found in all four developmental stages but in only one reproductive mode.”
Contributors
- Timothy F. Sharbel
- Marie-Luise Voigt
- Jose M. Corral
- Giulio Galla
- Jochen Kumlehn
- Christian Klukas
- Falk Schreiber
- Heiko Vogel
- Bjorn Rotter
SAMPLES
This section describes the SAGE libraries.
The processed data files should be tab-delimited text files with TAG and COUNT columns. See an example processed data file in the next worksheet.
Sample Name | Title | Processed Data File | Source Name | Organism | Characteristics: Label | Characteristics: Label | Characteristics: Label | Molecule | Anchor | Tag Length | Tag Count |
---|---|---|---|---|---|---|---|---|---|---|---|
LIBRARY 1 | Sexual ovule stage 1 | NS1.txt | Sexual ovule stage 1 | Boechera polyantha | Sexual | total RNA | NlaIII | 22 | 112539 | ||
LIBRARY 2 | Sexual ovule stage 2 | NS2.txt | Sexual ovule stage 2 | Boechera polyantha | Sexual | total RNA | NlaIII | 22 | 112539 | ||
LIBRARY 3 | Sexual ovule stage 3 | NS3.txt | Sexual ovule stage 3 | Boechera polyantha | Sexual | total RNA | NlaIII | 22 | 112539 | ||
LIBRARY 4 | Sexual ovule stage 4 | NS4.txt | Sexual ovule stage 4 | Boechera polyantha | Sexual | total RNA | NlaIII | 22 | 112539 | ||
LIBRARY 5 | Apomictic ovule stage 1 | NA1.txt | Apomictic ovule stage 1 | Boechera retrofracta | Apomictic | total RNA | NlaIII | 22 | 112539 | ||
LIBRARY 6 | Apomictic ovule stage 2 | NA2.txt | Apomictic ovule stage 2 | Boechera retrofracta | Apomictic | total RNA | NlaIII | 22 | 112539 | ||
LIBRARY 7 | Apomictic ovule stage 3 | NA3.txt | Apomictic ovule stage 3 | Boechera retrofracta | Apomictic | total RNA | NlaIII | 22 | 112539 | ||
LIBRARY 8 | Apomictic ovule stage 4 | NA4.txt | Apomictic ovule stage 4 | Boechera retrofracta | Apomictic | total RNA | NlaIII | 22 | 112539 | ||
LIBRARY 9 | Sexual ovule stage 1 | DS1.txt | Sexual ovule stage 1 | Boechera polyantha | Sexual | total RNA | DpnII | 22 | 112539 | ||
LIBRARY 10 | Sexual ovule stage 2 | DS2.txt | Sexual ovule stage 2 | Boechera polyantha | Sexual | total RNA | DpnII | 22 | 112539 | ||
LIBRARY 11 | Sexual ovule stage 3 | DS3.txt | Sexual ovule stage 3 | Boechera polyantha | Sexual | total RNA | DpnII | 22 | 112539 | ||
LIBRARY 12 | Sexual ovule stage 4 | DS4.txt | Sexual ovule stage 4 | Boechera polyantha | Sexual | total RNA | DpnII | 22 | 112539 | ||
LIBRARY 13 | Apomictic ovule stage 1 | DA1.txt | Apomictic ovule stage 1 | Boechera retrofracta | Apomictic | total RNA | DpnII | 22 | 112539 | ||
LIBRARY 14 | Apomictic ovule stage 2 | DA2.txt | Apomictic ovule stage 2 | Boechera retrofracta | Apomictic | total RNA | DpnII | 22 | 112539 | ||
LIBRARY 15 | Apomictic ovule stage 3 | DA3.txt | Apomictic ovule stage 3 | Boechera retrofracta | Apomictic | total RNA | DpnII | 22 | 112539 | ||
LIBRARY 16 | Apomictic ovule stage 4 | DA4.txt | Apomictic ovule stage 4 | Boechera retrofracta | Apomictic | total RNA | DpnII | 22 | 112539 |
PROTOCOLS
This section includes protocols and fields which are common to all Samples.
Growth Protocol
“One obligate sexual Boechera polyantha and one highly expressive apomeiotic Boechera retrofracta accession, both of which are diploid and had been used in a previous SuperSAGE experiment were used. The plants were grown from seedlings onwards in a phytotron under controlled environmental conditions. The gynoecia of both accessions were dissected out from selfed flowers at four different development stages in a 0.55 M sterile mannitol solution, at a standardized time (between 8 and 9 AM) over multiple days.”
Treatment Protocol
Sexual and apomictic Boechera plants were compared.
Extract Protocol
RNA from dissected ovules of different developmental stages was isolated using the PicoPure RNA isolation kit (Arcturus Bioscience).
Data Processing
“Automatic tag detection and counting was done at GenXPro, D-60438 Frankfurt am Main, Germany”
In this paper, we have compared the transcriptomic profiles of microdissected live ovules at four developmental stages between a diploid sexual and diploid apomictic Boechera. We sequenced >2 million SuperSAGE tags and identified (1) heterochronic tags (n = 595) that demonstrated significantly different patterns of expression between sexual and apomictic ovules across all developmental stages, (2) stage-specific tags (n = 577). These are the original data files we recieved from the company GeneXPro, who performed the SuperSAGE and DNA Sequencing. The libraries files (*.txt) are described in Supersage.md, whereby eached sequenced SuperSAGE tag and it's frequency in that library are listed.