DOI: 10.5061/dryad.jwstqjqkc
title: Data from: Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns

description: We have compared the transcriptomic profiles of microdissected live ovules
 at four developmental stages between a diploid sexual and diploid
 apomictic Boechera. We sequenced &gt;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.
description: 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 &gt;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.  
description: # SERIES ## 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](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 &gt;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"