Data from: Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns

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.