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 over 2 million SuperSAGE tags, and identified: (1) heterochronic tags (N=595) which demonstrated significantly different patterns of expression between sexual and apomictic ovules across all developmental stages, (2) stage-specific tags (N=577) which 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 which were found in all 4 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. 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. 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 analysed 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.