CNV in sexual and apomictic Boechera

The absence of meiosis and sex are expected to lead to mutation accumulation in asexual (apomictic) plants. We have performed a double-validated analysis of copy number variation (CNV) on 10 biological replicates each of diploid sexual and diploid apomictic Boechera using a high-density (>700K) custom microarray, in order to compare mutation accumulation in the form of CNV between the transcribing regions of their genomes. The Boechera genome demonstrated higher levels of depleted compared to enriched CNV, irrespective of reproductive mode. Genome-wide patterns of CNV revealed four divergent lineages, three of which were characterized by both sexual and apomictic genotypes. Hence genome-wide CNV is reflective of at least 3 independent origins (i.e. expression) of apomixis from different sexual genetic backgrounds. CNV distributions for different families of transposable elements (TEs) were lineage specific, and a trend for enrichment in LINE/L1 and LTR/Copia elements in lineage 3 apomicts is consistent with sex and meiosis being mechanisms for purging genomic parasites. We hypothesize that significant overrepresentation of specific gene ontology classes (e.g. pollen-pistil interaction) in apomicts implies that gene enrichment could be an adaptive mechanism for genome stability in diploid apomicts by providing a polyploid-like system for buffering the effects of deleterious mutations. 10 biological replicates each of sexual and apomictic Boechera genotypes, 720K NimbleGen custom CGH array based on 454 sequenced Boechera cDNA, Cy3 and Cy5 dye swap approach