Comparative Promoter Analysis of APOLLO for Identification of Regulatory Networks Involved in Apomixis

Abstract

The genus Boechera is a complex case study of reproductive plant biology stemming from its ability to produce seed sexually and asexually (apomixis). Previous work accomplished by the Sharbel Laboratory discovered an exclusive differentially expressed gene during early megasporogenesis with a 20nt indel differentiating two alleles of a gene called APOLLO. APOLLO is a gene encoding a DEDDH 5’-3’ exonuclease with extensive copy number variation of both alleles throughout the genus, but what makes APOLLO such an important candidate is that only one allele (sex allele) is found in sexual Boechera while apomictic Boechera have both alleles (sex and apo allele). To understand the cause of differential expression between the sex and apo allele of APOLLO, the promoter has been called into question. Unlike genes that present a conserved exon-intron structure, promoters are non-coding DNA elements with no distinct organizational patterns in relation to the motifs that attract transcriptional machinery, and therefore the understanding of promoter evolution is unresolved.

During gene duplication events it is assumed that the promoter is a single unit with the gene, but not all duplications are entitled to that degree of certainty because there is plenty of evidence for the formation of chimeric and fusion genes. What happens when a gene is duplicated but its promoter is left behind and how does it affect gene expression? This is in fact the case of the APOLLO apo allele. By sequencing 1kb upstream of a conserved area within the first exon of APOLLO a compelling case has been put together showing that a novel promoter is highly conserved, apoallele specific, and preliminarily responsible for the differential expression of APOLLO in pre-meiotic ovules of sexual and apomictic Boechera