The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the paleohexaploid Brassica rapa

Abstract

Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana-A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene,would be unlikely to lose function compared with amore redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, eachmechanism of CNS loss was assigned ametric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not mattermuchto their detectability frequency), whereas those lostby inferreddeletionor indels are approximately75% likely to be nonfunctional.Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72%chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with "deletion" in its description, but base substitutions do cause loss. Similarly,proved-functional G-boxes goundetectable by deletion 82%of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a "deletion machine" in the Brassica lineage. © 2013 The Author(s).