Speaker
Description
Detecting and predicting heritable changes in DNA that lead to adaptation is an essential goal in evolutionary biology. Copy number variants (CNVs) -- gains and losses of genomic sequences -- are a pervasive class of mutation and source of genetic variation that frequently underlie rapid adaptation. Although mechanisms of CNV formation have been identified, the role of local genomic architecture on CNV formation, selection, and subsequent dynamics remains elusive. To begin answering this question, we investigated the effect of proximate elements of general amino acid permease GAP1 on CNV formation and dynamics in Saccharomyces cerevisiae. GAP1 is flanked by two long terminal repeat (LTR) elements and has one downstream autonomously replicating sequence (ARS) element. First, we engineered strains lacking either an ARS, two LTRs, or all three elements in the background of an existing GAP1 CNV reporter strain, wherein a constitutively expressed fluorescent mCitrine gene was inserted adjacent to GAP1 (Lauer et al 2018). Then we experimentally evolved these strains in glutamine-limited media for 260 generations and detected GAP1 CNVs using this single-cell resolution CNV reporter system. Our study validated that these elements were indeed cis-acting to GAP1 CNV formation. Our results recapitulate previous findings that GAP1 CNVs are repeatedly generated and selected for early during adaptive evolution before undergoing more complex dynamics. We found the engineered mutants have different dynamics relative to the wild type, surprisingly appearing to reach higher copy numbers. This suggests mutants lacking any of these cis-acting elements employ different mechanism(s) to generate higher copy CNVs. Whole-genome-sequencing of isolated clones by a mixture of Nanopore and Illumina methods revealed CNV structure. Subsequent breakpoint analysis uncovered the mechanisms prevalently used. This study brings us closer to understanding the role of local genomic architecture on the evolutionary dynamics of adaptation.
