Genome sequencing projects typically produce a single reference genome. While tremendously useful, this glosses over potentially important variation in the sequence or structure of the genome within that species. Until recently, it has not even been possible to systematically survey sub-microscopic genome structural variations after the fact, due to the lack of suitable methodology. The investigators will apply a novel method for the genome-wide identification of structural variants in which the chromosomal location of one or more genes differs among individuals. This will be achieved by combining a particular genetic cross with massively-parallel DNA hybridization technology. The study will be done using closely related species of the model evolutionary plant, Mimulus. The specific goal of this work is to identify the frequency, position, size and gene content of chromosomal regions that are variable in position. The availability of genomic resources in Mimulus, its amenability to field studies in natural populations, and the tremendous diversity of the genus, make it an excellent model in which to study the ecological and evolutionary consequences of naturally-occurring genome structural variation.
Recent findings suggest that gene content routinely differs among individuals within a species. For example, pairs of humans have been found to differ from each other in the copy number of approximately a dozen chromosomal regions of nearly half a million base pairs each. These regions contain genes of neurological, developmental, and metabolic importance. Though studies such as this suggest that structural variation may be common, and despite the potential contribution of structural variation to adaptation and speciation, almost nothing is currently known about the abundance of gene copy number and gene location variation in natural populations. Thus, this work sets the stage for understanding the functional, ecological and evolutionary consequences of a class of molecular variation that has been hitherto largely neglected.
