Transposon Density Affects Homeolog Specific Gene Expression in Allopolyploid Monkeyflower (Mimulus)

Here we use allopolyploid species in the Mimulus genus (including a 140-generation-old neo-allopolyploid), as models to understand how genome structure, specifically transposon class and local transposon density, explain homeolog specific expression differences. Young allopolyploid lineages face the unique challenge of organizing two genomes, contributed by different parent species, evolved in separate contexts, now forced to share a most intimate environment – a nucleus. In the wake of allopolyploidy, homeologous genes (homologous genes derived from different parental subgenomes) are often expressed at non-equal levels. Typically, genome-wide patterns of homeolog expression bias are highly skewed – one parental genome (subgenome) is expressed at higher levels than the other. It is unknown how homeologs become biased over another. More broadly, it is also unknown how one subgenome becomes biasedly expressed as a whole over the other subgenome. A mechanistic understanding of these phenomena is fundamental to understanding allopolyploid gene expression, subgenome fractionation, and allopolyploid evolution.