Data from: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower
Edger, Patrick P., Michigan State University
Smith, Ronald D., College of William & Mary
McKain, Michael R., Donald Danforth Plant Science Center
Cooley, Arielle M., Whitman College
Vallejo-Marin, Mario, University of Stirling
Yuan, Yao-Wu, University of Connecticut
Bewick, Adam J., University of Georgia
Ji, Lexiang, University of Georgia
Platts, Adrian E., McGill University
Bowman, Megan J., Michigan State University
Childs, Kevin, Michigan State University
Washburn, Jacob D., University of Missouri
Schmitz, Robert, University of Georgia
Smith, Gregory D., College of William & Mary
Pires, J. Chris, University of Missouri
Puzey, Joshua R., College of William & Mary
Published Sep 06, 2017 on Dryad.
Cite this dataset
Edger, Patrick P. et al. (2017). Data from: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower [Dataset]. Dryad. https://doi.org/10.5061/dryad.d4vr0
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, less than 140 year old allopolyploid (Mimulus peregrinus), a resynthesized inter-species triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and diploid progenitors (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of two divergent genomes and significantly increases over generations. Additionally, CHH methylation levels are significantly reduced in regions near genes and within TEs in the first generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and recessive subgenomes in the natural allopolyploid. In addition, subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following hybridization. These findings provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events.
Mimulus Annotation and Expression Analyses
Gene expression data (raw counts and RPKM) for all transcriptome libraries analyzed in the manuscript. In addition, genome annotation and orthogroups for syntenic orthologs that were further analyzed, with full descriptions, are in the zipped file.