Data from: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower

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National Science Foundation


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 AnalysesGene 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.Mimulus_TPC_Dryad.zipMimulus_luteus.faaFasta file of M. luteus genome assemblyMimulus_luteus_complete_w_single_exons_standard_renamed_genes.gffGFF genome annotation file of Mimulus luteus. This GFF file provides gene annotation for the M. luteus genome assembly published in this paper.Mimulus_guttatus_complete_w_single_exons_standard_renamed_genes.gffGFF genome annotation file of Mimulus guttatus. This GFF file provides gene annotation for the M. guttatus genome v2.0 on available on Phytzome.AlignmentsThis folder contains coding sequence alignments and single copy ortholog alignments used to conduct phylogenetic analyses in this paper.alignments.tar,



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