title: Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella.
abstract: The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.
authors: Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
authors: Kim A
authors: KA
authors: Steige
authors: Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
authors: Johan
authors: J
authors: Reimegård
authors: Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
authors: Daniel
authors: D
authors: Koenig
authors: Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala Sweden.
authors: Douglas G
authors: DG
authors: Scofield
authors: Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden tanja.slotte@su.se.
authors: Tanja
authors: T
authors: Slotte
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D029687:Capsella / Q000235:genetics* / Q000502:physiology*; D004251:DNA Transposable Elements / Q000235:genetics; D035264:Flowers / Q000235:genetics* / Q000502:physiology*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056726:Genetic Association Studies; D006579:Heterozygote; D006824:Hybridization, Genetic; D016254:Mutagenesis, Insertional / Q000235:genetics; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012098:Reproduction / Q000235:genetics; D057945:Self-Fertilization
chemical_list: D004251:DNA Transposable Elements; D018749:RNA, Plant
keywords: adaptation; allele-specific expression; cis-regulatory evolution; gene expression; mating system evolution; self-fertilization