title: Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species.
abstract: OBJECTIVE
  Molecular phylogenies derived from all three plant genomes can provide insight into the evolutionary history of plant groups influenced by reticulation. We sought to reconstruct mitochondrial exome, chloroplast, and nuclear genome phylogenies for octoploid Fragaria and their diploid ancestors and to document patterns of incongruence between and within the cytoplasmic genomes and interpret these in the context of evolutionary origin of the octoploid strawberries.
  
  
  METHODS
  Using a genome-skimming approach, we assembled chloroplast genomes and mitochondrial exomes, and we used the POLiMAPS method to assemble nuclear sequence for octoploid species and constructed phylogenies from all three genomes. We assessed incongruence between and within cytoplasmic genomes using topology-based phylogenetic incongruence tests.
  
  
  RESULTS
  The incongruent cytoplasmic genome phylogeny with respect to the placement of octoploids suggests potential breakage in linkage disequilibrium of cytoplasmic genomes during allopolyploid origin of the octoploids. Furthermore, a single mitochondrial chimeric gene with a putative role in cytoplasmic male sterility yields a phylogeny that is inconsistent with the rest of the mitochondrial genome but consistent with the chloroplast phylogeny, suggesting intracellular gene transfer between heteroplasmic mitochondria, possibly driven by selection to overcome the effects of mito-nuclear incompatibility in octoploid origins.
  
  
  CONCLUSIONS
  This work expands on the current understanding of evolutionary history of the octoploid ancestors of cultivated strawberry. It demonstrates phylogenetic incongruence between cytoplasmic genomes in octoploids with respect to diploid ancestors, indicating breakage in linkage disequilibrium of cytoplasmic genomes. We discuss potential organism-level processes that may have contributed to the observed incongruence in Fragaria.
authors: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA.
authors: Rajanikanth
authors: R
authors: Govindarajulu
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA.
authors: Matthew
authors: M
authors: Parks
authors: Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331 USA.
authors: Jacob A
authors: JA
authors: Tennessen
authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA.
authors: Aaron
authors: A
authors: Liston
authors: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA.
authors: Tia-Lynn
authors: TL
authors: Ashman
mesh_terms: D002467:Cell Nucleus / Q000235:genetics; D019143:Evolution, Molecular; D031985:Fragaria / Q000235:genetics* / Q000378:metabolism; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
keywords: Fragaria; Rosaceae; chloroplast; chromosomal phylogeny; cytoplasmic male sterility; genome assembly; incongruence; linkage disequilibrium; mitochondria