title: Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid.
abstract: OBJECTIVE
  We explored the phylogenetic utility of entire plastid DNA sequences inDaucusand compared the results with prior phylogenetic results using plastid and nuclear DNA sequences.
  
  
  METHODS
  We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20Daucustaxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP).
  
  
  RESULTS
  Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade ofD. carotaand its most closely related speciesD. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously namedDcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations.
  
  
  CONCLUSIONS
  Our data have allowed us to (1) produce a well-resolved plastid phylogeny ofDaucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.
authors.affiliation: U. S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit; and Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA david.spooner@ars.usda.gov.
authors.forename: David M
authors.initials: DM
authors.lastname: Spooner
authors.affiliation: U. S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit; and Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA.
authors.forename: Holly
authors.initials: H
authors.lastname: Ruess
authors.affiliation: Plants for Human Health Institute, Department of Horticultural Sciences, North Carolina State University, 600 Laureate Way, Kannapolis, North Carolina 28081 USA.
authors.forename: Massimo
authors.initials: M
authors.lastname: Iorizzo
authors.affiliation: U. S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit; and Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA.
authors.forename: Douglas
authors.initials: D
authors.lastname: Senalik
authors.affiliation: U. S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit; and Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA.
authors.forename: Philipp
authors.initials: P
authors.lastname: Simon
mesh_terms: D002467:Cell Nucleus / Q000235:genetics*; D018742:DNA, Chloroplast / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000145:classification / Q000235:genetics; D018552:Daucus carota / Q000145:classification / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D054629:Genome, Mitochondrial / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D054627:Genome, Plastid / Q000235:genetics*; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D018087:Plastids / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018742:DNA, Chloroplast; D004272:DNA, Mitochondrial; D018744:DNA, Plant; D010940:Plant Proteins
keywords: Apiaceae; Daucus; DcMP; carrot; germplasm; mitochondria; next-generation sequencing; nuclear-to-plastid DNA transfer; plastid phylogeny