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Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial , Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid

David M. Spooner, Holly Ruess, Massimo Iorizzo, Douglas Senalik, Philipp Simon
American journal of botany 2017 v.104 no.2 pp. 296-312
Daucus, carrots, data collection, genes, mitochondria, mitochondrial DNA, mutation, nuclear genome, nucleotide sequences, phylogeny, plastid DNA, plastid genome
We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results to prior phylogenetic results using plastid, nuclear, and mitochondrial DNA sequences. We obtained, using Illumina sequencing, full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups. Phylogenetic trees of the entire dataset were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence to the entire dataset. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP, and identified the first instance in flowering plants of a nuclear gene inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA but none of non-synonymous mutations to the phylogeny. Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (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.