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

Author
item Spooner, David
item Ruess, Holly
item IORIZZO, MASSIMO - North Carolina State University
item Senalik, Douglas
item Simon, Philipp

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2017
Publication Date: 2/15/2017
Publication URL: https://handle.nal.usda.gov/10113/5642528
Citation: Spooner, D.M., Ruess, H., Iorizzo, M., Senalik, D., Simon, P. 2017. Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid. American Journal of Botany. 104(2):296-312. doi: 10.3732/ajb.1600415.

Interpretive Summary: DNA sequences are powerful tools to examine relationships among different species of plants, but have been hindered by insufficient length of these sequences. Our study overcame this by examining the entire chloroplast genome composing about 155,00o characters in wild carrots. We compared the results to prior relationship results using various other classes of DNA sequences. The relationship trees gave great precision in most part of the tree with high statistical support. Subsets of the data, including regions traditionally used as to examine relationships, often gave poorer results, showing the value of this increased set of DNA data. We also extended knowledge of a DNA transfer of another DNA type, called the mitochondrion, and alfro from the nucleus, into the chloroplast. Our data have allowed us to (1) produce a well-resolved relationship tree of wild carrots, (2) evaluate subsets of the entire chloroplast DNA tree data for relationships, (3) and to examine evidence for mitochondrial and nuclear DNA into the chloroplast. These data will guide taxonomists into better ways to examine relationships with the choice of sufficient quantities of data and proper DNA sequences to examine.

Technical Abstract: 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.