Location: Vegetable Crops ResearchTitle: A complete plastid phylogeny of Daucus – concordance to nuclear results, and markers necessary for phylogenetic resolution
Submitted to: Botany
Publication Type: Abstract Only
Publication Acceptance Date: 3/28/2016
Publication Date: 7/30/2016
Citation: Spooner, D.M., Ruess, H.M., Senalik, D.A., Simon, P.W. 2016. A complete plastid phylogeny of Daucus – concordance to nuclear results, and markers necessary for phylogenetic resolution [abstract]. Botany. Paper No. 119.
Technical Abstract: Premise of study: Our purposes were to (1) obtain a well-resolved plastid counterpart to the 94 gene nuclear ortholog gene phylogeny of Arbizu et al. (2014, Amer. J. Bot. 101:1666-1685; and Syst. Bot., in press), and (2) to investigate various classes and numbers of plastid markers necessary for a complete plastid phylogeny with resolution comparable to previously used plastid markers, barcoding genes, and a recent study identifying highly divergent non-coding plastid regions useful for phylogeny reconstruction in the Apiales (Downie and Jansen 2015, [DJ], Syst. Bot. 40:336-351). Methods: De novo assembly of whole plastid genomes using paired-end Illumina HiSeq2500 reads for 38 accessions: Daucus aureus (1 accession), 5 subspecies of D. carota (11 accessions), D. bicolor (2), D. conchitae (3), D. crinitus (2), D. glochidiatus (1), D. guttatus (2), D. involucratus (2), D. littoralis (1), D. muricatus (2), D. pusillus (2), D. sahariensis (1), D. setulosus (2), D. syrticus (1), D. tenuisectus (1); Daucus generic ingroups Pseudorlaya pumila and Rouya polygama, and outgroups Oenanthe virgata and Caucalis platycarpos (1 accession each). Key results: Plastid lengths varied from 154,218 bp (Oenanthe virgata) to 170,793 bp (Caucalis virgata), with the Daucus ingroups varying from 155,441 bp (D. involucratus) to 157,336 bp (D. setulosus). The entire plastid genome, excluding one of the inverted repeat regions, provided a highly resolved tree with 100% bootstrap support values on all of the branches except as noted below. This tree was almost entirely concordant with the nuclear results, except (1) for the clade including the 18-chromosome species (D. carota, D. sahariensis, D. syrticus) that was highly unresolved, and (2) an apparent plastid capture event in one accession of D. conchitae relative to D. bicolor. Identical topological results with bootstrap support values 70% or greater were obtained with the following subsets of the plastid data, ordered from best to worst: large single copy, exons, small single copy, functional genes, DJ fast evolving regions, gapped characters, intergenic regions. Intermediate congruent results to the dominant gene the topology but exhibiting only soft incongruence were: introns, DJ informative characters, matK, ndhF, tRNA characters, rbcL+tRNA+psbA. The following regions gave very poor topology: rbcL, trnH+psbA intergenic region, ribosomal RNA, tRNA exons. Conclusions: Plastid characters are only a small subset of the phylogenetic results to be obtained from whole genome datasets. We recommend that despite initial high costs, this approach be utilized for many phylogenetic studies.