Abstract
Our paper analyzes full plastid DNA sequence data of 202 wild and cultivated diploid potatoes, Solanum section Petota, to explore its phylogenetic utility compared to prior analyses of the same accessions using genome-wide nuclear SNPs, and plastid DNA restriction site data. The present plastid analysis discovered the same major clades as the nuclear data but with some substantial differences in topology within the clades. The considerably larger plastid and nuclear data sets add phylogenetic resolution within the prior plastid DNA restriction site data, highlight plastid/nuclear incongruence that supports hypotheses of hybridization/introgression to help explain the taxonomic difficulty in the section.
Highlights
The main phylogenetic utility of generation sequencing techniques is to produce data quantities far above that needed for well-resolved phylogenies
We obtained 202 complete plastid genomes with lengths ranging from 155,231 bp (S. polyadenium) to 155,696 bp (S. gourlayi), and an average read coverage depth of 403 (S. andreanum) to 4,050 (S. gourlayi) (Supplemental Table 1)
The SNPs are uniformly distributed in the plastid genome except with fewer in the inverted repeats (Fig. 2), which indicated the conservation of the IR region and is consistent with the observation in other species[21,22,23,24]
Summary
The main phylogenetic utility of generation sequencing techniques is to produce data quantities far above that needed for well-resolved phylogenies. Jansen and Ruhlman[4] provided a review of the many advantages of plastid DNA as a phylogenetic marker and reported the public availability of 200 plastid genomes that presently (September 2018) has grown to nearly 3000 for eukaryotes (https://www.ncbi.nlm.nih.gov/genome/browse#!/organelles/Viridiplantae) Despite these advantages of plastid DNA as a phylogenetic marker, incongruence between plastid and nuclear genes are common in phylogenetic studies throughout the angiosperms, with plastid phylogenies often the most discordant relative to other molecular markers[5]. Spooner et al.[12] provided the last conspectus of the section and recognized 107 wild species and four cultivated species partitioned into three main nuclear clades but not recognized as series, basing their decisions on a variety of morphological and molecular datasets including DNA markers (e.g., AFLPs, microsatellites), DNA sequence data of single and multiple nuclear orthologs www.nature.com/scientificreports/. The purpose of this study is to examine concordance of our new whole-genome plastid data with the nuclear data of the same accessions[19] and with the prior plastid phylogeny based on restriction site data
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