Analyses of 202 plastid genomes elucidate the phylogeny of Solanum section Petota

Authors: HUANG, BINQUAN - University Of Oxford; Ruess, Holly; LIANG, QIQI - Novogene Bioinformatics Institue; COLLEONI, CHRISTOPHE - Universite De Lille; Spooner, David

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2019
Publication Date: 2/14/2019
Citation: Huang, B., Ruess, H.M., Liang, Q., Colleoni, C., Spooner, D.M. 2019. Full genome analyses of 203 plastid genomes elucidates the phylogeny of Solanum section Petota. Scientific Reports. 9:4454. https://doi.org/10.1038/s41598-019-40790-5.
DOI: https://doi.org/10.1038/s41598-019-40790-5

Interpretive Summary: Every cell includes DNA in various compartments: 1) the nucleus where most of the DNA is located, 2), the mitochondrion or the energy factory of the cell, and 3) the chloroplast, where photosynthesis occurs. This study obtained DNA sequences from the chloroplast and used these sequences to construct a tree of relationships (a "phylogenetic tree") of 203 collections of wild potatoes. We compared these results to a prior phylogenetic tree published using DNA from the nucleus. Both phylogenetic trees have many points of agreement, but there were significant differences in the trees that provide useful information about how wild potatoes are related to each other. Because the chloroplast DNA is inherited from the mother plant in potatoes (as in most flowering plants) we can deduce who was the mother of those plants where hybridization between different species produced hybrid plants. These results are significant because they show relationships that are useful in classifying wild potatoes, and show genetic relationships that may guide breeders in useful species to use in their breeding programs.

Technical Abstract: We explored the phylogenetic utility of entire plastid DNA sequences of diploid accessions of Solanum section Petota. We used Illumina sequencing to obtain full plastid sequences of 203 diploid accessions representative of the cladistic diversity of section Petota, analyzed the data with three phylogenetic methods (maximum parsimony, SVD quartets, maximum likelihood), and compared the results to a parallel set of the same accessions previously examined with whole-genome next generation sequencing (NGS) to obtain nuclear sequence data. The present plastid analysis discovered 2036 parsimony informative characters, a great improvement over prior plastid DNA restriction site data of section Petota built from 89 parsimony-informative characters generated from 22 restriction site endonucleases. The same major clades were discovered in these plastid datasets, but there was much greater resolution within clades with the NGS data. The prior nuclear data are much larger, more than an order of magnitude larger than the NGS plastid data. However, the same major clades were discovered but with substantial differences in topology within the plastid vs. nuclear clades. The present plastid results have significant instances of plastid/nuclear incongruence that document hybridization or introgression within members of section Petota.