Data from: Systematics of Mukdenia and Oresitrophe (Saxifragaceae): Insights from genome skimming data

<p><span><i>Oresitrophe</i> and <i>Mukdenia</i> (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. However, the taxonomy of <i>Mukdenia</i>, especially of<i> M. acanthifolia</i>, has been controversial. Genome skimming of <i>M. acanthifolia</i> and <i>M. rossii</i>, including three individuals for each species is reported and complete plastomes, partial mitogenomes and ETS/ITS sequences were assembled using these data. Their plastomes ranged from 156,341 bp to 157,018 bp in length and had similar structural characteristics and gene content of other flowering plants. These genomes were typically quadripartite, comprising 113 unique genes (79 protein coding genes, 30 tRNAs and 4 rRNAs). Comparative analysis showed that the plastomes of <i>Mukdenia</i> and <i>Oresitrophe</i> were relatively conservative, reflecting the genome size and structure, gene contents, RNA editing sites and codon usage. Five plastid regions that were hotspots of change (<i>trn</i>H-<i>psb</i>A, <i>psb</i>C-<i>trn</i>S, <i>trn</i>M-<i>atp</i>E, <i>pet</i>A-<i>psb</i>J and <i>ccs</i>A-<i>ndh</i>D) were identified within <i>Mukdenia</i>, and six regions (<i>trn</i>H-<i>psb</i>A, <i>pet</i>N-<i>psb</i>M, <i>trn</i>M-<i>atp</i>E, <i>rps</i>16-<i>trn</i>Q, <i>ycf</i>1 and <i>ndh</i>F) contained a higher number of species-specific parsimony-informative sites that can serve as potential DNA barcodes for species identification. To infer phylogenetic relationships between <i>Mukdenia</i> and <i>Oresitrophe</i>, we combined our data with published data based on three different datasets. The monophyly of each species (<i>O. rupifraga</i>, <i>M. acanthifolia</i> and <i>M. rossii</i>) and the inferred topology ((<i>M. rossii</i>, <i>M. acanthifolia</i>), <i>O. rupifraga</i>) were well supported in trees reconstructed using the complete plastomes, but <i>M. acanthifolia</i> and <i>M. rossii</i> did not form separate clade in the ETS+ITS data. We found low recovery of genes in the Angiosperms 353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordances between the trees reconstructed from plastid and nuclear data. The results from this study suggest that <i>M. acanthifolia</i> should be treated as a distinct species.</span></p>