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

Oresitrophe and Mukdenia (Saxifragaceae) are epilithic sister genera used
in traditional Chinese medicine. However, the taxonomy of Mukdenia,
especially of M. acanthifolia, has been controversial. Genome skimming of
M. acanthifolia and M. rossii, 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 Mukdenia and Oresitrophe 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
(trnH-psbA, psbC-trnS, trnM-atpE, petA-psbJ and ccsA-ndhD) were identified
within Mukdenia, and six regions (trnH-psbA, petN-psbM, trnM-atpE,
rps16-trnQ, ycf1 and ndhF) 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
Mukdenia and Oresitrophe, we combined our data with published data based
on three different datasets. The monophyly of each species (O. rupifraga,
M. acanthifolia and M. rossii) and the inferred topology ((M. rossii, M.
acanthifolia), O. rupifraga) were well supported in trees reconstructed
using the complete plastomes, but M. acanthifolia and M. rossii 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 M. acanthifolia
should be treated as a distinct species.