J Syst Evol ›› 2023, Vol. 61 ›› Issue (1): 99-114.DOI: 10.1111/jse.12833

• Original Article • Previous Articles     Next Articles

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

Lu‐Xian Liu1†, Pan Deng1†, Meng‐Zhen Chen1, Li‐Min Yu2, Joongku Lee3, Wei‐Mei Jiang4, Cheng‐Xin Fu4, Fu‐De Shang1*, and Pan Li4*   

  1. 1 State Key Laboratory of Cotton Biology, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng 475000, China
    2 Xianrendong Nature Reserve, Zhuanghe 116407, China
    3 Department of Environment and Forest Resources, Chungnam National University, Daejeon 34134, South Korea
    4 Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China

    These authors contributed equally to this work.
    * Authors for correspondence. Fu‐De Shang. E‐mail: fudeshang@henu.edu.cn; Pan Li. E‐mail: panli_zju@126.com
  • Received:2021-06-03 Accepted:2022-01-17 Online:2022-01-20 Published:2023-01-01


Oresitrophe and Mukdenia (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. The taxonomy of Mukdenia, especially of M. acanthifolia, has been controversial. To address this, we produced plastid and mitochondrial data using genome skimming for Mukdenia acanthifolia and Mukdenia rossii, including three individuals of each species. We assembled complete plastomes, mitochondrial CDS and nuclear ribosomal ETS/ITS sequences using these data. Comparative analysis shows that the plastomes of Mukdenia and Oresitrophe are relatively conservative in terms of genome size, structure, gene content, RNA editing sites and codon usage. Five plastid regions that represent hotspots of change (trnH-psbA, psbC-trnS, trnM-atpE, petA-psbJ and ccsA-ndhD) are identified within Mukdenia, and six regions (trnH-psbA, petN-psbM, trnM-atpE, rps16-trnQ, ycf1 and ndhF) contain a higher number of species-specific parsimony-informative sites that may 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 (Oresitrophe rupifraga, M. acanthifolia and M. rossii) and the inferred topology ((M. rossii, M. acanthifolia), O. rupifraga) are well supported in trees reconstructed using the complete plastome sequences, but M. acanthifolia and M. rossii did not form a separate clade in the trees based on ETS + ITS data, while the mitochondrial CDS trees are not well-resolved. We found low recovery of genes in the Angiosperms353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordance between trees reconstructed from organellar and nuclear data. Considering its morphological distinctiveness and our molecular phylogenetic results, we strongly recommend that M. acanthifolia be treated as a distinct species.

Key words: DNA barcode, phylogenomics, phylogeny, plastome, species identification, taxonomy