The complete chloroplast genome sequences of eight Orostachys species: Comparative analysis and assessment of phylogenetic relationships

• Published in: PloS one Vol. 17; no. 11; p. e0277486
• Main Authors: Lee, Ha-Rim, Kim, Kyung-Ah, Kim, Bo-Yun, Park, Yoo-Jung, Lee, Yoo-Bin, Cheon, Kyeong-Sik
• Format: Journal Article
• Language: English
• Published: San Francisco Public Library of Science 10.11.2022
• Subjects: Analysis; Biology and Life Sciences; Chloroplasts; Classification; Comparative analysis; Computer and Information Sciences; Crassulaceae; Engineering and Technology; Gene sequencing; Genera; Genes; Genetic aspects; Genomes; Genomics; Hylotelephium; Introns; Morphology; Nucleotides; Phylogenetics; Phylogeny; Proteins; rRNA; Species; Taxonomy; Transfer RNA; tRNA; South Korea; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0277486

We analyzed the complete chloroplast genomes of eight Orostachys species and compared the sequences to those of published chloroplast genomes of the congeneric and closely related genera, Meterostachys and Hylotelephium. The total chloroplast genome length of thirteen species, including the eight species analyzed in this study and the five species analyzed in previous studies, ranged from 149,860 (M. sikokianus) to 151,707 bp (H. verticillatum). The overall GC contents of the genomes were almost identical (37.6 to 37.8%). The thirteen chloroplast genomes each contained 113 unique genes comprising 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among the annotated genes, sixteen genes contained one or two introns. Although the genome structures of all Orostachys and Hylotelephium species were identical, Meterostachys differed in structure due to a relatively large gene block (trnS-GCU-trnS-GGA) inversion. The nucleotide diversity among the subsect. Orostachys chloroplast genomes was extremely low in all regions, and among the subsect. Appendiculatae, genus Orostachys, and all thirteen chloroplast genomes showed high values of Pi (>0.03) in one, five, or three regions. The phylogenetic analysis showed that Orostachys formed polyphyly, and subsect. Orostachys and Appendiculatae were clustered with Hylotelephium and Meterostachys, respectively, supporting the conclusion that each subsection should be considered as an independent genus. Furthermore, the data supported the taxonomic position of O. margaritifolia and O. iwarenge f. magnus, which were treated as synonyms for O. iwarenge in a previous study, as independent taxa. Our results suggested that O. ramosa and O. japonica f. polycephala were individual variations of O. malacophylla and O. japonica, respectively. The exact taxonomic position of O. latielliptica and the phylogenetic relationship among the three species, O. chongsunensis, O. malacophylla and O. ramosa, should be a topic of future study.