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

Abstract

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.

First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae)

“…nivea , where the rps19 gene was present at the boundary between the LSC and Irb. The fate of genes located at the boundaries of each region also depends on the extension or contraction of specific regions of the plastome, which can be used for the phylogenetic classification of taxa [ 49 , 50 , 51 , 52 ]. For example, in the genus Camellia (Theaceae), variations in the length of the IR regions due to various indels in the plastome have been observed [ 51 ].…”

Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis

“…Most studies utilizing cp. genomes have successfully yielded high-resolution and well-supported phylogenetic trees, even in phylogenetically challenging plant taxa [ 15 , 16 , 31 , 33 ]. In our study, we constructed a phylogenetic tree based on the alignment of chloroplast whole-genome sequences from Q. disciformis , Q. dinghuensis , Q. blakei , and Q. hui , along with 17 other closely related species of section Cyclobalanopsis .…”

The complete chloroplast genome sequences of six Hylotelephium species: Comparative genomic analysis and phylogenetic relationships

“…Hylotelephium is known to be a very difficult group to classify due to the high external morphological variation of each taxon and the very similar morphological characteristics between species [ 15 , 24 ]. According to these findings, many morphological and molecular phylogenetic studies have been conducted, but the delimitation of this genus and phylogenetic relationships between its species remain insufficiently resolved [ 16 – 23 , 71 ].…”

“…Since then, various molecular phylogenetic studies [ 16 – 23 ] have been performed and revealed a large phylogenetic distance between the two genera; Hylotelephium formed a clade with Sinocrassula A. Berger, Orostachys , and Meterostachys Nakai ( Telephium clade), and Sedum was in the Acre clade. However, in most studies, including studies using ITS of nuclear DNA [ 16 , 18 ] and some marker regions of the chloroplast genome [ 19 ], as well as whole chloroplast genome sequences [ 23 ], the taxonomic position of Hylotelephium as an independent genus was not supported because it formed a paraphyletic clade with Orostachys species. Therefore, studies are needed to evaluate an accurate taxonomic position by identifying the exact phylogenetic relationship between two genera.…”