Complete chloroplast genome sequence of Adenophora racemosa (Campanulaceae): Comparative analysis with congeneric species

Abstract

Adenophora racemosa, belonging to the Campanulaceae, is an important species because it is endemic to Korea. The goal of this study was to assemble and annotate the chloroplast genome of A. racemosa and compare it with published chloroplast genomes of congeneric species. The chloroplast genome was reconstructed using de novo assembly of paired-end reads generated by the Illumina MiSeq platform. The chloroplast genome size of A. racemosa was 169,344 bp. In total, 112 unique genes (78 protein-coding genes, 30 tRNAs, and 4 rRNAs) were identified. A Maximum likelihood (ML) tree based on 76 protein-coding genes divided the five Adenophora species into two clades, showing that A. racemosa is more closely related to Adenophora stricta than to Adenophora divaricata. The gene order and contents of the LSC region of A. racemosa were identical to those of A. divaricata and A. stricta, but the structure of the SSC and IRs was unique due to IR contraction. Nucleotide diversity (Pi) >0.05 was found in eleven regions among the three Adenophora species not included in sect. Remotiflorae and in six regions between two species (A. racemosa and A. stricta).

A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea

“…In addition, the fragment from 8,966 to 52,067 bp was in inverse order in the LSC region, which was different from the reported cp genome of K. obovata (Chen et al, 2019;Yang et al, 2019). This inversion has been previously reported in other cp genomes (Wei et al, 2020;Cui et al, 2021;Kim & Cheon, 2021;Wang et al, 2021).…”

Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species

“…The A/T type accounted for the largest proportion of SSRs. The obvious nucleotide bias may be due to the lower number of hydrogen bonds and lower energy consumption of A/T bases ( Niu et al., 2017 ; Kim and Cheon, 2021 ). Previous studies have reported a higher A/T than G/C content in most plants, which may be due to the large number of A/T-type SSRs ( Wang et al., 2021 ; Wu et al., 2021 ; Han et al., 2022 ).…”

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

“…plants, but structural changes in chloroplast genomes, such as gene duplication and deletion and inversion due to occasional rearrangements, provide important taxonomic data [34][35][36][37][38][39][40][41][42]. This study showed that the genome structures of Orostachys and Hylotelephium species were identical, and the sequence identities were also very similar among species in most of the chloroplast regions (Fig 2…”

“…Many recent studies have been carried out to clarify the taxonomy of related taxa using complete cp genome sequences. The cp genome is known to be highly conserved in most land plants, but structural changes in chloroplast genomes, such as gene duplication and deletion and inversion due to occasional rearrangements, provide important taxonomic data [ 34 – 42 ]. This study showed that the genome structures of Orostachys and Hylotelephium species were identical, and the sequence identities were also very similar among species in most of the chloroplast regions ( Fig 2 and S1 Fig ).…”