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The complete chloroplast genome of an endemic plant to Korea, Cardamine amaraeformis Nakai.: genome structure and phylogenetic analysis.

ABSTRACT: The plant Cardamine amaraeformis Nakai. is considered an endemic plant to Korea. However, due to the similar morphological characteristics of C. amaraeformis with C. scutata, it is not easy to distinguish these two species. Here, the complete chloroplast genome of C. amaraeformis was sequenced and characterized. The chloroplast genome of C. amaraeformis was 155,598 bp in length, comprising a large single-copy (LSC) region of 84,574 bp and a small single-copy (SSC) region of 17,976 bp and a pair of inverted repeats (IRs) of 26,524 bp. The genome contained 131 genes, including 86 protein-coding (PCGs), 37 tRNA and 8 rRNA genes. Of those, 6 PCGs, 8 tRNA and 4 rRNA genes were duplicated in the IR region and one gene was a pseudogene. The GC content of the C. amaraeformis chloroplast genome was 36.3%. Phylogenetic analysis revealed that all Cardamine species formed a monophyletic clade and C. amaraeformis was closely associated with C. parviflora. Therefore, the present study could help to distinguish C. scutata and resolve the phylogenetic relationships among the Cardamine lineage.

SUBMITTER: Raman G

PROVIDER: S-EPMC8405106 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of an endemic plant to Korea, Cardamine amaraeformis Nakai.: genome structure and phylogenetic analysis.

Raman Gurusamy G Park Kyu Tae KT Park SeonJoo S

Mitochondrial DNA. Part B, Resources 20210825 9

The plant Cardamine amaraeformis Nakai. is considered an endemic plant to Korea. However, due to the similar morphological characteristics of C. amaraeformis with C. scutata, it is not easy to distinguish these two species. Here, the complete chloroplast genome of C. amaraeformis was sequenced and characterized. The chloroplast genome of C. amaraeformis was 155,598 bp in length, comprising a large single-copy (LSC) region of 84,574 b ...[more]

PMID: 34471692

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Project description:Dendropanax oligodontus, which belongs to the family Araliaceae, is an endemic and endangered species of Hainan Island, China. It has potential economic and medicinal value owing to the presence of phenylpropanoids, flavonoids, triterpenoids, etc. The analysis of the structure and characteristics of the D. oligodontus chloroplast genome (cpDNA) is crucial for understanding the genetic and phylogenetic evolution of this species. In this study, the cpDNA of D. oligodontus was sequenced for the first time using next-generation sequencing methods, assembled, and annotated. We observed a circular quadripartite structure comprising a large single-copy region (86,440 bp), a small single-copy region (18,075 bp), and a pair of inverted repeat regions (25,944 bp). The total length of the cpDNA was 156,403 bp, and the GC% was 37.99%. We found that the D. oligodontus chloroplast genome comprised 131 genes, with 86 protein-coding genes, 8 rRNA genes, and 37 tRNAs. Furthermore, we identified 26,514 codons, 13 repetitive sequences, and 43 simple sequence repeat sites in the D. oligodontus cpDNA. The most common amino acid encoded was leucine, with a strong A/T preference at the third position of the codon. The prediction of RNA editing sites in the protein-coding genes indicated that RNA editing was observed in 19 genes with a total of 54 editing sites, all of which involved C-to-T transitions. Finally, the cpDNA of 11 species of the family Araliaceae were selected for comparative analysis. The sequences of the untranslated regions and coding regions among 11 species were highly conserved, and minor differences were observed in the length of the inverted repeat regions; therefore, the cpDNAs were relatively stable and consistent among these 11 species. The variable hotspots in the genome included clpP, ycf1, rnK-rps16, rps16-trnQ, atpH-atpI, trnE-trnT, psbM-trnD, ycf3-trnS, and rpl32-trnL, providing valuable molecular markers for species authentication and regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. Evolutionary selection pressure analysis indicated that the atpF gene was strongly subjected to positive environmental selection. Phylogenetic analysis indicated that D. oligodontus and Dendropanax dentiger were the most closely related species within the genus, and D. oligodontus was closely related to the genera Kalopanax and Metapanax in the Araliaceae family. Overall, the cp genomes reported in this study will provide resources for studying the genetic diversity and conservation of the endangered plant D. oligodontus, as well as resolving phylogenetic relationships within the family.

Dataset Information

The complete chloroplast genome of an endemic plant to Korea, Cardamine amaraeformis Nakai.: genome structure and phylogenetic analysis.

Publications

The complete chloroplast genome of an endemic plant to Korea, <i>Cardamine amaraeformis</i> Nakai.: genome structure and phylogenetic analysis.

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