Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates

Choi, Kyoung Su; Ha, Young‐Ho; Gil, Hee-Young; Choi, Kyung; Kim, Dong-Kap; Oh, Seung-Hwan

doi:10.3390/plants10020397

Cited by 20 publications

(21 citation statements)

References 80 publications

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“…The contraction and expansion of IR regions are the main contributors to the size variation in cp genomes and alter the evolutionary rate of the cp genome [ 41 , 42 ]. We compared the IR boundaries in 20 Dipterocarpoideae species and found that the IR boundary regions varied slightly, especially IRb/SSC, SSC/IRa, and IRa/LSC (Fig.…”

Section: Resultsmentioning

confidence: 99%

Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

et al. 2021

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Background In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as “Bingpian” in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency. Methods In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci. Results The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae. Conclusions Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.

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Section: Resultsmentioning

confidence: 99%

Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

et al. 2021

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“…However, the IR region has contracted and expanded in different species during CP evolution [46]. Recently, an expansion of the IR region in Clematis was confirmed [47]. In Symplocos, the IR is very stable, with the only differences in the length of ψycf1 [10,[48][49][50].…”

Section: Discussionmentioning

confidence: 96%

Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Kim

Lee

Choi

2021

Forests

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In the present study, chloroplast genome sequences of four species of Symplocos (S. chinensis for. pilosa, S. prunifolia, S. coreana, and S. tanakana) from South Korea were obtained by Ion Torrent sequencing and compared with the sequences of three previously reported Symplocos chloroplast genomes from different species. The length of the Symplocos chloroplast genome ranged from 156,961 to 157,365 bp. Overall, 132 genes including 87 functional genes, 37 tRNA genes, and eight rRNA genes were identified in all Symplocos chloroplast genomes. The gene order and contents were highly similar across the seven species. The coding regions were more conserved than the non-coding regions, and the large single-copy and small single-copy regions were less conserved than the inverted repeat regions. We identified five new hotspot regions (rbcL, ycf4, psaJ, rpl22, and ycf1) that can be used as barcodes or species-specific Symplocos molecular markers. These four novel chloroplast genomes provide basic information on the plastid genome of Symplocos and enable better taxonomic characterization of this genus.

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“…The chloroplast and nuclear genomes of Clematis are well sequenced and provided valuable information for their phylogeny ( Yan et al, 2016 ; Xiang et al, 2019 ; Wang et al, 2021 ), evolution ( Sheng et al, 2014 ), and conservation ( Choi et al, 2021 ). However, it has been reported that the chloroplast genomes provided insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the cultivars’ recent origin and the genome conserved sequences ( Evans et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

Liu

Yuan

et al. 2023

Front. Genet.

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Clematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult to classify systematically, and in particular, the phylogenetic position of the endangered Clematis acerifolia is highly controversial. The use of the mitochondrial complete genome is a powerful molecular method that is frequently used for inferring plants phylogenies. However, studies on Clematis mitogenome are rare, thus limiting our full understanding of its phylogeny and genome evolution. Here, we sequenced and annotated the C. acerifolia mt genome using Illumina short- and Nanopore long-reads, characterized the species first complete mitogenome, and performed a comparative phylogenetic analysis with its close relatives. The total length of the C. acerifolia mitogenome is 698,247 bp and the main structure is multi-branched (linear molecule 1 and circular molecule 2). We annotated 55 genes, including 35 protein-coding, 17 tRNA, and 3 rRNA genes. The C. acerifolia mitogenome has extremely unconserved structurally, with extensive sequence transfer between the chloroplast and mitochondrial organelles, sequence repeats, and RNA editing. The phylogenetic position of C. acerifolia was determined by constructing the species mitogenome with 24 angiosperms. Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants.

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Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates

Cited by 20 publications

References 80 publications

Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

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