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

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Institute of Natural Science, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea
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Department of Life Sciences, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea
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Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea
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Department of Life Science, Gachon University, Seongnam-si, Gyeonggi-do 13120, Korea
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DMZ Botanic Garden, Korea National Arboretum, 916-70, Punchbowl-ro, Haean-myeon, Yanggu, Gangwon-do 24564, Korea
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Research Planning and Coordination Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea
*
Author to whom correspondence should be addressed.
Academic Editor: Brent L. Nielsen
Plants 2021, 10(2), 397; https://doi.org/10.3390/plants10020397
Received: 22 January 2021 / Revised: 13 February 2021 / Accepted: 16 February 2021 / Published: 19 February 2021
Previous studies on the chloroplast genome in Clematis focused on the chloroplast structure within Anemoneae. The chloroplast genomes of Cleamtis were sequenced to provide information for studies on phylogeny and evolution. Two Korean endemic Clematis chloroplast genomes (Clematis brachyura and C. trichotoma) range from 159,170 to 159,532 bp, containing 134 identical genes. Comparing the coding and non-coding regions among 12 Clematis species revealed divergent sites, with carination occurring in the petD-rpoA region. Comparing other Clematis chloroplast genomes suggested that Clematis has two inversions (trnH-rps16 and rps4), reposition (trnL-ndhC), and inverted repeat (IR) region expansion. For phylogenetic analysis, 71 protein-coding genes were aligned from 36 Ranunculaceae chloroplast genomes. Anemoneae (Anemoclema, Pulsatilla, Anemone, and Clematis) clades were monophyletic and well-supported by the bootstrap value (100%). Based on 70 chloroplast protein-coding genes, we compared nonsynonymous (dN) and synonymous (dS) substitution rates among Clematis, Anemoneae (excluding Clematis), and other Ranunculaceae species. The average synonymoussubstitution rates (dS)of large single copy (LSC), small single copy (SSC), and IR genes in Anemoneae and Clematis were significantly higher than those of other Ranunculaceae species, but not the nonsynonymous substitution rates (dN). This study provides fundamental information on plastid genome evolution in the Ranunculaceae. View Full-Text
Keywords: chloroplast genome; Clematis; rearrangement; inversion; IR expansion; nucleotide substitution rate chloroplast genome; Clematis; rearrangement; inversion; IR expansion; nucleotide substitution rate
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MDPI and ACS Style

Choi, K.S.; Ha, Y.-H.; Gil, H.-Y.; Choi, K.; Kim, D.-K.; Oh, S.-H. Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. Plants 2021, 10, 397. https://doi.org/10.3390/plants10020397

AMA Style

Choi KS, Ha Y-H, Gil H-Y, Choi K, Kim D-K, Oh S-H. Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. Plants. 2021; 10(2):397. https://doi.org/10.3390/plants10020397

Chicago/Turabian Style

Choi, Kyoung S., Young-Ho Ha, Hee-Young Gil, Kyung Choi, Dong-Kap Kim, and Seung-Hwan Oh. 2021. "Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates" Plants 10, no. 2: 397. https://doi.org/10.3390/plants10020397

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