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Peer-reviewedCC BY 4.0Ecology and Evolution

Comparative Chloroplast Genomics Reveals Phylogenetic Relationships Among Korean Dioscorea Species

  • Ji Eun Kim1
  • Min Su Jo1
  • Kyung‐Bae Nam1
  • Jun Hyeok Kim1
  • Jun‐Ho Song2
  • Hyeok‐Jae Choi3
  • Gyu Young Chung4
  • Chae Sun Na1
4 affiliations
  1. 1Wild Plant Seed Division Baekdudaegan National Arboretum Bonghwa‐gun Gyeongsangbuk‐do Republic of Korea
  2. 2Department of Biology Chungbuk National University Cheongju‐si Chungcheongbuk‐do Republic of Korea
  3. 3Department of Biology and Chemistry Changwon National University Changwon‐si Gyeongsangnam‐do Republic of Korea
  4. 4Department of Forest Science Gyeongkuk National University Andong‐si Gyeongsangbuk‐do Republic of Korea
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Abstract

Crop wild relatives represent important sources of genetic variation for crop improvement, particularly as climate change and increasing global food demand require the development of more resilient and productive crop varieties. However, genomic information on many wild Dioscorea species in East Asia remains limited. In this study, we sequenced and assembled the complete chloroplast genomes of six Dioscorea species native to Korea, including the first reported complete chloroplast genome of D. coreana . The assembled genomes exhibited a conserved quadripartite structure with similar gene contents and GC compositions across species. Despite this overall conservation, comparative analyses revealed localized sequence variation, particularly in noncoding regions. Several loci, including ndhF and ycf1 , exhibited increased nucleotide diversity, indicating their potential as informative markers. In addition, simple sequence repeats were composed mainly of A/T‐rich motifs and predominantly distributed in the large single‐copy region. Phylogenetic analysis based on concatenated chloroplast protein‐coding gene sequences provided a well‐resolved framework for the studied taxa and clarified the relationships among Korean Dioscorea species. Furthermore, the close genetic relationship between cultivated yam and its wild relatives was supported. These results provide new genomic data for previously underrepresented Korean taxa, including the first chloroplast genome of D. coreana , and offer a basis for future studies on genetic diversity, species identification, and the utilization of wild germplasm.

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Cite

BibTeXRIS
BibTeX
@article{kim2026comparative,
  title = {{Comparative Chloroplast Genomics Reveals Phylogenetic Relationships Among Korean Dioscorea Species}},
  author = {Ji Eun Kim and Min Su Jo and Kyung‐Bae Nam and Jun Hyeok Kim and Jun‐Ho Song and Hyeok‐Jae Choi and Gyu Young Chung and Chae Sun Na},
  journal = {Ecology and Evolution},
  year = {2026},
  month = nov,
  doi = {10.1002/ece3.74651},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.74651},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Comparative Chloroplast Genomics Reveals Phylogenetic Relationships Among Korean Dioscorea Species
AU  - Ji Eun Kim
AU  - Min Su Jo
AU  - Kyung‐Bae Nam
AU  - Jun Hyeok Kim
AU  - Jun‐Ho Song
AU  - Hyeok‐Jae Choi
AU  - Gyu Young Chung
AU  - Chae Sun Na
PY  - 2026
DA  - 2026/11/08
JO  - Ecology and Evolution
DO  - 10.1002/ece3.74651
UR  - https://onlinelibrary.wiley.com/doi/10.1002/ece3.74651
AB  - Crop wild relatives represent important sources of genetic variation for crop improvement, particularly as climate change and increasing global food demand require the development of more resilient and productive crop varieties. However, genomic information on many wild Dioscorea species in East Asia remains limited. In this study, we sequenced and assembled the complete chloroplast genomes of six Dioscorea species native to Korea, including the first reported complete chloroplast genome of D. coreana . The assembled genomes exhibited a conserved quadripartite structure with similar gene contents and GC compositions across species. Despite this overall conservation, comparative analyses revealed localized sequence variation, particularly in noncoding regions. Several loci, including ndhF and ycf1 , exhibited increased nucleotide diversity, indicating their potential as informative markers. In addition, simple sequence repeats were composed mainly of A/T‐rich motifs and predominantly distributed in the large single‐copy region. Phylogenetic analysis based on concatenated chloroplast protein‐coding gene sequences provided a well‐resolved framework for the studied taxa and clarified the relationships among Korean Dioscorea species. Furthermore, the close genetic relationship between cultivated yam and its wild relatives was supported. These results provide new genomic data for previously underrepresented Korean taxa, including the first chloroplast genome of D. coreana , and offer a basis for future studies on genetic diversity, species identification, and the utilization of wild germplasm.
SN  - 2045-7758
SN  - 2045-7758
ER  -