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Peer-reviewedCC BY 4.0PLOS One

Plastome evolution in Aurantioideae and plastome-based classification of Citrus

  • Eranga Pawani Witharana1
  • Myat Htoo San2
  • Nadeeka U. Jayawardana3
  • Nobuhiro Kotoda4
  • Masashi Yamamoto5
  • Yukio Nagano6
6 affiliations
  1. 1Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
  2. 2Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan
  3. 3Graduate School of Advanced Health Science, Saga University, Saga, Japan
  4. 4The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
  5. 5Faculty of Agriculture, Saga University, Saga, Japan
  6. 6Applied BioSciences, Macquarie University, Sydney, New South Wales, Australia
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Abstract

Plastomes are widely used in plant systematics and also retain signals of structural evolution. In this study, we investigated plastome evolution in the subfamily Aurantioideae of Rutaceae, focusing on structural variation at the LSC–IR boundary regions, putative pseudogenization of plastid genes, plastome-based classification of Citrus, and divergence-time patterns. Comparative analyses revealed substantial structural variation around the rpl22 and rps19 regions at the LSC–IR boundaries and repeated pseudogenization of plastid genes such as rpl22, ycf68, and orf56. Additional lineage-specific sequence disruptions were detected in cemA, ycf15, rps4, and ycf1. Phylogenetic analyses of complete plastomes from 56 Citrus accessions resolved eight major plastome clusters within Citrus. Divergence-time analysis indicated two comparable Asia–Africa splits within Aurantioideae, whereas the divergence between Australian and Asian Citrus lineages was more recent. These results show that plastome evolution in Aurantioideae combines phylogenetically informative sequence variation with recurrent local structural change and provides useful information for classification and evolutionary interpretation in this economically important plant group.

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Cite

BibTeXRIS
BibTeX
@article{witharana2026plastome,
  title = {{Plastome evolution in Aurantioideae and plastome-based classification of Citrus}},
  author = {Eranga Pawani Witharana and Myat Htoo San and Nadeeka U. Jayawardana and Nobuhiro Kotoda and Masashi Yamamoto and Yukio Nagano},
  journal = {PLOS One},
  year = {2026},
  month = oct,
  doi = {10.1371/journal.pone.0349882},
  url = {https://doi.org/10.1371/journal.pone.0349882},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Plastome evolution in Aurantioideae and plastome-based classification of Citrus
AU  - Eranga Pawani Witharana
AU  - Myat Htoo San
AU  - Nadeeka U. Jayawardana
AU  - Nobuhiro Kotoda
AU  - Masashi Yamamoto
AU  - Yukio Nagano
PY  - 2026
DA  - 2026/10/07
JO  - PLOS One
DO  - 10.1371/journal.pone.0349882
UR  - https://doi.org/10.1371/journal.pone.0349882
AB  - Plastomes are widely used in plant systematics and also retain signals of structural evolution. In this study, we investigated plastome evolution in the subfamily Aurantioideae of Rutaceae, focusing on structural variation at the LSC–IR boundary regions, putative pseudogenization of plastid genes, plastome-based classification of Citrus, and divergence-time patterns. Comparative analyses revealed substantial structural variation around the rpl22 and rps19 regions at the LSC–IR boundaries and repeated pseudogenization of plastid genes such as rpl22, ycf68, and orf56. Additional lineage-specific sequence disruptions were detected in cemA, ycf15, rps4, and ycf1. Phylogenetic analyses of complete plastomes from 56 Citrus accessions resolved eight major plastome clusters within Citrus. Divergence-time analysis indicated two comparable Asia–Africa splits within Aurantioideae, whereas the divergence between Australian and Asian Citrus lineages was more recent. These results show that plastome evolution in Aurantioideae combines phylogenetically informative sequence variation with recurrent local structural change and provides useful information for classification and evolutionary interpretation in this economically important plant group.
SN  - 1932-6203
ER  -