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Peer-reviewedCC BY 4.0Ecology and Evolution

Plastid Phylogenomics of Elatostemateae (Urticaceae): Insights Into Structural Variation and Phylogenetic Relationships

  • Long‐Fei Fu1
  • Zi‐Bing Xin1
  • Chi Xiong1
  • Fang Wen1
  • Yi‐Gang Wei1
  • Alexandre K. Monro2
  1. 1Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany Guilin China
  2. 2Identification & Naming Department The Royal Botanic Gardens, Kew Richmond UK
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Abstract

The tribe Elatostemateae, with approximately 1300 species, is the most species‐rich group within Urticaceae, yet plastome evolution and several intergeneric relationships remain incompletely resolved. We analyzed 40 species representing the major extant lineages of Elatostemateae using complete plastomes and nuclear ribosomal DNA (nrDNA); Metapilea was excluded because suitable DNA material was unavailable. Plastomes retained the typical angiosperm quadripartite structure and ranged from 143,738 to 163,969 bp. Comparative analyses revealed large inversions in the large single‐copy (LSC) region, pronounced inverted‐repeat (IR) boundary shifts, and a rare plastid mitochondrial DNA‐derived sequence (PTMT) insertion. Seven highly variable regions were identified as candidate markers for DNA barcoding. Plastome, protein‐coding sequence (CDS), nrDNA, and combined analyses recovered the same three major Elatostemateae clades, although several internal nrDNA nodes had lower support. Plastid and nrDNA data placed Gyrotaenia as sister to Pilea s.l . within Elatostemateae, whereas recent low‐copy nuclear evidence places Gyrotaenia + Myriocarpa sister to core Elatostemateae, revealing cytonuclear discordance. These results provide a framework for Elatostemateae systematics and document substantial plastome structural variation; denser low‐copy nuclear or whole‐genome sampling will be needed to distinguish incomplete lineage sorting from historical introgression.

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Cite

BibTeXRIS
BibTeX
@article{fu2026plastid,
  title = {{Plastid Phylogenomics of Elatostemateae (Urticaceae): Insights Into Structural Variation and Phylogenetic Relationships}},
  author = {Long‐Fei Fu and Zi‐Bing Xin and Chi Xiong and Fang Wen and Yi‐Gang Wei and Alexandre K. Monro},
  journal = {Ecology and Evolution},
  year = {2026},
  month = oct,
  doi = {10.1002/ece3.74416},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.74416},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Plastid Phylogenomics of Elatostemateae (Urticaceae): Insights Into Structural Variation and Phylogenetic Relationships
AU  - Long‐Fei Fu
AU  - Zi‐Bing Xin
AU  - Chi Xiong
AU  - Fang Wen
AU  - Yi‐Gang Wei
AU  - Alexandre K. Monro
PY  - 2026
DA  - 2026/10/06
JO  - Ecology and Evolution
DO  - 10.1002/ece3.74416
UR  - https://onlinelibrary.wiley.com/doi/10.1002/ece3.74416
AB  - The tribe Elatostemateae, with approximately 1300 species, is the most species‐rich group within Urticaceae, yet plastome evolution and several intergeneric relationships remain incompletely resolved. We analyzed 40 species representing the major extant lineages of Elatostemateae using complete plastomes and nuclear ribosomal DNA (nrDNA); Metapilea was excluded because suitable DNA material was unavailable. Plastomes retained the typical angiosperm quadripartite structure and ranged from 143,738 to 163,969 bp. Comparative analyses revealed large inversions in the large single‐copy (LSC) region, pronounced inverted‐repeat (IR) boundary shifts, and a rare plastid mitochondrial DNA‐derived sequence (PTMT) insertion. Seven highly variable regions were identified as candidate markers for DNA barcoding. Plastome, protein‐coding sequence (CDS), nrDNA, and combined analyses recovered the same three major Elatostemateae clades, although several internal nrDNA nodes had lower support. Plastid and nrDNA data placed Gyrotaenia as sister to Pilea s.l . within Elatostemateae, whereas recent low‐copy nuclear evidence places Gyrotaenia + Myriocarpa sister to core Elatostemateae, revealing cytonuclear discordance. These results provide a framework for Elatostemateae systematics and document substantial plastome structural variation; denser low‐copy nuclear or whole‐genome sampling will be needed to distinguish incomplete lineage sorting from historical introgression.
SN  - 2045-7758
SN  - 2045-7758
ER  -