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Peer-reviewedCC BY 4.0Ecology and Evolution

Phylogenomics Clarifies Plastome Reduction and Phylogenetic Relationships in Monotropoideae

  • Guocui Deng1,2,3
  • Kaili Duan1,2
  • Niyan Xiang4
  • Feng Gao3
  • Peng Zhan5
  • Rui Shu3
  • Qingsong Lin6
  • Qing Zuo7
  • Tao Yuan1,2,3
7 affiliations
  1. 1College of Life Science and Technology Xinjiang University Ürümqi China
  2. 2Xinjiang Key Laboratory of Biological Resources and Genetic Engineering Ürümqi China
  3. 3State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences Wuhan University Wuhan China
  4. 4School of Resources and Environmental Science Hubei University Wuhan China
  5. 5Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences South‐Central Minzu University Wuhan China
  6. 6Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences Zhejiang Agriculture & Forestry University Hangzhou Zhejiang China
  7. 7Institute of Intelligent Chinese Medicine Chongqing University of Chinese Medicine Chongqing College of Traditional Chinese Medicine Chongqing China
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Abstract

Plastome evolution and biogeographic history remain poorly understood in mycoheterotrophic lineages. Here, we sequenced and assembled the complete plastome of Monotropa callistoma (Ericaceae), a fully mycoheterotrophic species, and compared it with other mycoheterotrophic plastomes. The M. callistoma plastome is 29,784 bp long, lacks the canonical quadripartite structure, and contains 40 genes, representing an intermediate level of reduction within Monotropoideae. Comparative analyses revealed extreme contraction in some lineages, including Sciaphila (12.8–21.5 kb), and a weak positive correlation between GC content and genome size. Within Monotropoideae, plastomes become smaller from the early‐branching Pterospora lineage to the more recently diverged Monotropa lineage. This reduction is accompanied by progressively poorer synteny and lineage‐specific loss of rps23 in Monotropa . Phylogenomic analyses of 30 Ericaceae plastomes strongly supported Monotropoideae (bootstrap = 100) and clarified relationships among its 10 sampled genera. Divergence‐time estimation and ancestral‐range reconstruction placed the origin of Clade 1 (Pyroloideae, Arbutoideae and Monotropoideae) in Asia during the late Cretaceous to early Cenozoic. The lineage subsequently dispersed to North America via Beringia, whereas the Monotropsis + Monotropastrum + Monotropa clade later dispersed back to Asia during the late Eocene to early Oligocene. This history gave rise to East Asian endemics, including Monotropa humile and M. callistoma . These findings illuminate plastome reduction in mycoheterotrophs, resolve relationships within Monotropoideae, and support a complex history of bidirectional intercontinental dispersal.

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Cite

BibTeXRIS
BibTeX
@article{deng2026phylogenomics,
  title = {{Phylogenomics Clarifies Plastome Reduction and Phylogenetic Relationships in Monotropoideae}},
  author = {Guocui Deng and Kaili Duan and Niyan Xiang and Feng Gao and Peng Zhan and Rui Shu and Qingsong Lin and Qing Zuo and Tao Yuan},
  journal = {Ecology and Evolution},
  year = {2026},
  month = oct,
  doi = {10.1002/ece3.74449},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.74449},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Phylogenomics Clarifies Plastome Reduction and Phylogenetic Relationships in Monotropoideae
AU  - Guocui Deng
AU  - Kaili Duan
AU  - Niyan Xiang
AU  - Feng Gao
AU  - Peng Zhan
AU  - Rui Shu
AU  - Qingsong Lin
AU  - Qing Zuo
AU  - Tao Yuan
PY  - 2026
DA  - 2026/10/02
JO  - Ecology and Evolution
DO  - 10.1002/ece3.74449
UR  - https://onlinelibrary.wiley.com/doi/10.1002/ece3.74449
AB  - Plastome evolution and biogeographic history remain poorly understood in mycoheterotrophic lineages. Here, we sequenced and assembled the complete plastome of Monotropa callistoma (Ericaceae), a fully mycoheterotrophic species, and compared it with other mycoheterotrophic plastomes. The M. callistoma plastome is 29,784 bp long, lacks the canonical quadripartite structure, and contains 40 genes, representing an intermediate level of reduction within Monotropoideae. Comparative analyses revealed extreme contraction in some lineages, including Sciaphila (12.8–21.5 kb), and a weak positive correlation between GC content and genome size. Within Monotropoideae, plastomes become smaller from the early‐branching Pterospora lineage to the more recently diverged Monotropa lineage. This reduction is accompanied by progressively poorer synteny and lineage‐specific loss of rps23 in Monotropa . Phylogenomic analyses of 30 Ericaceae plastomes strongly supported Monotropoideae (bootstrap = 100) and clarified relationships among its 10 sampled genera. Divergence‐time estimation and ancestral‐range reconstruction placed the origin of Clade 1 (Pyroloideae, Arbutoideae and Monotropoideae) in Asia during the late Cretaceous to early Cenozoic. The lineage subsequently dispersed to North America via Beringia, whereas the Monotropsis + Monotropastrum + Monotropa clade later dispersed back to Asia during the late Eocene to early Oligocene. This history gave rise to East Asian endemics, including Monotropa humile and M. callistoma . These findings illuminate plastome reduction in mycoheterotrophs, resolve relationships within Monotropoideae, and support a complex history of bidirectional intercontinental dispersal.
SN  - 2045-7758
SN  - 2045-7758
ER  -