Comparative genomics of Begonia chloroplasts: insights into molecular evolution, species identification, and phylogeny.
4 affiliations
- 1College of Tourism and Landscape Architecture, Guilin University of Technology, Guilin, 541006, Guangxi, China.
- 2Guangxi Zhuang Autonomous Region, Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, 541006, Guangxi, China.
- 3School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, Hubei, China. [email protected].
- 4Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China. [email protected].
Abstract
Background
Begonia, a hyperdiverse genus with ecological and medicinal values, confronts challenges in species identification and phylogenetic resolution due to remarkable morphological plasticity and ambiguous taxonomic boundaries. Chloroplast genomes (plastomes) serve as powerful molecular tools for addressing these issues, yet comprehensive plastomic data for Chinese Begonia species remain insufficient. This study presents the largest plastome dataset for Chinese Begonia (76 plastomes total), identifies hypervariable markers, and resolves a specific taxonomic issue, clarifying the phylogenetic position.Methods
We sequenced and assembled plastomes of 25 Chinese Begonia species, integrating 51 public plastomes for comparative analyses, including plastome structure, repeat dynamics, codon usage, nucleotide polymorphism, phylogenetics (ML/BI), and positive selection (Ka/Ks, BEB tests).Results
All 25 assembled plastomes exhibited a conserved quadripartite structures (167,365 - 169,901 bp) with 142-143 genes. Eleven hypervariable regions (e.g., ycf1, petB, ndhF-rpl32) were identified as potential DNA barcodes. Phylogenetic tree aligned with geographic distributions, clarifying taxonomic positions (e.g., B. mashanica). Five genes (matK, ndhB, ndhD, rps8, and rps15) showed candidate signals of positive selection, suggesting candidate loci for shade adaptation that require functional validation.Conclusion
This study enriches Begonia plastome resources, provides reliable molecular markers for species authentication, and sheds light on adaptive evolution. The findings support sustainable utilization of medicinal Begonia and advancing genus-level evolutionary and taxonomic research.
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BibTeX
@article{huang2026comparative,
title = {{Comparative genomics of Begonia chloroplasts: insights into molecular evolution, species identification, and phylogeny.}},
author = {Yang Huang and Wenxiu Tang and Secai Huang and Chao Xiong and Lan Wu},
journal = {BMC genomics},
year = {2026},
month = jul,
doi = {10.1186/s12864-026-13066-2},
url = {https://europepmc.org/article/MED/42928148},
note = {CC BY},
}
RIS
TY - JOUR
TI - Comparative genomics of Begonia chloroplasts: insights into molecular evolution, species identification, and phylogeny.
AU - Yang Huang
AU - Wenxiu Tang
AU - Secai Huang
AU - Chao Xiong
AU - Lan Wu
PY - 2026
DA - 2026/07/29
JO - BMC genomics
DO - 10.1186/s12864-026-13066-2
UR - https://europepmc.org/article/MED/42928148
AB - Background Begonia, a hyperdiverse genus with ecological and medicinal values, confronts challenges in species identification and phylogenetic resolution due to remarkable morphological plasticity and ambiguous taxonomic boundaries. Chloroplast genomes (plastomes) serve as powerful molecular tools for addressing these issues, yet comprehensive plastomic data for Chinese Begonia species remain insufficient. This study presents the largest plastome dataset for Chinese Begonia (76 plastomes total), identifies hypervariable markers, and resolves a specific taxonomic issue, clarifying the phylogenetic position.Methods We sequenced and assembled plastomes of 25 Chinese Begonia species, integrating 51 public plastomes for comparative analyses, including plastome structure, repeat dynamics, codon usage, nucleotide polymorphism, phylogenetics (ML/BI), and positive selection (Ka/Ks, BEB tests).Results All 25 assembled plastomes exhibited a conserved quadripartite structures (167,365 - 169,901 bp) with 142-143 genes. Eleven hypervariable regions (e.g., ycf1, petB, ndhF-rpl32) were identified as potential DNA barcodes. Phylogenetic tree aligned with geographic distributions, clarifying taxonomic positions (e.g., B. mashanica). Five genes (matK, ndhB, ndhD, rps8, and rps15) showed candidate signals of positive selection, suggesting candidate loci for shade adaptation that require functional validation.Conclusion This study enriches Begonia plastome resources, provides reliable molecular markers for species authentication, and sheds light on adaptive evolution. The findings support sustainable utilization of medicinal Begonia and advancing genus-level evolutionary and taxonomic research.
SN - 1471-2164
ER -