Comparative Analysis of Chloroplast Genomes and Phylogenetic Relationships of Eight Quercus Species
Xin Li#, Xiaoming Tian#,*, Guangfeng Xiang, Lan Zhou, Gaofei Li, Lu Zhu, Chao Liu, Xiangpeng Li, Li Liu, Tianyi Jiang, Cun Mou, Hao Lv*
Institute of Plant Conservation, Hunan Botanical Garden, Changsha, China
* Corresponding Author: Xiaoming Tian. Email: 
; Hao Lv. Email: 
# These authors contributed equally to this work
Phyton-International Journal of Experimental Botany https://doi.org/10.32604/phyton.2026.079853
Received 29 January 2026; Accepted 06 May 2026; Published online 26 May 2026
Abstract
Quercus is widely distributed globally and holds significant ecological and economic value. However, the morphological classification of this genus has long been controversial, with the core issue being whether the
Cyclobalanopsis should be treated as an independent genus or as a subgenus within
Quercus. In this study, the chloroplast genomes of eight
Quercus species were determined and analyzed. Among these, the complete chloroplast genome of
Quercus pachyloma is reported for the first time, alongside newly published chloroplast genome data for seven other
Quercus species collected from Hunan and Jiangxi provinces in China. All eight species exhibited a typical quadripartite chloroplast genome structure, with genome sizes ranging from 160,716 to 160,842 bp. The gene composition and arrangement were highly conserved, with each species containing 131 genes. Three highly variable regions (
psaI,
infA,
rpl22) were identified as candidate DNA barcodes. The total number of simple sequence repeats (SSRs) was similar across species, with all types distributed among them; however, dispersed repetitive sequences exhibited distinct regional characteristics and interspecific differences, providing potential marker resources for distinguishing closely related species. Phylogenetic analysis revealed that all eight species nested within
Quercus, with
Quercus shennongii and
Cyclobalanopsis edithae clustered together as a distinct branch with 100% bootstrap support. Samples from different geographic sources within the same species did not cluster directly, suggesting the potential for intraspecific genetic variation and geographic population structure differentiation within
Quercus. This study provides new chloroplast genomic evidence for the taxonomic status of
Cyclobalanopsis. The phylogenetic results are compatible with treating
Cyclobalanopsis as a subgenus within
Quercus but may not be the sole explanation. Final taxonomic treatment requires careful evaluation integrating nuclear genomic, phytogeographic, and population data.
Keywords
Chloroplast genome;
quercus;
cyclobalanopsis; phylogeny; molecular markers
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