Open Access

ARTICLE

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 Authors: Xiaoming Tian. Email: ; Hao Lv. Email:
# These authors contributed equally to this work

Phyton-International Journal of Experimental Botany 2026, 95(6), 8 https://doi.org/10.32604/phyton.2026.079853

Received 29 January 2026; Accepted 06 May 2026; Issue published 29 June 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.

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Keywords

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Supplementary Material

Supplementary Material File

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