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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Systematics and Evolution
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1430191

Comparative and Phylogenetic Analysis of Chloroplast Genomes from Ten Species in Quercus section Cyclobalanopsis

Provisionally accepted
Ke Huang Ke Huang Buyu Li Buyu Li *Xiaoli Chen Xiaoli Chen *Chun Qin Chun Qin *Xuemei Zhang Xuemei Zhang *
  • China West Normal University, Nanchong, China

The final, formatted version of the article will be published soon.

    The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.

    Keywords: chloroplast (cp) genome, phylogenetic analysis, Quercus section Cyclobalanopsis, DNA SEQUENCING, sequence annotation

    Received: 09 May 2024; Accepted: 31 Jul 2024.

    Copyright: © 2024 Huang, Li, Chen, Qin and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Buyu Li, China West Normal University, Nanchong, China
    Xiaoli Chen, China West Normal University, Nanchong, China
    Chun Qin, China West Normal University, Nanchong, China
    Xuemei Zhang, China West Normal University, Nanchong, China

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