Complete chloroplast genome sequence of Quercus salicina Blume (Fagaceae)

Abstract

Quercus salicina Blume 1851, an evergreen broad-leaved species belonging to the family Fagaceae, is primarily distributed from southern Korea to Japan. In this study, we comprehensively analyzed the chloroplast genome of Q. salicina. Its genome, with a quadripartite structure, spanned 160,801 bp and had a GC content of 36.58%. Annotation revealed 131 genes, including 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. These intricacies in the genome were further confirmed by the presence of introns in multiple genes. Phylogenetic analysis of 19 Fagales species elucidated their evolutionary relationships, with Fagus engleriana branching early and Q. salicina showing a close relationship with Q. gilva. This study enhances our understanding of the genetic makeup of Q. salicina and its evolutionary dynamics within the Fagales.

Keywords: Chloroplast genome; Fagaceae; Phylogenetic analysis; Quercus salicina.

Figure 1.

Morphological characteristics of the leaves and branches of quercus salicina, an evergreen broad-leaved tree native to the temperate regions of Southern Korea. This photograph was taken by hyunmo choi on May 17, 2024, in Jinju, Korea. The lanceolate leaves with a glossy surface are characteristic of the species.

Figure 2.

Circular map of the chloroplast genome of Quercus salicina. Genes, tRNAs, and rRNAs are displayed as differently colored boxes on the outer circle, while the inner circle shows the quadripartite structure of the chloroplast genome. The dark grey graph inside the inner circle represents the GC content, while the light grey graph indicates the AT content along the genome. LSC, large single-copy; IRA, inverted repeat A; SSC, small single-copy; IRB, inverted repeat B.

Figure 3.

Phylogenetic tree of Quercus salicina (highlighted in bold and underlined, GenBank accession number or_458923) with other species of the order Fagales. The Betulaceae family, represented by Alnus japonica, was selected as the outgroup for the analysis. A corresponding phylogram is displayed in the upper left corner. Phylogenetic analyses were conducted using protein-coding sequences with Clustal Omega for sequence alignment and IQ-TREE version 2.3.6 for maximum likelihood (ML) tree construction. The optimal substitution model, TVM+F + G4, was selected using ModelFinder based on the Bayesian information criterion (BIC). Bootstrap analysis with 1,000 replicates was performed to assess branch support, with values displayed at the corresponding nodes. The following sequences with GenBank accession numbers and references were used: Castanopsis sieboldii MZ_028444 (Park et al. 2021), Castanea crenata MN_402457, Castanea mollissima HQ_336406, Quercus gilva MK_986651, Quercus glauca KX_852399, Quercus variabilis KU_240009, Quercus aliena KP_301144, Quercus dentata MG_967555, Fagus engleriana KX_852398 (Zeng et al. 2019), Quercus acuta MT_742291, Quercus phillyraeoides NC_048488 (Li et al. 2021), Quercus myrsinifolia MN_199025, Quercus acutissima MH_607377 (Li et al. 2019), Quercus mongolica MK_089571 (Kang et al. 2019), Quercus serrata MN_602452 (Gantsetseg et al. 2024), Corylus heterophylla NC_031856 (Xu and Wu 2021), Corylus sieboldiana MH_628456 (Hu et al. 2020), and Alnus japonica NC_036753 (Zhang et al. 2021).