The complete chloroplast genome sequence of the North American sclerophyllous evergreen shrub, Quercus turbinella (Fagaceae)

Abstract

Quercus turbinella (section Quercus; Fagaceae) is an evergreen shrub characteristic in central Arizona and it concerns one of the most abundant and economically important genera of Quercus in the Northern Hemisphere. Here, we have sequenced the complete chloroplast genome to provide insight into the phylogenetic relationship of Q. turbinella. The whole genome is 161,208 bp in length with two inverted repeat regions of 25,827 bp each, which separate a large single-copy region of 90,552 bp and a small single-copy region of 19,002 bp. A total of 136 genes were annotated, including 88 protein-coding genes, eight ribosomal RNAs, and 40 transfer RNAs. The result of the maximum-likelihood phylogenetic analysis strongly suggested that Quercus turbinella had a close relationship to Quercus macrocarpa with strong bootstrap support.

Keywords: Chloroplast genome; Quercus turbinella; phylogenetic analysis.

Figure 1.

The habit (A) and morphological characteristics (B) of Quercus turbinella. Q. turbinella is an evergreen desert scrub oak, that is predominantly found in pinyon-juniper forests and desert slopes. Bark light gray or brown; twigs brown to gray, 1–3 mm diam., usually tomentose or sometimes glabrous, becoming glabrate. Leaf-blade elliptic or ovate, thick, leathery, base cordate or rounded, margins planar or slightly crisped-undulate, apex acute or obtuse; abaxial surface yellow or reddish, usually glaucous, adaxial surface grayish, glaucous, or yellowish glandular, sparsely and minutely stellate-pubescent or glabrous. Photos taken by professor Jung-Hyun Lee in Thunder Mountain Trail, Sedona, AZ, United States, February 2023, without any copyright issues.

Figure 2.

Schematic map of overall features of the chloroplast genome of Quercus turbinella. The circular map of the chloroplast genome was generated using CPGview (Liu et al. 2023). The map comprised seven circles, each depicting different features. Starting from the center and moving outwards, the first circle illustrated distributed repeats with red arcs indicating the forward direction and green arcs indicating the reverse direction. The second circle depicted tandem repeats through short bars. The third circle displayed microsatellite sequences represented by short bars. The fourth circle indicated the sizes of the LSC and SSC regions. The fifth circle represented the IRA and IRB regions. The sixth circle demonstrated the GC contents across the plastome. Lastly, the seventh circle displayed genes distinguished by different colors corresponding to their functional groups.

Figure 3.

Construction of phylogenetic tree (ML) based on complete chloroplast genome of Q. turbinella and 18 other Quercus species. The sequence of Fagus engleriana was used as the outgroup. The following sequences were used: Q. acutissima MH899015 (Zhang et al. 2020), Q. variabilis KU240009 (Yang et al. 2016), Q. baronii KT963087 (Yang et al. 2015), Q. glaucoides MG678003 (Yang et al. 2021), Q. multinervi MG678004 (Yang et al. 2021), Q. myrsinifolia MG678005 (Yang et al. 2021), Q. pachyloma OP442517, Q. aliena KP301144, Q. serrata MN602452 (Liu et al. 2021), Q. yunnanensis MW876863 (Yang 2021), Q. stewardii MG678022 (Yang et al. 2021), Q. dentata MK105455, Q. fabri MK922346 (Xu et al. 2019), Q. wutaishanica MN602450 (Liu et al. 2021), Q. griffithii MG678034 (Yang et al. 2021), Q. mongolica MK089571, Q. robur MG678035 (Yang et al. 2021), Q. macrocarpa MK105459 (Pang et al. 2019), Fagus engleriana KX852398 (Yang et al. 2018). The numbers above the nodes indicate bootstrap values with 1,000 replicates.