The complete chloroplast genome sequence of Quercus ningangensis and its phylogenetic implication

Tian-Rui Wang,Gregor Kozlowski,Zheng-Wei Wang,Yi-Gang Song

doi:10.35535/pfsyst-2021-0014

Abstract

Quercus ningangensis is an economically and ecologically important tree species belonging to the family Fagaceae. In this study, the complete chloroplast (cp) genome of Q. ningangensis was sequenced and assembled, and 18 published cp genomes of Quercus were retrieved for genomic analyses (including sequence divergence, repeat elements, and structure) and phylogenetic inference. With this study, we found that complete cp genomes in Quercus are conserved, and we discovered a codon composition bias, which may be related to genomic content and genetic characteristics. In addition, we detected considerable structural variations in the expansion and contraction of inverted repeat regions. Six regions with relatively high variable (matK-rps16, psbC, ycf3 intron, rbcL, petA-psbJ, and ycf1) were detected by conducting a sliding window analysis, which has a high potential for developing effective genetic markers. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods resulted in a robust phylogenetic tree of Quercus with high resolution for nearly all identified nodes. The phylogenetic relationships showed that the phylogenetic position of Q. ningangensis was located between Q. sichourensis and Q. acuta. The results of this study contribute to future research into the phylogenetic evolution of Quercus section Cyclobalanopsis (Fagaceae).

Highlights

Woody species have received much scientific and media attention over the past decade due to their very significant economic value, as well as their importance with respect to ecology and biodiversity (Häggström 2019; Carrero et al 2020; Fazan et al 2020)
Quercus ningangensis belongs to the Quercus section Cyclobalanopsis, which diverged at the transition of the Oligocene and Miocene (~26 million years ago (Ma)) (Deng et al 2018)
Most of the genes occurred as single copies in the LSC and SSC, but 18 genes were duplicated in the IR regions, including seven protein-coding genes, seven tRNA genes, and four rRNA genes (16S, 23S, 4.5S, and 5S)

Summary

Introduction

Woody species have received much scientific and media attention over the past decade due to their very significant economic value, as well as their importance with respect to ecology and biodiversity (Häggström 2019; Carrero et al 2020; Fazan et al 2020). Quercus ningangensis belongs to the Quercus section Cyclobalanopsis, which diverged at the transition of the Oligocene and Miocene (~26 Ma) (Deng et al 2018) The distribution of this species is very narrow in Guangxi, Hunan, and Jiangxi provinces, and its conservation status is uncertain due to data deficiency (Huang et al 1999; Carrero et al 2020). The single-celled trichome base supported Q. ningangensis as a member of the single-celled trichome bases (STB) lineage in the section Cyclobalanopsis (Deng et al 2014). Recent phylogenetic and phylogenomic studies have not included samples of this species (Deng et al 2018; Hipp et al 2020; Yang et al 2020)

Methods

Results

Conclusion