ORIGINAL ARTICLE
The complete chloroplast genome sequence of Quercus ningangensis and its phylogenetic implication
| 1 | Eastern China Conservation Centre for Wild Endangered Plant Resources,
Shanghai Chenshan Botanical Garden, Shanghai, 201602,
China |
| 2 | Horticulture and Landscape Department, Shanghai Chenshan Botanical
Garden, Shanghai, 201602, China |
| 3 | Department of Biology and Botanic Garden, University of Fribourg,
Fribourg, Switzerland |
| 4 | Natural History Museum Fribourg, Fribourg, Switzerland |
Online publication date: 2021-12-31
Publication date: 2021-12-31
Plant and Fungal Systematics 2021; 66(2): 155–165
KEYWORDS
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).
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