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Article

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

by
Xue Liu
1,
Er-Mei Chang
1,
Jian-Feng Liu
1,*,
Yue-Ning Huang
1,
Ya Wang
1,
Ning Yao
1 and
Ze-Ping Jiang
1,2
1
Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2
Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
*
Author to whom correspondence should be addressed.
Forests 2019, 10(7), 587; https://doi.org/10.3390/f10070587
Submission received: 5 June 2019 / Revised: 7 July 2019 / Accepted: 12 July 2019 / Published: 15 July 2019
(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)
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Abstract

Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant. No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex Wenz. (KU240009), Q. baronii Skan (KT963087), Q. aquifolioides Rehd. et Wils. (KX911971), Q. variabilis Bl. (KU240009), Fagus engleriana Seem. (KX852398), Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus.
Keywords: chloroplast (cp) genome; Q. bawanglingensis; comparative analysis; phylogenetics; interspecific relationships chloroplast (cp) genome; Q. bawanglingensis; comparative analysis; phylogenetics; interspecific relationships

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MDPI and ACS Style

Liu, X.; Chang, E.-M.; Liu, J.-F.; Huang, Y.-N.; Wang, Y.; Yao, N.; Jiang, Z.-P. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China. Forests 2019, 10, 587. https://doi.org/10.3390/f10070587

AMA Style

Liu X, Chang E-M, Liu J-F, Huang Y-N, Wang Y, Yao N, Jiang Z-P. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China. Forests. 2019; 10(7):587. https://doi.org/10.3390/f10070587

Chicago/Turabian Style

Liu, Xue, Er-Mei Chang, Jian-Feng Liu, Yue-Ning Huang, Ya Wang, Ning Yao, and Ze-Ping Jiang. 2019. "Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China" Forests 10, no. 7: 587. https://doi.org/10.3390/f10070587

APA Style

Liu, X., Chang, E.-M., Liu, J.-F., Huang, Y.-N., Wang, Y., Yao, N., & Jiang, Z.-P. (2019). Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China. Forests, 10(7), 587. https://doi.org/10.3390/f10070587

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