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Int. J. Mol. Sci. 2018, 19(8), 2443; https://doi.org/10.3390/ijms19082443

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

1
Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
2
Genepioneer Biotechnologies Co. Ltd., Nanjing 210014, China
*
Author to whom correspondence should be addressed.
Received: 13 July 2018 / Revised: 14 August 2018 / Accepted: 16 August 2018 / Published: 18 August 2018
(This article belongs to the Special Issue Chloroplast)
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Abstract

Quercus acutissima, an important endemic and ecological plant of the Quercus genus, is widely distributed throughout China. However, there have been few studies on its chloroplast genome. In this study, the complete chloroplast (cp) genome of Q. acutissima was sequenced, analyzed, and compared to four species in the Fagaceae family. The size of the Q. acutissima chloroplast genome is 161,124 bp, including one large single copy (LSC) region of 90,423 bp and one small single copy (SSC) region of 19,068 bp, separated by two inverted repeat (IR) regions of 51,632 bp. The GC content of the whole genome is 36.08%, while those of LSC, SSC, and IR are 34.62%, 30.84%, and 42.78%, respectively. The Q. acutissima chloroplast genome encodes 136 genes, including 88 protein-coding genes, four ribosomal RNA genes, and 40 transfer RNA genes. In the repeat structure analysis, 31 forward and 22 inverted long repeats and 65 simple-sequence repeat loci were detected in the Q. acutissima cp genome. The existence of abundant simple-sequence repeat loci in the genome suggests the potential for future population genetic work. The genome comparison revealed that the LSC region is more divergent than the SSC and IR regions, and there is higher divergence in noncoding regions than in coding regions. The phylogenetic relationships of 25 species inferred that members of the Quercus genus do not form a clade and that Q. acutissima is closely related to Q. variabilis. This study identified the unique characteristics of the Q. acutissima cp genome, which will provide a theoretical basis for species identification and biological research. View Full-Text
Keywords: Quercus; chloroplast genome; phylogenetic relationship Quercus; chloroplast genome; phylogenetic relationship
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Li, X.; Li, Y.; Zang, M.; Li, M.; Fang, Y. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima. Int. J. Mol. Sci. 2018, 19, 2443.

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