Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

• Published in: International journal of molecular sciences Vol. 19; no. 8; p. 2443
• Main Authors: Li, Xuan, Li, Yongfu, Zang, Mingyue, Li, Mingzhi, Fang, Yanming
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 18-08-2018; MDPI
• Subjects: Base Composition; Bioinformatics; chloroplast genome; Chloroplasts; Chloroplasts - genetics; Deoxyribonucleic acid; Divergence; DNA; Ecological monitoring; Forestry; Genes; Genes, Plant; Genome, Chloroplast; Genomes; Genomics; Inverted repeat; Loci; Morphology; Nucleotide sequence; phylogenetic relationship; Phylogenetics; Phylogeny; Plant Proteins - genetics; Population; Population genetics; Proteins; Quercus; Quercus - genetics; Quercus acutissima; RNA, Plant - genetics; RNA, Ribosomal - genetics; RNA, Transfer - genetics; rRNA; Structural analysis; Studies; Transfer RNA; Trees; China; Quercus; chloroplast genome; phylogenetic relationship
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms19082443

, an important endemic and ecological plant of the
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
was sequenced, analyzed, and compared to four species in the Fagaceae family. The size of the
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
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
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
genus do not form a clade and that
is closely related to
. This study identified the unique characteristics of the
cp genome, which will provide a theoretical basis for species identification and biological research.