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.
Highlights
Oak trees provide humans with materials used in food, clothing, and houses, while oak forests supply living organisms and animals with comfortable habitats, good air, and sufficient and pure moisture
The DNA G + C contents of the large single copy (LSC), small single copy (SSC), and inverted repeat (IR) regions, and the whole genome are 34.62, 30.84, 42.78, and 36.08 mol %, respectively, which is similar to the chloroplast genomes of other Quercus species (Figure A1; Table 2)
We reported and analyzed the complete cp genome of Q. acutissima, an endemic and ecological tree species in China
Summary
Oak trees provide humans with materials used in food, clothing, and houses, while oak forests supply living organisms and animals with comfortable habitats, good air, and sufficient and pure moisture. Complete chloroplast (cp) genome size data will be necessarily used to infer the phylogenetic relationship of Quercus or Fagaceae in future studies. Q. acutissima is an ecological and economic tree species in deciduous broad-leaved forests in the temperate zone of East Asia, widely distributed on the Hu Huanyong line or in Southeast China (latitude from 18◦ to 41◦ N and longitude from 91◦ to 123◦ E) [16]. This line from Heilongjiang Province to Tengchong, Yunnan Province, is roughly inclined in a 45◦ straight line. It is expected that the results will provide a theoretical basis for the determination of phylogenetic status and future scientific research
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