Complete Chloroplast Genome of Castanopsis sclerophylla (Lindl.) Schott: Genome Structures, Comparative and Phylogenetic Analysis

Abstract

Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved forest in subtropical area and has important ecological and economic value. However, there are little studies on its chloroplast genome. In this study, the complete chloroplast genome sequences of C. sclerophylla was reported based on the Illumina Hiseq 2500 platform. The complete chloroplast genome of C. sclerophylla was 160,497bp, including a pair of inverted repeated (IRs) regions (25,675bp) that were separated by a large single copy (LSC) region of 90,255bp, and a small single copy (SSC) region of 18,892bp. The overall GC content of chloroplast genome was 36.82%. A total of 131 genes were found, of these 111 genes were unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the relatively smaller chloroplast genome size of C. sclerophylla compared with other three congeneric species. Sequence analysis detected that the LSC and SSC regions were more divergent than the IR regions within the Castanopsis, furthermore, a higher divergence was found in non-coding regions than in coding regions. The maximum likelihood (ML) phylogenetic analysis showed that these four species of the genus Castanopsis formed a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide basic knowledge about characteristics of C. sclerophylla and also enhance our understanding of Castanopsis species evolution within the Fagaceae family. Meanwhile, these findings will contribute to the exploration, utilization and conservation genetics of C. sclerophylla.