Abstract
Lithocarpus konishii, a rare species endemic to islands in South China, was evaluated as a vulnerable species (VU) by the 'China Species Red List.' Here, we first presented the complete chloroplast genome sequence of L. konishii. The chloroplast genome was 161,059 bp in length with 36.76% GC content, containing a small single-copy region (SSC, 18,967 bp), a large single-copy region (LSC, 90,250 bp), and a pair of inverted repeats (IRs, 25,921 bp each). A total of 139 genes were predicted, including 87 protein-coding genes (CDS), 8 rRNAs, and 44 tRNAs. Based on the concatenated shared unique CDS sequence dataset, maximum-likelihood and Bayesian inference methods were used to build the phylogenetic trees of 18 species from the Fagaceae family. Results indicated that L. konishii is closely related to L. longnux and L. pachyphyllus var. fruticosus, and forms a monophyly of the subfamily Castaneoideae with Castanopsis and Castanea. This study provides a theoretical basis for the conservation genomics of this endangered plant.