The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis.

, an important economic nut tree, is narrowly endemic to eastern China in the wild. The complete cp genome of was sequenced with NGS using an Illumina HiSeq2500, analyzed, and compared to its closely related species. The cp genome is 160,825 bp in length with an overall GC content of 36.13%, presenting a quadripartite structure comprising a large single copy (LSC; 90,115 bp), a small single copy (SSC; 18,760 bp), and a pair of inverted repeats (IRs; 25,975 bp). The genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 252 simple sequence repeats (SSRs) and 55 long repeats were identified. Gene selective pressure analysis showed that seven genes (, , , , , , and ) were possibly under positive selection compared with the other species. Phylogenetic relationships of 46 species inferred that is monophyletic, and that is sister to and . The genome comparison revealed that there is a wide variability of the junction sites, and there is higher divergence in the noncoding regions than in coding regions. These results suggest a great potential in phylogenetic research. The newly characterized cp genome of provides valuable information for further studies of this economically important species.