Abstract
Cephalotaxus sinensis is an endangered Tertiary relict tree endemic to China with high medicinal values. To contribute to its conservation genetics studies, its complete chloroplast (cp) genome was assembled using Illumina high-throughput sequencing technology in this study. The cp genome is 135,646 bp long with an asymmetric base composition (32.5% A, 17.6% C, 17.5% G and 32.4% T). It encodes a set of 113 unique genes (incl. 82 protein coding, 27 tRNA and 4 rRNA genes) with one of them (trnQ-UUG) being duplicated. Besides, 14 genes (atpF, ndhA, ndhB, petB, petD, rpl2, rpl16, rpoC1, rps12, rps16, trnA-UGC, trnG-UCC, trnI-GAU and trnK-UUU) possess a single intron, and another gene (ycf3) has a couple of introns. Phylogenetic analysis generally supported the current family-level taxonomy of the order Cupressales, and suggested that C. sinensis is closely related to the congeneric C. oliveri.
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