| Summary: | <i>Fokienia hodginsii</i> (Dunn) Henry et Thomas is a relic gymnosperm with broad application value. It is a fit candidate when choosing species for the construction of artificial forests. We determined the complete chloroplast genome sequence of <i>F. hodginsii</i>, which is 129,534 bp in length and encodes 83 protein genes, 33 transfer RNA (tRNA) genes, as well as four ribosomal RNA genes. The GC content of the complete sequence and protein coding regions is 34.8% and 36.2%, respectively. We identified 11 tandem repeats, 11 forward repeats, and three palindromic repeats and classified them by size. Following our microsatellite analysis, a total number of 73 simple sequence repeats were detected, preferentially within the intergenic space. Being a member of Cupressophyta, <i>F. hodginsii</i> owns several common characters; the <i>trnR-CCG</i> gene has been deleted, while the <i>trnI-CAU</i> and <i>trnQ-UUG</i> genes have been duplicated. Moreover, the <i>accD</i> gene, which encodes acetyl-CoA carboxylase, contains 771 codons in <i>F. hodginsii</i>, similar to <i>Cryptomeria japonica</i> (L. F.) D. Don, further supporting the diversity of <i>accD</i> and its size expansion in Cupressophyta. Concerning the loss of inverted repeat (IR) regions, the 86-bp sequence with the duplicated <i>trnI-CAU</i> gene is inferred to be the footprint of IR contraction. Phylogenetically, <i>F. hodginsii</i> is placed as a sister taxon to <i>Chamaecyparis hodginsii</i> (Dunn) Rushforth. This work offers meaningful guidance as well as reference value to the breeding research and improvement of <i>F. hodginsii</i>. Moreover, it gives us a better understanding of the genomic structure and evolutionary history of gymnosperms, especially coniferales.
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