Complete chloroplast genomes of wild and cultivated Cryptomeria japonica var. sinensis

The tree Cryptomeria japonica var. sinensis is native to China and is an important forest species widely used for wood production. Here, we sequenced the complete chloroplast (cp) genomes of six wild and six cultivated accessions of this tree. The 12 cp genomes ranged from 131,379 to 131,528 bp. The GC content was 35.4%, similar to other gymnosperm species. The cp genomes lacked typical inverted repeat (IR) regions and encoded 118 genes. Most genes appeared in one copy and 17 genes contained introns. Two multi-copy genes (trnM-CAU × 3, trnQ-UUG × 2) were identified. And 59–61 simple sequence repeats (SSRs) were identified in the whole cp genomes, and most SSR loci consisted of A or T bases. Phylogenetic analysis indicated that wild and cultivated accessions were not clearly differentiated. Our results will provide useful information for the conservation and utilization of this variety. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1932592