Vernicia montana and Vernicia fordii are considered to have great economic importance in terms of having industrial oil and ornamental greening properties. However, wild resources of Vernicia trees have been reduced because of their ecology and habitat destruction. To better understand the genetic differences between V. montana and V. fordii, collecting more molecular data was necessary for further analysis. Here, we sequenced, assembled, and annotated the complete chloroplast (CP) genome of two tung trees based on the genome skimming approach. The whole CP genomes of V. montana and V. fordii were 160,906 bp and 161,494 bp in length, respectively, both of which comprised 135 genes, including 81 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 21 duplicated genes. The overall GC contents in V. montana and V. fordii CP genome were 36.13% and 36.03%, respectively. By comparing the CP genome sequences between V. montana and V. fordii, a total of 2,280 SNPs and 257 indels were identified. Among them, 1,807 SNPs and 153 indels were within the large single copy region, while 93 SNPs and 74 indels were within the small single copy region. The phylogenic analysis showed that V. montana was closely related to V. fordii and is considered a sister group. Hence, this study will be useful in investigating the conservation genetics and potential breeding applications of this oil shrub.
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