Myristica teysmannii Miq. is an endemic and endangered plant, with narrow distribution to the southern part of East Java, Indonesia. This study was aimed to determine the complete chloroplast genome sequence of M. teysmannii using the Illumina NextSeq 500 platform and reconstruct the phylogenetic relationship with selected Magnoliids taxa. Results showed that the chloroplast genome of M. teysmannii is 155,975 bp in size, with a large single copy region (87,187 bp), a small single copy region (20,656 bp), and two inverted repeat regions (24,066 bp each). The chloroplast genome consists of 126 genes, including 85 protein-coding genes and eight ribosomal RNA and 35 transfer RNA genes. Phylogenetic analysis showed that M. teysmannii is placed in the Myristica clade along with M. yunnanensis, M. fatua, M. fragrans, and M. argentea. This phylogeny may be used as a foundation for further studies of this endemic and endangered plant species. Additionally, the position of Eusyderoxylon zwageri in the Endocomia clade instead of Lauraceae is surprising; further studies need to be conducted to confirm this finding.
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