| Summary: | The two varieties of mangosteen (<i>Garcinia mangostana</i> L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety that was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely, 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single-nucleotide polymorphism (SNP). Comparative analyses with other publicly available <i>Garcinia</i> plastomes, including <i>G. anomala</i>, <i>G. gummi-gutta</i>, <i>G. mangostana</i> var. Thailand, <i>G. oblongifolia</i>, <i>G. paucinervis</i>, and <i>G. pedunculata</i>, found that the gene content, gene order, and gene orientation were highly conserved among the <i>Garcinia</i> species. Phylogenomic analysis divided the six <i>Garcinia</i> plastomes into three groups, with the Mesta and Manggis varieties clustered closer to <i>G. anomala</i>, <i>G. gummi-gutta</i>, and <i>G. oblongifolia</i>, while the Thailand variety clustered with <i>G. pedunculata</i> in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the <i>Garcinia</i> genus to better understand their evolutionary history.
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