The complete chloroplast genome of Garcinia binucao (Blanco) Choisy, an indigenous fruit from the Philippines

Abstract

Garcinia binucao (Blanco) Choisy is an indigenous species endemic to the Philippines. Its fruit is traditionally used as a souring agent in local cuisine and has been reported to possess nutritional and medicinal properties. Despite its ethnobotanical significance and promising bioactive properties, the species remains underutilized. To date, no genomic resources have been published for G. binucao, limiting its application in food systems, genetic studies, and conservation programs. This study reports the first complete chloroplast genome of G. binucao from an accession conserved at the Institute of Plant Breeding, University of the Philippines Los Banos. The assembled plastome is circular with a length of 156,570 base pairs (bp). It displays the typical quadripartite structure of most angiosperms, consisting of a large single-copy (LSC) region (85,357 bp), a small single-copy (SSC) region (17,129 bp), and a pair of inverted repeats (IR), each 27,042 bp in size. A total of 128 genes were annotated, including 83 protein-coding genes, 37 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs), consistent with the majority of Garcinia species. Of the protein-coding genes, 45 are involved in photosynthesis, 28 genes for self-replication, five genes with conserved open reading frames, and five genes are associated with other functions. The GC content was 36.2%. Leucine (10.6%) was the most abundant amino acid, with a codon usage bias toward UUA. Additionally, 98 simple sequence repeats (SSRs) were detected, 88.78% consisting of A/T motifs. Phylogenomic analysis based on assembled plastome and publicly available cpDNA sequences of 17 other species in the order Malpighiales revealed that G. indica is the closest relative of G. binucao. These findings provide a framework for future research on the species, including its conservation and potential use as a genetic resource.