Pometia pinnata (J.R.Forst. & G.Forst.) as urban tree species: A chloroplast genome and phylogenetic studies

Abstract Pometia pinnata (J.R.Forst. & G.Forst.) is a native Indonesian forest plant increasingly used in urban landscaping. It produces both edible fruits and valuable timber. As with other tree species, enhancing its genetic quality is essential to maximize the utilization of this promising species. However, the information on genetic and genomic data is still lacking, including the analysis of the genetic relationship of this species. This study aims to generate the chloroplast genome of P. pinnata , identify the most suitable DNA marker, and evaluate the relationship within the Sapindaceae family using long-read sequence data generated by MinION Oxford Nanopore Technologies (ONT). The study involved several steps: DNA extraction, DNA quality and quantity tests, DNA sequencing, assembly of the chloroplast genome, and reconstruction of a phylogenetic tree using three markers, i.e., rbcL, matK , and rbcL+matK combinations. The DNA sequencing yielded 449,068 reads, with 2,856 reads after mapping, an N50 read length of 4,188 bp, a total base of 1,135,927 Mb, and a chloroplast genome of 160,372 bp. These results indicated that the DNA isolated from P. pinnata is good quality. Phylogenetic tree analysis revealed that the combination of rbcL and matK markers effectively differentiates groups within the Sapindaceae family, revealing P. pinnata as closely related to Nephelium lappaceum, Nephelium mutabile, Sapindus mukorossi, Dimocarpus longan, Bligia sapida, Litchi chinensis, Acer yangbiense , and Lepisanthes alata . This study enriches genetic studies on P. pinnata , establishing a foundation for species identification based on the rbcL and matK marker and supporting future tree improvement programs.