Long-read sequencing of Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree endemic to Nusakambangan Island, Indonesia: Resource for chloroplast genome, phylogenetic, and biosynthetic gene clusters studies

<ns3:p> Abstract* Background Long-read sequencing of <ns3:italic>Dipterocarpus littoralis</ns3:italic> (Blume) Kurz. (Dipterocarpaceae) is essential for generating important genetic data to support biodiversity conservation, taxonomy resolution, and the sustainable management of this critically endangered species. However, this type of study remains largely unaddressed. Therefore, this study aims to generate genetic information for <ns3:italic>D. littoralis,</ns3:italic> including the characterization of chloroplast genome (cp genome) sequences, the construction of a phylogenetic tree, and the identification of the biosynthetic gene cluster (BGC). Methods The genomic DNA extracted from <ns3:italic>D. littoralis</ns3:italic> leaf tissue was sequenced using the MinION Oxford Nanopore Technologies. The cp genome was reconstructed from an assembly with GetOrganelle, and the resulting genome was annotated with GeSeq. A maximum-likelihood (ML) phylogenetic tree was inferred using IQ-TREE2, while biosynthetic gene clusters were annotated and classified through BRAKER2 and PlantiSMASH. Conclusions This study revealed that the length of the chloroplast genome was 153,775 base pairs (bp) with a GC content of 37%, and it consists of four subregions: a large single-copy (LSC) region of 85,079 bp, a small single-copy (SSC) region of 20,232 bp, and two inverted repeats (IR) regions (IRA 24,232 bp; IRB 24,232 bp). The cp genome of D <ns3:italic>. littoralis</ns3:italic> encodes 111 genes, including 78 protein-coding genes, 29 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The phylogenetic tree derived from the cp genome indicated that <ns3:italic>D. littoralis</ns3:italic> formed a monophyletic group alongside other species within the same genus. Furthermore, a total of 77 genes coding for BGCs were identified, comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters. The findings of this study may enhance molecular identification, clarify phylogenetic relationships, and support comparative genomics within the genus <ns3:italic>Dipterocarpus,</ns3:italic> as well as facilitate the discovery of potential natural products from <ns3:italic>D. littoralis.</ns3:italic> </ns3:p>