Abstract

Kapur (Dryobalanops aromatica) is an important dipterocarp species currently classified as vulnerable by the IUCN Red List Threatened Species. Science-based conservation and restoration efforts are needed, which can be supported by new genomic data generated from new technologies, including MinION Oxford Nanopore Technology (ONT). ONT allows affordable long-read DNA sequencing, but this technology is still rarely applied to native Indonesian forest trees. Therefore, this study aimed to generate whole genome datasets through ONT and use part of these data to construct the draft of the chloroplast genome and analyze the universal DNA barcode-based genetic relationships for D. aromatica. The method included DNA isolation, library preparation, sequencing, bioinformatics analysis, and phylogenetic tree construction. Results showed that the DNA sequencing of D. aromatica resulted in 1.55 Gb of long-read DNA sequences from which a partial chloroplast genome (148,856 bp) was successfully constructed. The genetic relationship was analyzed using two selected DNA barcodes (rbcL and matK), and its combination showed that species of the genus Dryobalanops had a close relationship as indicated by adjacent branches between species. The phylogenetic tree of matK and the combination of the matK and rbcL genes showed that D. aromatica was closely related to Dryobalanops rappa, whereas the rbcL gene showed group separation between D. aromatica and D. rappa. Therefore, a combination of the matK and rbcL genes is recommended for future use in the phylogenetic or phylogenomic analysis of D. aromatica.

Highlights

  • Dipterocarpaceae is an ecologically and economically important tree family widely used for timber and non-timber forest products

  • The sequence of D. aromatica obtained in this study is good for long-read sequencing

  • Chloroplast genome sequencing of D. aromatica was successfully carried out with the aid of D. turbinatus as reference for assembly, which resulted in 148,856 bp of D. aromatica chloroplast DNA (cpDNA)

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Summary

Introduction

Dipterocarpaceae is an ecologically and economically important tree family widely used for timber and non-timber forest products. The non-timber forest products of Dipterocarpaceae, such as resin, sap, and camphor, have high economical values [1]. Dryobalanops aromatica, an important species from this family that produces camphor, is native to Indonesia and is distributed in North Sumatra, Riau Islands, and Borneo (West Kalimantan, Sabah, and Sawarak) [2]. The camphor of D. aromatica contains a borneol compound [6] that can be utilized in the form of crystals and resins as a material for preparing perfumes and various medicine [7]. Borneol can dilute the blood in the human brain blood vessels and exert cerebral protective effects. A concerted effort is needed to increase the population of D. aromatica through tree regeneration, which could be aligned with ecosystem restoration programs promoted by the United Nations [13]

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