Understanding Diospyros rumphii Bakh from North Sulawesi through Long-read sequences analysis using MinION Oxford Nanopore Technologies

Abstract

Diospyros rumphii (Ebony) is a high-value timber species native to Indonesia, which is listed as a Data Deficient species by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Therefore, additional data to enrich knowledge on the distribution, ecology, and genetics of this species is urgently needed. Furthermore, this study aimed to generate whole-genome sequencing data, including the low-coverage data for D. rumphii using MinION Oxford Nanopore Technologies (ONT). The sequence data generated from leaf and cambium genomic DNA was assembled to result in a draft of the chloroplast genome and constructed the phylogenetic tree based on partial nucleotide sequences of the rbcL gene. The results showed that DNA sequencing of D. rumphii generated a 3.25 Gb of long-read sequences data and a draft of a partial chloroplast genome with a size of 150,578 bp. Genetic relationship analysis using the rbcL gene showed that D. rumphii was positioned in one clade with Diospyros oblonga, which has a bootstrap value of 87% suggesting that the rbcL gene can be considered as recommended molecular marker for genetic analysis of D. rumphii in the future.

Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study

“…One of the long-read sequence technologies is MinION Oxford Nanopore Technologies (https:// nanoporetech.com) (Mikheyev & Tin, 2014). This technology has successfully generated genetic information in several tree species such as Diospyros celebica (Siregar et al, 2021), Diospyros rumphii (Salindeho et al, 2023), and Dryobalanops aromatica (Wahyuni et al, 2021). In general, this technology can be applied to balsa trees (Ochroma pyramidale).…”