Characterization of the chloroplast genome sequence of Calophyllum inophyllum, a bioenergy tree species, using Oxford Nanopore Technologies

Abstract

Abstract Calophyllum inophyllum is a forest tree species that offers significant renewable energy benefits. However, the genetic information of these bioenergy tree species for the study of tree improvement is still limited. This study aimed to assemble the draft chloroplast genome using MinION Oxford Nanopore Technologies (ONT) and analyze the genetic relationship based on molecular markers for C. inophyllum. The study involved several steps: DNA extraction and isolation using the CTAB method, DNA library preparation, DNA sequencing using MinION Oxford Nanopore Technologies (ONT), and phylogenetic analysis based on selected DNA markers. The results showed that 115.1 Mb of high-quality DNA was successfully generated using ONT long-read sequencing, and 114.708 bp was annotated into partial genome chloroplast. The genetic relationship analysis using two selected DNA barcodes, namely rbcL and accD showed that the accD gene is more recommended for constructing a phylogenetic tree for the genus Calophyllum than the rbcL gene as it has a high bootstrap value (93%). Furthermore, the accD gene can also be considered a potential marker for further genetic analysis of C. inophyllum.