Chloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study
Kapur (<i>Dryobalanops aromatica</i>) 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,...
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| Main Authors: | , , , , , |
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| Format: | article |
| Language: | EN |
| Published: |
MDPI AG
2021
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| Subjects: | |
| Online Access: | https://doaj.org/article/840aec2d38a14d508528050bcf4a55e5 |
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| Summary: | Kapur (<i>Dryobalanops aromatica</i>) 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 <i>D. aromatica</i>. The method included DNA isolation, library preparation, sequencing, bioinformatics analysis, and phylogenetic tree construction. Results showed that the DNA sequencing of <i>D. aromatica</i> 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 (<i>rbc</i>L and <i>mat</i>K), and its combination showed that species of the genus <i>Dryobalanops</i> had a close relationship as indicated by adjacent branches between species. The phylogenetic tree of <i>matK</i> and the combination of the <i>mat</i>K and <i>rbc</i>L genes showed that <i>D. aromatica</i> was closely related to <i>Dryobalanops rappa</i>, whereas the <i>rbc</i>L gene showed group separation between <i>D. aromatica</i> and <i>D. rappa</i>. Therefore, a combination of the <i>mat</i>K and <i>rbc</i>L genes is recommended for future use in the phylogenetic or phylogenomic analysis of <i>D. aromatica.</i> |
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