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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Autores principales:	Dwi Wahyuni, Fifi Gus Dwiyanti, Rahadian Pratama, Muhammad Majiidu, Henti Hendalastuti Rachmat, Iskandar Zulkarnaen Siregar
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Dryobalanops aromatica</i> genome markers MinION sequencing Plant ecology QK900-989
Acceso en línea:	https://doaj.org/article/840aec2d38a14d508528050bcf4a55e5
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spelling	oai:doaj.org-article:840aec2d38a14d508528050bcf4a55e52021-11-25T17:38:10ZChloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study10.3390/f121115151999-4907https://doaj.org/article/840aec2d38a14d508528050bcf4a55e52021-11-01T00:00:00Zhttps://www.mdpi.com/1999-4907/12/11/1515https://doaj.org/toc/1999-4907Kapur (<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>Dwi WahyuniFifi Gus DwiyantiRahadian PratamaMuhammad MajiiduHenti Hendalastuti RachmatIskandar Zulkarnaen SiregarMDPI AGarticle<i>Dryobalanops aromatica</i>genomemarkersMinIONsequencingPlant ecologyQK900-989ENForests, Vol 12, Iss 1515, p 1515 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Dryobalanops aromatica</i> genome markers MinION sequencing Plant ecology QK900-989
spellingShingle	<i>Dryobalanops aromatica</i> genome markers MinION sequencing Plant ecology QK900-989 Dwi Wahyuni Fifi Gus Dwiyanti Rahadian Pratama Muhammad Majiidu Henti Hendalastuti Rachmat Iskandar Zulkarnaen Siregar Chloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study
description	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>
format	article
author	Dwi Wahyuni Fifi Gus Dwiyanti Rahadian Pratama Muhammad Majiidu Henti Hendalastuti Rachmat Iskandar Zulkarnaen Siregar
author_facet	Dwi Wahyuni Fifi Gus Dwiyanti Rahadian Pratama Muhammad Majiidu Henti Hendalastuti Rachmat Iskandar Zulkarnaen Siregar
author_sort	Dwi Wahyuni
title	Chloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study
title_short	Chloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study
title_full	Chloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study
title_fullStr	Chloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study
title_full_unstemmed	Chloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study
title_sort	chloroplast genome draft of <i>dryobalanops aromatica</i> generated using oxford nanopore technology and its potential application for phylogenetic study
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/840aec2d38a14d508528050bcf4a55e5
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Chloroplast Genome Draft of <i>Dryobalanops aromatica</i> Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study

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