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

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 gene...

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Bibliographic Details
Published in:IOP conference series. Earth and environmental science 2023-06, Vol.1188 (1), p.12035
Main Authors: Salindeho, R A, Dwiyanti, F G, Pratama, R, Matra, D D, Majiidu, M, Fatlan, K F, Siregar, I Z
Format: Article
Language:English
Subjects:
Chloroplasts
Deoxyribonucleic acid
Diospyros
DNA
DNA sequencing
Genetic analysis
Genetic relationship
Genetics
Genomes
Geographical distribution
Indigenous species
Nature conservation
Nucleotide sequence
Nucleotides
Phylogeny
RbcL gene
Threatened species
Whole genome sequencing
Wildlife conservation
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Summary: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 rbc L 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 rbc L gene showed that D. rumphii was positioned in one clade with Diospyros oblonga , which has a bootstrap value of 87% suggesting that the rbc L gene can be considered as recommended molecular marker for genetic analysis of D. rumphii in the future.
ISSN:1755-1307
1755-1315
DOI:10.1088/1755-1315/1188/1/012035