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Peer-reviewedCC BY-NCData in brief

Chloroplast genome assembly of lagan bras (Dipterocarpus cinereus Slooten) using Oxford Nanopore MinION long-read sequencing dataset.

  • R Amelia Siti Ina Mardiah1
  • Rahadian Pratama2
  • Irsyad Kamal1
  • Muhammad Majiidu1
  • Fifi Gus Dwiyanti1
  • Henti Hendalastuti Rachmat3
  • Kesuma Wijaya4
  • Iskandar Z Siregar1
4 affiliations
  1. 1Department of Silviculture, Faculty of Forestry and Environment, Institut Pertanian Bogor (IPB University), Bogor, West Java, 16680, Indonesia.
  2. 2Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Institut Pertanian Bogor (IPB University), Bogor, West Java, 16680, Indonesia.
  3. 3Research Center for Ecology, National Research and Innovation Agency (BRIN), Cibinong, West Java, 16911, Indonesia.
  4. 4Protected Forest Management (KPHL) Unit II Batam, Riau Islands, 29425, Indonesia.
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Abstract

Dipterocarpus cinereus Slooten is a tree species endemic to Mursala Island, North Sumatra, that was once declared extinct in the wild and is currently classified as critically endangered. To support future conservation, genomic data are crucial as a fundamental basis for modern conservation. However, genomic data for this species have not been characterized. This study presents a chloroplast genome (cp genome) dataset for D. cinereus obtained using Oxford Nanopore MinION long-read sequencing. Genomic DNA was extracted from leaf tissue using the modified CTAB method, followed by sequencing, assembly, and gene annotation. The annotated cp genome was used to construct the phylogenetic tree. The assembled chloroplast genome dataset is 154,987 bp in length with a GC content of 36.89%. It exhibits a typical quadripartite structure, consisting of a large single-copy (LSC) region of 85,979 bp, a small single-copy (SSC) region of 20,450 bp, and a pair of inverted repeat (IR) regions, each 24,279 bp long. The annotated cp genome of D. cinereus contains 136 genes, comprising 88 protein-coding genes, 36 tRNA genes, and 12 rRNA genes, of which 17 genes contain introns (13 with a single intron and 4 with two introns). The phylogenetic tree revealed that D. cinereus is closely related to Dipterocarpus alatus. This finding provides an initial genomic dataset and baseline information as a reference for further genetic studies of D. cinereus and helps fill a gap in dipterocarp data to support its conservation initiatives.

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Cite

BibTeXRIS
BibTeX
@article{mardiah2026chloroplast,
  title = {{Chloroplast genome assembly of lagan bras (Dipterocarpus cinereus Slooten) using Oxford Nanopore MinION long-read sequencing dataset.}},
  author = {R Amelia Siti Ina Mardiah and Rahadian Pratama and Irsyad Kamal and Muhammad Majiidu and Fifi Gus Dwiyanti and Henti Hendalastuti Rachmat and Kesuma Wijaya and Iskandar Z Siregar},
  journal = {Data in brief},
  year = {2026},
  month = aug,
  doi = {10.1016/j.dib.2026.113354},
  url = {https://europepmc.org/article/MED/42927273},
  note = {CC BY-NC},
}
RIS
TY  - JOUR
TI  - Chloroplast genome assembly of lagan bras (Dipterocarpus cinereus Slooten) using Oxford Nanopore MinION long-read sequencing dataset.
AU  - R Amelia Siti Ina Mardiah
AU  - Rahadian Pratama
AU  - Irsyad Kamal
AU  - Muhammad Majiidu
AU  - Fifi Gus Dwiyanti
AU  - Henti Hendalastuti Rachmat
AU  - Kesuma Wijaya
AU  - Iskandar Z Siregar
PY  - 2026
DA  - 2026/08/01
JO  - Data in brief
DO  - 10.1016/j.dib.2026.113354
UR  - https://europepmc.org/article/MED/42927273
AB  - Dipterocarpus cinereus Slooten is a tree species endemic to Mursala Island, North Sumatra, that was once declared extinct in the wild and is currently classified as critically endangered. To support future conservation, genomic data are crucial as a fundamental basis for modern conservation. However, genomic data for this species have not been characterized. This study presents a chloroplast genome (cp genome) dataset for D. cinereus obtained using Oxford Nanopore MinION long-read sequencing. Genomic DNA was extracted from leaf tissue using the modified CTAB method, followed by sequencing, assembly, and gene annotation. The annotated cp genome was used to construct the phylogenetic tree. The assembled chloroplast genome dataset is 154,987 bp in length with a GC content of 36.89%. It exhibits a typical quadripartite structure, consisting of a large single-copy (LSC) region of 85,979 bp, a small single-copy (SSC) region of 20,450 bp, and a pair of inverted repeat (IR) regions, each 24,279 bp long. The annotated cp genome of D. cinereus contains 136 genes, comprising 88 protein-coding genes, 36 tRNA genes, and 12 rRNA genes, of which 17 genes contain introns (13 with a single intron and 4 with two introns). The phylogenetic tree revealed that D. cinereus is closely related to Dipterocarpus alatus. This finding provides an initial genomic dataset and baseline information as a reference for further genetic studies of D. cinereus and helps fill a gap in dipterocarp data to support its conservation initiatives.
SN  - 2352-3409
ER  -