Abstract
<ns3:p> Abstract* Background Long-read sequencing of <ns3:italic>Dipterocarpus littoralis</ns3:italic> (Blume) Kurz. (Dipterocarpaceae) is essential for generating important genetic data to support biodiversity conservation, taxonomy resolution, and the sustainable management of this critically endangered species. However, this type of study remains largely unaddressed. Therefore, this study aims to generate genetic information for <ns3:italic>D. littoralis,</ns3:italic> including the characterization of chloroplast genome (cp genome) sequences, the construction of a phylogenetic tree, and the identification of the biosynthetic gene cluster (BGC). Methods The genomic DNA extracted from <ns3:italic>D. littoralis</ns3:italic> leaf tissue was sequenced using the MinION Oxford Nanopore Technologies. The cp genome was reconstructed from an assembly with GetOrganelle, and the resulting genome was annotated with GeSeq. A maximum-likelihood (ML) phylogenetic tree was inferred using IQ-TREE2, while biosynthetic gene clusters were annotated and classified through BRAKER2 and PlantiSMASH. Conclusions This study revealed that the length of the chloroplast genome was 153,775 base pairs (bp) with a GC content of 37%, and it consists of four subregions: a large single-copy (LSC) region of 85,079 bp, a small single-copy (SSC) region of 20,232 bp, and two inverted repeats (IR) regions (IRA 24,232 bp; IRB 24,232 bp). The cp genome of D <ns3:italic>. littoralis</ns3:italic> encodes 111 genes, including 78 protein-coding genes, 29 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The phylogenetic tree derived from the cp genome indicated that <ns3:italic>D. littoralis</ns3:italic> formed a monophyletic group alongside other species within the same genus. Furthermore, a total of 77 genes coding for BGCs were identified, comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters. The findings of this study may enhance molecular identification, clarify phylogenetic relationships, and support comparative genomics within the genus <ns3:italic>Dipterocarpus,</ns3:italic> as well as facilitate the discovery of potential natural products from <ns3:italic>D. littoralis.</ns3:italic> </ns3:p>
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Claims 14
Claim · model-written summary
The chloroplast genome of Dipterocarpus littoralis is 153,775 bp long with a GC content of 37%.
- Taxon
- Dipterocarpus littoralis
Dipterocarpus littoralist0 - Outcome
- length of the chloroplast genomee1
- Value
- 153,775 base pairs (bp)e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e1“the length of the chloroplast genome was 153,775 base pairs (bp) with a GC content of 37%”
Claim · model-written summary
The chloroplast genome of Dipterocarpus littoralis encodes 111 genes.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- genese2
- Value
- 111 genese2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e2“encodes 111 genes, including 78 protein-coding genes, 29 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes”
Claim · model-written summary
The phylogenetic tree derived from the chloroplast genome places Dipterocarpus littoralis in a monophyletic group with other species of its genus.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- monophyletic groupe3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e3“formed a monophyletic group alongside other species within the same genus”
Claim · model-written summary
A total of 77 genes coding for biosynthetic gene clusters were identified in Dipterocarpus littoralis.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- genes coding for BGCse4
- Value
- 77e4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e4“a total of 77 genes coding for BGCs were identified”
Claim · model-written summary
Dipterocarpus littoralis has 44 terpene clusters.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- terpene clusterse5
- Value
- 44e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e5“comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters”
Claim · model-written summary
Dipterocarpus littoralis has 6 alkaloid clusters.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- alkaloid clusterse5
- Value
- 6e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e5“comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters”
Claim · model-written summary
Dipterocarpus littoralis has 1 lignan cluster.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- lignan clustere5
- Value
- 1e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e5“comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters”
Claim · model-written summary
Dipterocarpus littoralis has 4 saccharide clusters.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- saccharide clusterse5
- Value
- 4e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e5“comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters”
Claim · model-written summary
Dipterocarpus littoralis has 1 Saccharide-Polyketide cluster.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- Saccharide-Polyketide clustere5
- Value
- 1e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e5“comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters”
Claim · model-written summary
Dipterocarpus littoralis has 1 saccharide-terpene cluster.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- saccharide-terpene clustere5
- Value
- 1e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e5“comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters”
Claim · model-written summary
Dipterocarpus littoralis has 20 putative biosynthetic gene clusters.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- putative clusterse5
- Value
- 20e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e5“comprising 44 terpene clusters, 6 alkaloid clusters, 1 lignan cluster, 4 saccharide clusters, 1 Saccharide-Polyketide cluster, 1 saccharide-terpene cluster, and 20 putative clusters”
Claim · model-written summary
The large single-copy region of the chloroplast genome of Dipterocarpus littoralis is 85,079 bp.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- large single-copy (LSC) regione6
- Value
- 85,079 bpe6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e6“a large single-copy (LSC) region of 85,079 bp”
Claim · model-written summary
The small single-copy region of the chloroplast genome of Dipterocarpus littoralis is 20,232 bp.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- small single-copy (SSC) regione7
- Value
- 20,232 bpe7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e7“a small single-copy (SSC) region of 20,232 bp”
Claim · model-written summary
The inverted repeat regions of the chloroplast genome of Dipterocarpus littoralis are 24,232 bp each.
- Taxon
- Dipterocarpus littoralisDipterocarpus littoralist0
- Outcome
- inverted repeats (IR) regionse0
- Value
- 24,232 bpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Dipterocarpus littoralis (Dipterocarpaceae), a critically endangered tree”
e0“two inverted repeats (IR) regions (IRA 24,232 bp; IRB 24,232 bp)”