Transcriptome dataset of gall-rust infected Sengon (Falcataria falcata) seedlings using long-read PCR-cDNA sequencing.

Sengon (Falcataria falcata) is an economically important legume tree widely cultivated in community forests, especially in Java Island. However, attacks of gall rust disease by Uromycladium falcatariae is difficult to manage. Understanding sengon genes expressions when artificially infected with gall rust fungi can help unravel its resistance mechanisms. Total RNA was extracted from sengon seedlings samples inoculated with U. falcatariae fungi at 7, 21, and 35 days after inoculation (DAI) and from the control group. Total RNA sequencing was performed using the PCR-cDNA Sequencing protocol (SQK-PCB109) from Oxford Nanopore Technologies. The RNA-Seq obtained varies from 1.3 million to 1.9 million total reads. The assembled full-length transcript was constructed using the RATTLE program, resulting in 21,819 transcripts. The TransDecoder program used to define open reading frames (ORFs) generated 2,342 transcripts, of which 34.15% were 5'prime_partial, 8.15% were 3'prime_partial, 8.5% were internal, and 49.14% were complete. Analysis of differentially expressed genes (DEGs) between resistant and susceptible seedlings, found that 1,013 genes that were up-regulated and 1,130 genes that were down-regulated in the resistant lines. The transcriptome data discussed in this article have been deposited in the DDBJ with accession number DRA015681.

Chloroplast genome draft assembly of Falcataria moluccana using hybrid sequencing technology.

OBJECTIVES: Falcataria moluccana, known locally as Sengon, is a fast-growing legume tree that is commonly planted in community forests of Java Island, Indonesia. However, the plantations face attacks of Boktor stem borer (Xystrocera festiva) and gall-rust disease (Uromycladium falcatariae) as major threats to its productivity. To control those pest and disease, it is necessary to grow resistant sengon clones, which are developed through tree improvement program, of which needs genetic and genomic information. This dataset was created to construct draft of sengon chloroplast genome and to study the evolution of sengon based on matK and rbcL barcode genes. DATA DESCRIPTION: Genomic DNA was extracted from leaf samples of one individual healthy tree in a private plantation. The DNA was sequenced using Illumina Novaseq 6000 (Novogen AIT, Singapore) for short-reads data, and MinION of Nanopore following manufacture's protocols SQK-LSK110 for long-reads data. The 66,3 Gb short-reads and 12 Gb long-reads data were hybrid assembled and used to construct a 128.867 bp of F. moluccana chloroplast genome with a quadripartite structure, containing a pair of inverted repeats, a large single-copy and a small single-copy region. Phylogenetic tree constructed using matK and rbcL showed monophyletic origin of F. moluccana and other legume trees.

Effects of two contrasting potting media on the leaf development index, photosynthetic rate, and metabolite profile of camphor (Dryobalanops aromatica) seedlings.

Camphor (Dryobalanops aromatica C. F. Gaertn.) is a vulnerable tropical tree species that has been exploited for its timber as well as its resin, which is used for medicinal uses. The use of camphor in Indonesia is limited owing to the decreasing size of the species' population in its native habitat. Therefore, replanting programs have been encouraged for this species owing to its adaptability to mineral soils and shallow peatlands. However, experimental evidence of the effect of different growing media on morphology, physiology, and biochemistry is very limited, which is needed to evaluate the replanting program's success. Therefore, this study aimed to determine the responses of camphor (D. aromatica) seedlings grown in two different types of potting media i.e. mineral and peat, for 8 weeks of planting. In particular, the types of bioactive compounds produced in camphor leaves and their levels were assessed by analyzing their metabolite profiles. Leaf growth was evaluated morphologically using the plastochron index, while photosynthetic rates were measured with LI-6800 Portable Photosynthesis System. Metabolites were identified by using liquid chromatography-tandem mass spectrometry. The percentage of LPI of 5 or more was lower in the peat medium at 8% than in the mineral medium at 12%. The photosynthetic rate of camphor seedlings was 1-9 µmol CO2 m⁻2 s⁻1, with a higher rate in the peat medium than in the mineral medium, suggesting that the peat medium was better for growth. Lastly, the metabolomic analysis in the leaf extract revealed the presence of 21 metabolites, which were dominated by flavonoid compounds.

De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media.

OBJECTIVES: Efforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socio-economic factors and ecological dynamics attributed to lack of knowledge on the adaptive mechanisms of potential tree species such as Kapur (Dryobalanops aromatica C.F.Gaertn Syn. Dryobalanops sumatrensis J.F. Gmelin A.J.G.H Kostermans). This species is a multi-purpose tree that, commonly grows in mineral soils, but also in peat swamp as previously reported, which raised a fundamental question regarding the molecular mechanism of this adaptation. Therefore, a dataset was created aiming to detect candidates of adaptive genes in D. aromatica seedlings, cultivated in two contrasting potting media, namely mineral soil and peat media, based on RNA Sequencing Transcriptome Analysis. DATA DESCRIPTION: The RNA transcriptome data of D. aromatica's seedlings derived from young leaves of three one-year-old seedlings, raised in each dry mineral soil media and peat media, were generated by using Illumina HiSeq 4000 platform in NovogenAIT, Singapore. The acquired data, as the first transcriptome dataset for D. aromatica, is of a great importance in understanding molecular mechanism and responses of the involved genes of D. aromatica to the contrasting, growing potting media conditions that could also be useful to generate molecular markers.

Datasets for genome assembly of six underutilized Indonesian fruits.

Indonesia has a high genetic diversity of tropical fruits. However, studies on genomics are still very limited. In this data article, six underutilized Indonesian fruits were analyzed for the estimated genome size and partial data of genome assembly including Artocarpus nangkadak (Artocarpus heterophyllus x Artocarpus integer), Salacca sumatrana, Flacourtia inermis, Lansium domesticum, Pometia pinnata, and Syzygium samarangense. These genome data may be used to construct molecular markers for plant systematics and breeding program of these species. Our genome data were sequenced paired-end libraries using BGISeq-500 and generated approximately 5 Gb of bases per species. The raw sequences have been deposited in the DNA Data Bank of Japan (DDBJ) under the DDBJ BioProject umbrella with accession number PRJDB7265 and to the DDBJ Read Archive for each species following Artocarpus nangkadak (DRA007398), Salacca sumatrana (DRA007394), Flacourtia inermis (DRA007395), Lansium domesticum (DRA007393), Pometia pinnata (DRA007396), Syzygium samarangense (DRA007397).