Transcriptome dataset from Solanum lycopersicum L. cv. Micro-Tom; wild type and two mutants of INDOLE-ACETIC-ACID (SlIAA9) using long-reads sequencing oxford nanopore technologies.

OBJECTIVE: Tomatoes are the most widely consumed fruit vegetable and are relatively easy to cultivate. However, an increase in temperature causes some plants to respond with a decrease in fruit production. So, it is necessary to develop plants resistant to extreme temperature changes. The tomato cv. Micro-Tom has genetic variations in the gene of INDOLE-ACETIC-ACID, namely SlIAA9-3 and SlIAA9-5. However, the genetic information regarding the full-length transcript of the gene from this type of tomato plant is unknown. Therefore, this study aimed to determine the full-length transcript of the genes of these three types of tomatoes using long-reads sequencing technology from Oxford Nanopore. DATA DESCRIPTION: The total RNA from three types of Micro-Tom was isolated with the RNeasy PowerPlant Kit. Then, the RNA sequencing process used PCR-cDNA Barcoding kit - SQK-PCB109 and continued with the processing of raw reads based on the protocol from microbepore protocol ( https://github.com/felixgrunberger/microbepore ). The resulting raw reads were 578 374, 409 905, and 851 948 for wildtype, iaa9-3, and iaa9-5, respectively. After obtaining cleaned reads, each sample was mapped to the tomato reference genome (S. lycopersicum ITAG4.0) with the Minimap2 program. In particular, 965 genes were expressed only in the iaa9-3 mutant, and 2332 genes were expressed only in the iaa9-5 mutant. Whereas in the wild type, 1536 genes are specifically expressed. In cluster analysis using the heatmap analysis, separate groups were obtained between the wild type and the two mutants. This proves an overall difference in transcript levels between the wild type and the mutants.

Agro-Physiological Traits of Kaffir Lime in Response to Pruning and Nitrogen Fertilizer under Mild Shading.

Mild shading has been reported to increase leaf production in kaffir lime (Citrus hystrix) through the improvement of agro-physiological variables, such as growth, photosynthesis, and water-use efficiency; however, there is still a knowledge gap concerning its growth and yield after experiencing severe pruning in harvest season. Additionally, a specific nitrogen (N) recommendation for leaf-oriented kaffir lime is still unavailable due to its lesser popularity compared to fruit-oriented citrus. The present study determined the best pruning level and N dose based on agronomy and the physiology of kaffir lime under mild shading. Nine-month-old kaffir lime seedlings grafted to rangpur lime (C. limonia) were arranged in a split-plot design, i.e., N dose as a main plot and pruning as a subplot. Comparative analysis resulted in 20% higher growth and a 22% higher yield in the high-pruned plants by leaving 30 cm of main stem above the ground rather than short ones with a 10 cm main stem. Both correlation and regression analysis strongly highlighted the importance of N for leaf numbers. Plants treated with 0 and 10 g N plant-1 experienced severe leaf chlorosis due to N deficiency, while those treated with 20 and 40 g N plant-1 showed N sufficiency; thus, the efficient recommendation for kaffir lime leaf production is 20 g N plant-1.

Dataset from de novo transcriptome assembly of Myristica fatua leaves using MinION nanopore sequencer.

Myristica fatua is a tropical fruit tree species originating from Indonesia. Very few genomic resources are available for the species. We developed a full-length transcriptome assembly using long-read sequencing (MinION Nanopore technology) and produced 4.3 million reads (3.5 G of bases). The assembled full-length transcript was constructed using the RATTLE program and assembled 21,098 transcripts. The transcript ranged from 201 - 14,174 bp, and N50 was 2,017 bp. The transcripts were annotated with the UNIPROT database using BlastX. The functional annotation was performed using Blast2go software. The 8,445 microsatellite motif-containing contigs were identified. The raw reads are deposited in the ENA (European Nucleotide Archive) with ENA experiment accession number ERX6798613.

The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm.

Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi's genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.

Relationship among Agroclimatic Variables, Soil and Leaves Nutrient Status with the Yield and Main Composition of Kaffir Lime (Citrus hystrix DC) Leaves Essential Oil.

Previous studies revealed the impact growing location has on the quantity and quality of essential oils derived from numerous Citrus spp., except on the kaffir lime. This study aims to analyze the relationship shared by agroclimatic variables and soil-plant nutrient status to kaffir lime leaves essential oil yield and main composition. The experiment was conducted between February and April 2019 in four growing locations, namely Bogor (6°36'36″ S, 106°46'47″ E), West Bandung (6°48'12″ S, 107°39'16″ E), Pasuruan (7°45'5″ S, 112°40'6″ E) and Tulungagung (8°6'27″ S, 112°0'35″ E). The highest essential oil yield was obtained from Bogor (1.5%), while the lowest one was from Tulungagung (0.78%). The yield was positively and significantly correlated with the rainfall, soil organic carbon, soil pH, and macronutrient levels, i.e., nitrogen, phosphorus, and magnesium. Citronellal, the major component in metabolites' profile of kaffir lime leaves essential oils, was significantly affected by the growing location. The absolute content of citronellal was positively and significantly correlated with the actual soil pH and leaf Ca content; furthermore, it negatively correlated with the leaf content of Fe, Mn, Zn, Cu. Pearson correlation analysis also showed (i) a negative significant correlation between the relative percentage of citronellol and annual rainfall intensity; (ii) a negative significant correlation between altitude and relative percentage of caryophyllene, and (iii) a positive significant correlation between the relative percentage of linalool and leaf K content.

Metabolomics dataset of underutilized Indonesian fruits; rambai (Baccaurea motleyana), nangkadak (Artocarpus nangkadak), rambutan (Nephelium lappaceum) and Sidempuan salak (Salacca sumatrana) using GCMS and LCMS.

The information of secondary metabolite compound from underutilized Indonesian fruits are still limited including rambai (Baccaurea motleyana Müll.Arg.), nangkadak (Artocarpus nangkadak or A. heterophyllus x A. integer), rambutan (Nephelium lappaceum L.) and Sidempuan salak (Salacca sumatrana Becc.). To identify the secondary metabolite, we used GC-MS (gas chromatography-mass spectrometry) and LC-MS (liquid chromatography-mass spectrometry) analyses. The accessions/varieties numbers used in this analysis including two accession for rambai, three accessions for nangkadak, four varieties for rambutan and three accessions for Sidempuan salak. All sample were collected from edible part such arilode/carpel and also rind for only rambutan. Based on, spectral data showed common and specific secondary metabolite compounds in each commodity. Preliminary GCMS analysis from the dataset obtained specific secondary metabolites contained in rambai; Decanoic acid, 1-Decene, Methyl salicylate and Stearyl alcohol, nangkadak; ß-Cyclocitral, 2-Furanmethanol and Linoleic acid, rambutan; Citraconic anhydride, 3,5-Dideuteropyridine-4-carboxylic acid, Isobutyl formate and n-Methyl-D3-Aziridine, and Sidempuan salak; 5-Formyl-2-furfurylmethanoate, 2-Methoxy-4-vinylphenol and Tiglic acid.

Comparative transcriptome analysis of translucent flesh disorder in mangosteen (Garcinia mangostana L.) fruits in response to different water regimes.

Translucent flash disorder (TFD) is one of the important physiological disorders in mangosteen (Garcinia mangostana L.). TFD has symptoms such as flesh arils that become firm and appear transparent similar to watercore in apple or pear. Information on the changes of gene expression in TFD-affected tissues remain limited, and investigations into the effects of different water regimes still need to be undertaken. Through an RNA sequencing approach using the Ion Proton, 183,274 contigs with length ranging from 173-13,035 bp were constructed by de novo assembly. Functional annotation was analyzed using various public databases such as non-redundant protein NCBI, SwissProt, and Gene Ontology, and KEGG pathway. Our studies compared different water regimes to incidence and differentially expressed genes of TFD-like physiological disorders. From the differentially expressed gene (DEG) between normal air and TFD-affected aril, we identified DEG-related TFD events, which 6228 DEGs in the control condition and 3327 DEGs in under water stress treatment condition remained, and confirmed these with RT-qPCR, including sucrose synthase (SUSY), endoglucanase (GUN), xyloglucan endotransglucosylase/hydrolase (XTH), and polygalacturonase (PG) showed statistically significant. In addition, transcription factors also indicated changes in MYB, NAC and WRKY between tissues and different water regimes.

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).

Dataset from de novo transcriptome assembly of Nephelium lappaceum aril.

Nephelium lappaceum (Rambutan), is one of tropical fruit in which - cultivated widely in Indonesia and has good taste and aroma. However, the transcriptomic study of rambutan has limited. In this study, we performed transcriptome assembly using paired-end Illumina technology. The assembled transcriptome was constructed using Trinity and after filtering and removal sequences redundancy produced 36,303 contigs. The contig ranged 201-11,770 bp and N50 has 1327 bp. The contig was annotated with several databases such as SwissProt, TrEMBL, and nr/nt of NCBI databases. The raw reads are deposited in the DDBJ with DRA accession number, DRA007359: https://www.ncbi.nlm.nih.gov/sra/?term=DRA007359. The assembled contigs of transcriptome are deposited in the DDBJ TSA repository with accession number IADQ01000001-IADQ01036303: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/tsa/IADQ.gz and also can be accessed at http://rujakbase.id.

Dataset of the first de novo transcriptome assembly of the arillode of Baccaurea motleyana.

Baccaurea motleyana Müll. Arg. (rambai) is one of the underutilized fruit natives to Indonesia, Thailand, and Malaya Peninsula and it is mostly cultivated in Java island (Lim, 2012) [1]. The edible part of fruits is white and reddish arillodes in which having sweet to acid-sweet tastes. However, nucleotide as well as transcriptome information of this species is still scarce, no information has been deposited in GenBank. In this data article, we performed for the first time of de novo assembly of transcriptome using paired-end Illumina technology. The assembled contigs were constructed using Trinity and after filtering and clustering, produced 37,077 contigs. The contig ranged 201-4972 bp and N50 has 696 bp. The contig was annotated with several database such as SwissProt, TrEMBL, nr and nt NCBI databases. The raw reads were deposited in DDBJ with DRA numbers, DRA007358. The assembled contigs of transcriptome are deposited in the DDBJ TSA with accession number, IADP01000001-IADP01037077 and also can be accessed at http://rujakbase.id.

In vitro Callus Induction of Sipahutar Pineapple (Ananas comosus L.) from North Sumatra Indonesia.

BACKGROUND AND OBJECTIVE: Sipahutar pineapple (Ananas comosus L.) is a indigenous of pineapple grown in Sipahutar district, North Sumatra, Indonesia. Propagation of Sipahutar pineapple that being done traditionally is less effective, because the number of seeds that produced is very limited and requires a long time. Propagation through in vitro culture is an alternative solution to solve this problem. It is necessary to add plant growth regulator (PGR) to stimulate callus formation in Sipahutar pineapple explants (Ananas comosus L.). Callus induction of pineapple from Sipahutar was carried out by PGR treatment on MS medium. The purpose of this study was to determine the effect MS medium treatment with added dichlorophenoxyacetic acid (2,4-D) and benzyl amino purin (BAP) PGR on Sipahutar pineapple callus formation (Ananas comosus L.) with light and dark treatment. MATERIALS AND METHODS: This callus induction research used a completely randomized design (CRD) with 2 factors, the first factor was treatment 2,4-D (0, 1, 2) ppm. The second factor is BAP (0, 0.5, 1) ppm. RESULTS: Nine combinations of treatments are obtained. Each combination of treatments is treated in both light and dark conditions. The parameters of this study were the percentage (%) of explants that formed callus, the time of callus formed, callus texture, callus biomass, callus surface height and callus surface area. Data were analyzed with two-way ANOVA, followed by Duncan Multiple Rate Test (DMRT). CONCLUSION: The study showed that the interaction between 2,4-D and BAP significantly affected the time of callus formed but 2,4-D and BAP did not significantly affect callus biomass, callus surface height and callus surface area. All explants can form callus, except explants without the addition of 2,4-D and BAP. The callus formed on 10 days after induction (DAI) and 12 DAI with the treatment of light and dark. The color of the produced callus were white, yellowish white, greenish white, brown, brownish yellow, brownish white, brownish green, yellowish green and greenish white. The callus formed is generally compact textures, except for explants which by giving 1 ppm 2,4-D produce friable callus.

De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit.

Garcinia mangostana L. (Mangosteen), of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.