Abstract
Shorea balangeran Burk locally known as balangeran has been widely used as recommended species for tropical peat swamp forest restoration, due to the capability of these species to grow in waterlogged and dry areas. However, the information concerning genetic basis of adaptation to ecological condition variation is limited and no transcriptome study has been reported in this context. Here we reported two sets of transcriptome data from a sample of leaf and basal stem that were taken from seedlings growing in potted media containing peat and mineral soil. The raw reads are stored in the DDBJ platform with accession number DRA008633.
Keywords: Shorea balangeran, Transriptome, RNA-seq, Adaptation
Specifications Table
| Subject | Agricultural and Biological Sciences: Forestry |
| Specific subject area | Molecular study in Forestry |
| Type of data | RNA Sequencing Data |
| How data were acquired | Illumina Hiseq 4000 |
| Data format | Raw sequencing reads and assembled contigs |
| Parameters for data collection | Leaf and basal steam of balangeran seedlings planted in waterlogged peat, dry peat, waterlogged mineral soil and dry mineral soil |
| Description of data collection | Total RNA was sequenced using Illumina Hiseq 4000 platform in NovogenAIT, Singapore |
| Data source location | Bogor, West Java Indonesia |
| Data accessibility | Repository name: DDBJ (DNA Data Bank of Japan) Data identification number: DRA008633 Direct URL to data: https://ddbj.nig.ac.jp/DRASearch/submission?acc=%20DRA008633 |
| Related research article | F. Indriani, D.D. Matra, U.J. Siregar, I.Z. Siregar Ecological aspects and genetic diversity of Shorea balangeran in two forest types of Muara Kendawangan Nature Reserve, West Kalimantan, Indonesia, Biodiversitas. 20 (2019) 482–488 https://doi.org/10.13057/biodiv/d200226 |
Value of the Data
|
1. Data
Shorea balangeran (balangeran) belongs to Dipterocarpaceae family that is distributed in peat and heath forest in Indonesia [1]. In this study the de novo transcriptome assembly of balangeran is reported for the first time. The transcriptome data were obtained from leaves and basal stem of seedling that were growing in potted media containing each of peat and mineral soil. The high quality of mRNA extracted were sequenced using Illumina Hiseq 4000. The statistics of the reads and assembled sequences are presented in Table 1. The overview of transcriptome data were showed in Table 2. Analysis showed that 113,998 contigs (63.62%) had significant matches in nr NCBI database and 78,407 (43.49%) in Swiss-Prot database and 90,875 (50.40%) in TrEMBL database. Out of 180,291 merged contigs, a total 130,314 open reading frames (ORFs) were identified (Table 3) with 5prime partial ORFs type 31,209 (23.95%), 3prime partial 17,633 (13.53%) and complete ORFs type 64,374 (49.40%) were identified. In this study, microsatellite motifs from merged contigs were identified (Table 4), mononucleotides were the most abundant type (44,626, 70.30%), followed by trinucleotides (11,160, 17.58%) and dinucleotides (6,270, 9.88%).
Table 1.
The properties of reads and assembled sequences of balangeran.
| Features | Numbers |
||
|---|---|---|---|
| Leaf | Basal Stem | Mergedb (Leaf and Basal Stem) | |
| Reads | |||
| Number of reads | 64,101,942 | 56,537,051 | 120,638,993 |
| Number of bases | 9,615,291,300 | 8,480,557,650 | 18,095,848,950 |
| Number of post-trimming reads | 62,400,243 (97.35) |
54,917,915 (97.14) |
117,318,158 (97.25) |
| Number of post-trimming bases | 9,360,036,450 (97.35) |
8,237,687,250 (97.14) |
17,597,723,700 (97.25) |
| Transcriptsa | |||
| Number of transcript | 279,598 | 574,875 | – |
| Number of bases | 175,610,736 | 342,696,076 | – |
| Length range (bp) | 201-16,510 | 201-16,960 | – |
| Average (bp) | 628.08 | 596.12 | – |
| N50 (bp) | 940 | 839 | – |
| GC contents (%) | 42.28 | 45.56 | – |
| Contigsb | |||
| Number of contig | 187,297 | 440,665 | 180,291 |
| Number of bases | 118,677,247 | 252,486,917 | 197,305,352 |
| Length range (bp) | 201-16,510 | 201-16,960 | 201-17,014 |
| Average (bp) | 633.63 | 572.97 | 1094.37 |
| N50 (bp) | 918 | 762 | 1489 |
| GC contents (%) | 42.6 | 46.2 | 44.3 |
Constructed by Trinity Program.
Constructed by CAP3, cd-hit-est, and corset (only for merged contig) programs.
Table 2.
Functional annotation of balangeran contigs using several database.
| Database Source | Number (percentage) |
|---|---|
| Contig Number | 180,291 |
| Non-redundant protein (nr) NCBI | 113,998 (63.62) |
| Non-redundant Nucleotide (nt) NCBI | 53,407 (29.62) |
| Swiss-Prot UniProt | 78,407 (43.49) |
| TrEMBL UniProt | 90,875 (50.40) |
Table 3.
Open Reading Frames (ORFs) prediction characteristics of balangeran contigs using TransDecoder.
| Features | Contigs Number (percentage) |
|---|---|
| ORF contig | 130,314 |
| ORFs Type : | |
| a. 5prime_partial | 31,209 (23.95) |
| b. 3prime_partial | 17,633 (13.53) |
| c. Internal | 17,104 (13.13) |
| d. Complete | 64,374 (49.40) |
Table 4.
Number and motif of microsatellite of balangeran contigs.
| Motifs | Number of Contigs (percentage) |
||
|---|---|---|---|
| Leaf | Basal Stem | Merged | |
| Mononucleotide | 26,259 (72.93) | 48,786 (68.83) | 44,626 (70.30) |
| Dinucleotide | 3939 (10.94) | 6943 (9.80) | 6270 (9.88) |
| Trinucleotide | 5192 (14.42) | 13,443 (18.97) | 11,160 (17.58) |
| Tetranucleotide | 421 (1.17) | 1221 (1.72) | 995 (1.57) |
| Pentanucleotide | 142 (0.39) | 292 (0.41) | 267 (0.42) |
| Hexanucleotide | 54 (0.15) | 193 (0.27) | 164 (0.26) |
2. Experimental design, materials, and methods
Balangeran seedlings were treated and raised in the nursery of Department of Silviculture, Faculty of Forestry, IPB University Bogor for 6 months. Two seedlings were grown in peat soil in which each seedling planted in waterlogged peat and dry peat. Two seedlings were grown in mineral soil in which each seedling planted in waterlogged soil and dry soil. Total RNA was isolated from leaves and basal stem using Plant Total RNA mini kit (Geneaid) following the protocol. The quantity and integrity were evaluated using P360 Nanophotometer (Implen, München, Germany) and Bioanalyzer 2100 (Agilent Technologies). RNA samples had RNA integrity number (RIN) values between 7.4 and 8.6. The total RNA extracted were used for Illumina Hiseq 4000 sequencing following the protocol (NovogeneAIT, Singapore). The quality of raw data were examined using FastQC [2] then performed using Trimmomatic 0.39 to remove adaptor sequences, contamination and low-quality reads with default parameters (TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25) [3]. Pre-processed read from each leaves and basal stem were de novo assembled using Trinity v.2.3.2 with default parameter (minimum length = 200) [4], generated high quality contigs [5]. The each contigs from leaves and basal stem were reconstructed using CAP3 [6] and CD-HIT-EST v.4.6.8 [7]. The contigs form leaves and basal stem were merged and reconstructed using CAP3, CD-HIT-EST, and Corset program [8,9]. The database such as NCBI non-redundant (nr) (downloaded by October 1, 2018) and NCBI nucleotide sequence (nt) (downloaded by October 1, 2018), SwissProt and TrEMBL of UniProt (downloaded by September 14, 2018) were used to annotate the contigs using BLAST + program [10]. Open reading frames (ORFs) of contigs were predicted by the TransDecoder package (https://github.com/TransDecoder/TransDecoder), with the minimum ORF length of 100 bp [11]. Microsatellite discovery was analyzed using MISA software (http://pgrc.ipk-gatersleben.de/misa) with parameter (unit size-minimum repeats) as follows: 1–10, 2–6, 3–5, 4–5, 5–5, 6–5 and the interruptions (maximum difference between microsatellites) was 100 bases.
Acknowledgments
This research was funded by PMDSU program (Master Program of Education Leading to Doctoral Degree for Excellent Graduates) from Ministry of Research, Technology and Higher Education of the Republic of Indonesia and it was also partially funded under World Class University (WCU) Program, managed by Institut Teknologi Bandung. We are thankful to FRDC, FOERDIA, MoEF, Bogor, West Java, Indonesia for providing seedlings of Shorea balangeran.
Conflict of Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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