Abstract
Sengon (Falcataria moluccana), formerly known as Albizia falcataria or Paraserianthes falcataria, is an essential tree species for the development of community-based timber plantation, especially in Indonesia. The plantations nowadays are facing a significant disease threat, namely infection of gall-rust fungi (Uromycladium falcatarium). However, a clear understanding of the molecular mechanisms of the tree response against the disease is still unknown. We carried out transcriptome assembly using BGISEQ-500 technology to provide assembled de novo transcriptome dataset generated from gall-rust infected and non-infected trees. The construction of assembled transcriptome was conducted using Trinity v.2.3.2 The raw reads are available in the DDBJ platform with accession number, DRA007983.
Keywords: De novo, Falcataria moluccana, Gall-rust (Uromycladium falcatarium) infected, Next-generation sequencing (NGS), RNA, Transcriptome
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 | The data acquired by Next-generation Sequencing technology using BGISEQ-500 platform |
| Data format | Raw Sequencing reads and assembled contigs |
| Parameters for data collection | The cambium was collected each from outer sapwood of gall-rust infected and non-infected Sengon tree. |
| Description of data collection | The RNA was sequenced with Next Generation Sequencing method using BGISEQ-500 platform in Beijing Genomic Institute, Hongkong. |
| Data source location | City/Region: Bogor/West Java Country: Indonesia Latitude and longitude (and GPS coordinates) for collected samples/data: 6°32′38.9″S 106°44′24.5″E |
| Data accessibility | Repository name: DDBJ (DNA Data Bank of Japan) Data identification number: DRA007983 Direct URL to data: https://ddbj.nig.ac.jp/DRASearch/submission?acc=DRA007983 |
| Related research article | N.E. Lelana, S. Wiyanto, Gianto, I.Z. Siregar. Genetic diversity of Falcataria moluccana and its relationship to the resistance of gall rust disease. Biodiversitas (2018): 12–17. DOI: https://doi.org/10.13057/biodiv/d190102 D. Rahmawati, N. Khumaida, U.J. Siregar. Morphological and phytochemical characterization of susceptible and resistant Sengon (Falcataria moluccana) tree to gall rust disease. Biodiversitas 20 (2019): 907–913. DOI: https://doi.org/10.13057/biodiv/d200340 |
Value of the data
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1. Data
This data presented the de novo transcriptome assembly of Falcataria moluccana (Miq.) Barneby & JW Grimes (Indonesia: Sengon, Malaysia: Batai, Hawaii: Albizia, East Timor: Madre de Cacao, Philippines: Falcata). The Sengon tree is cultivated widely in Indonesia as a material source for veneer, light construction, and pellet in bioenergy. However, the plantations are facing the most damaging threat that damaging the wood and lowering the productivity, gall-rust (Uromycladium falcatarium) fungi infection. Altough the fungi could infect any tissue, the wood or stem, which is the main product of the plantation, was the part that damaged badly. After the fungi entered the bark, the gall-rust fungi will wounded the cell in cambium, causing death in some cells and grow itself in cambium tissues by blocking the nutrient. The fungi also secretes growth hormones that caused the undifferentiated cell in cambium to grow rapidly and created wood deformity. The transcriptome of Sengon was derived from the RNA collected from the cambium part of the stem. The sequencing process was generated using BGISEQ-500 platform. The properties of the reads and the assembled sequences are shown in Table 1. Overview of the transcriptome data is presented in Table 2. The KEGG pathway analysis generated pathways with high number of contigs which involved in gall-rust infection incidence (Table 3). Among the microsatellite motifs from the merged sequences (Table 4), mono- (27,917; 39.83%) and dinucleotide (8,242; 11.76%) were the most common, and the three most frequent motifs were A/T (26,157; 64.33%), AG/CT (4,300; 10.58%), and AT/AT (2,195; 5.40%). The most frequent trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide were AAG/CTT (1,378; 3.39%), AAAG/CTTT (83; 0.2%), AAAAG/CTTTT (8; 0.02%), and AAACCC/GGGTTT (7; 0.02%) respectively.
Table 1.
The properties of raw reads and assembled sequences of Sengon cambium.
| Features | Numbers |
||
|---|---|---|---|
| infected | non-infected | Merged | |
| Raw Reads | |||
| Numbers | 79,054,112 | 79,037,484 | 158,090,000 |
| Bases | 7,905,411,200 | 7,903,748,400 | 15,810,000,000 |
| Unique Transcripts | |||
| Numbers | 380,032 | 118,171 | 400,633 |
| Bases | 278,860,152 | 114,550,451 | 325,278,365 |
| Length range (bp) | 201-17,824 | 201-8,098 | 201-12,634 |
| Average (bp) | 733.78 | 969.36 | 811.91 |
| N50 (bp) | 1324 | 1439 | 1521 |
| GC contents (%) | 40.1 | 40.6 | 39.8 |
| Contigs | |||
| Numbers | 72,968 | 41,332 | 70,089 |
| Bases | 100,689,847 | 57,231,623 | 115,068,922 |
| Length range (bp) | 201-21,986 | 201-8,098 | 181-15,997 |
| Average (bp) | 733.78 | 1385 | 1641 |
| N50 (bp) | 1074 | 1243 | 1382 |
| GC contents (%) | 41.1 | 40.8 | 40.6 |
Table 2.
Functional annotation of Sengon contigs.
| Source | Number (percentage) |
||
|---|---|---|---|
| Infected | Non-infected | Merged | |
| Contig Number | 72,968 | 41,332 | 70,089 |
| Contigs: | |||
| Nr NCBI | – | – | 68,927 (98.34) |
| Nt NCBI | 61,213 (83.89) | 37,986 (91.90) | 62,880 (89.71) |
| SwissProt | 40,694 (55.76) | 25,633 (62.02) | 42,783 (61.04) |
| TrEMBL | – | – | 58,593 (83.59) |
| Gene ontology | – | – | 17,134 (24.45) |
| KEGG | – | – | 3,256 (4.65) |
Table 3.
Top 20 KEGG pathway with the highest contig numbers of merged sequence.
| Pathway | Pathway ID | #Enzymes in pathway | #Contigs of Enzyme |
|---|---|---|---|
| Purine metabolism | map00230 | 7 | 54 |
| Thiamine metabolism | map00730 | 2 | 44 |
| Biosynthesis of antibiotics | map01130 | 8 | 31 |
| Pyrimidine metabolism | map00240 | 8 | 17 |
| Folate biosynthesis | map00790 | 2 | 16 |
| One carbon pool by folate | map00670 | 3 | 16 |
| beta-Lactam resistance | map01501 | 1 | 13 |
| Drug metabolism - other enzymes | map00983 | 2 | 13 |
| Penicillin and cephalosporin biosynthesis | map00311 | 1 | 13 |
| Terpenoid backbone biosynthesis | map00900 | 1 | 12 |
| Aminoacyl-tRNA biosynthesis | map00970 | 3 | 9 |
| Alanine, aspartate and glutamate metabolism | map00250 | 3 | 8 |
| Cysteine and methionine metabolism | map00270 | 3 | 8 |
| Porphyrin and chlorophyll metabolism | map00860 | 3 | 6 |
| Galactose metabolism | map00052 | 1 | 6 |
| Oxidative phosphorylation | map00190 | 1 | 5 |
| Glutathione metabolism | map00480 | 2 | 4 |
| Pantothenate and CoA biosynthesis | map00770 | 3 | 4 |
| Cyanoamino acid metabolism | map00460 | 1 | 3 |
| Glycine, serine and threonine metabolism | map00260 | 2 | 3 |
| Phenylalanine, tyrosine and tryptophan biosynthesis | map00400 | 2 | 3 |
Table 4.
The number and motif of microsatellite of Sengon contigs.
| Motifs | Number of contigs (percentage) |
||
|---|---|---|---|
| Infected | Non-infected | Merged | |
| Mononucleotide | 15,979 (21.90) | 18,786 (45.45) | 27,917 (39.83) |
| Dinucleotide | 7,157 (9,81) | 3,879 (9.38) | 8,242 (11.76) |
| Trinucleotide | 3,676 (5.04) | 2,258 (5.46) | 4,172 (5.95) |
| Tetranucleotide | 216 (0.30) | 94 (0.23) | 255 (0.36) |
| Pentanucleotide | 31 (0.04) | 6 (0.01) | 28 (0.04) |
| Hexanucleotide | 41 (0.06) | 22 (0.05) | 48 (0.07) |
2. Experimental design, materials, and methods
The cambiums of Sengon tree were collected from a private plantation in Bogor, West Java, Indonesia (6°32′38.9″S 106°44′24.5″E). The RNA was extracted from the cambium part originated from gall-rust infected and gall-rust free tree, each type of tree consist of one individual and no replication. The RNA extracted by BGI from 80 mg tissue sample using established CTAB-pBIOZOL method. The integrity and quantity of isolated-RNA were monitored and quantified by a NanoDrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer. The non-infected sample was treated with Ribozero due to ribosomal RNA contamination. The RNA sequencing was carried out using the BGISEQ-500 (BGI, Hong Kong) and produced pre-processing reads to discard the adaptors and low-quality reads. The pre-processed reads were de novo assembled by Trinity v.2.3.2 [1], and the high-quality contigs were obtained [2], [3]. These contigs were annotated using BLAST + program [4] against the NCBI non-redundant (Nr), Nucleotide sequences (Nt) and protein sequence database of UniProt (SwissProt and TrEMBL). The annotated-contigs from Nr database were performed using Blast2Go software [5] to obtain functional annotation of Gene Ontology and KEGG pathway. Identification of contigs containing microsatellites was performed using MISA program [6], with minimum repeats were: 10 for 1 base, 6 for 2 bases, and 5 for 3, 4, 5, and 6 bases; and the interruptions (the maximum difference between microsatellites) were 100 bases.
Acknowledgments
This research is partially funded by Master Program of Education Leading to Doctoral Degree for Excellent Graduates (PMDSU) Scheme from Ministry of Research, Technology and Higher Education of the Republic of Indonesia (KEMENRISTEKDIKTI) and The United States Agency for International Development (USAID) through the Sustainable Higher Education Research Alliances (SHERA) program - Centre for Development of Sustainable Region (CDSR). In 2017–2021, CDSR is led by Center for Energy Studies – Gadjah Mada University (UGM).
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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