Skip to main content

De novo transcriptome assembly data for sengon (Falcataria moluccana) trees displaying resistance and susceptibility to boktor stem borers (Xystrocera festiva Pascoe)

Abstract

Objectives

Sengon (Falcataria moluccana) is a popular tree species in community plantation forests in Java, Indonesia due to its fast-growing and multipurpose characteristics. However, without effective control measures sengon plantations are vulnerable to boktor stem borer (Xystrocera festiva) infestation. Previous research found some boktor-resistant trees amid mostly susceptible individuals. Resistant trees have higher levels of enzyme inhibitory activity than susceptible ones. However, efforts to differentiate between the two accessions using microsatellite markers failed to provide satisfactory answers. This dataset was created to study differences in gene expressions between resistant and susceptible accessions, and to identify candidate genes involved in boktor resistance in sengon.

Data description

RNA was extracted from fresh wood samples collected from two individual trees: one heavily infested with boktor larvae, and the other showing no signs of infestation. The sample trees grow in close proximity to each other within the same plantation. The RNA was sequenced using the BGISEQ-500 platform and produced 78.5 million raw reads. De novo transcriptome were assembled using Trinity and produced 96,164 contigs after filtering and clustering. This transcriptome data is important for understanding pest resistance mechanisms in sengon trees, serving as basis for an improvement program for resistance to boktor pest.

Objective

Sengon (Falcataria moluccana) is a multipurpose legume tree, often utilized in reforestation programs and widely grown in community forest plantations in Indonesia, especially in Java. The fast-growing tree has high economic value, and can provide significant and rapid returns [1]. However, plantation productivity is being adversely affected by serious infestations of the larvae of a coleopteran stem borer known locally as boktor (Xystrocera festiva) [2]. The larvae feed on the cambium and outer parts of sapwood [3] causing deformities, wood quality degradation, and tree death. As there is no known effective method for their control [4], the selection of resistant tree lines is becoming an important option for establishing healthy stands. Previous research has shown that among mostly susceptible trees, some trees are resistant and have higher levels of enzyme inhibitory activity [5]. Efforts to differentiate between these two accessions using microsatellite markers have failed to provide satisfactory answers [6] as the mechanisms involved in tropical tree resistance to phytophagous pests remain largely unknown. Technological advances have allowed us to perform large-scale and rapid sequencing using next-generation sequencing (NGS) platforms to obtain genomic and transcriptomic data for perennial plants, especially trees, to accelerate tree improvement programs [7,8,9]. Therefore, this dataset was created to obtain differential expression information on candidate genes involved in boktor larvae resistance in sengon trees.

Data description

Cambium samples were taken from two trees: resistant and susceptible trees in a community sengon plantation in Bogor, West Java, Indonesia (lat. -6.54416084, long. 106.7401301 DD). Trees showing no signs of infestation were considered resistant, while those heavily infested with Xystroscera festiva were deemed susceptible. A pair of trees, one heavily infested and the other showing no signs of infestation, were selected as samples. The sample trees had to be growing within the same cultivation plot in close proximity to each other in order to eliminate the possibility of environmental factors influencing the severity of pest infestation. Total RNA was extracted from 80 mg tissue samples using the established CTAB-pBIOZOL [10] method by following the manufacturer's instructions. The integrity and quantity of isolated-RNA were quantified by a NanoDrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer. Before sequencing library construction, samples were treated with Ribo-zero rRNA remover [11] to remove the ribosomal RNA contaminant. RNA sequencing was performed using the BGISEQ-500 platform (BGI, Hong Kong).

The resulting raw reads (dataset 1) were then quality controlled using FastQC software [12] to ensure only high-quality data were used for further analysis. Clean reads were de novo assembled using Trinity v. 2.3.2 software [13, 14] and, due to high transcript redundancy, were processed further through filtering and clustering by using CAP3 [15], CD-HIT-EST [16] and Corset [17]. The clean reads were also mapped to reference genomes using Bowtie [18]. The assembled contigs (Data file 1), contained 96,164 contigs with an average length of 1,604.13 bp (Data file 2). Candidate proteins in coding sequences in all contigs were then extracted using TransDecoder v.5.5.0 [19] to produce Open Reading Frames (ORFs) predictions (Data file 3). The assembled contigs were also annotated using BLAST + [20] against the NCBI non-redundant protein (nr) (Data file 5), nucleotide sequence (nt) (Data file 6), and SwissProt protein sequence databases (Data file 7) and TrEMBL from UniProt (Data file 8), with an E-value cut-off − 10 [21].

Transcriptome reference statistics were then analyzed using Blast2GO in OmicsBox [22] to produce distribution data on species blasted, top-hit species blasted, E-value, and sequence similarity (Data file 9). Gene ontology and KEGG pathway analyses were performed using contigs annotated with the Swiss-Prot database (Data file 10), locating 31 cellular components, 38 molecular functions, 60 biological processes (Data file 11), and 148 pathways (Data file 12). Microsatellite regions (Data file 13) in contigs were found using MISA [23] with minimum repeats: 10 for one base; 6 for two bases; and 5 for 3, 4, 5 and 6 bases; and the maximum interruptions allowed between two or more microsatellite sites were 100 bases. The number of contigs containing microsatellite regions was 37,956 contigs with 57,487 microsatellite sites identified (Data file 14).

Limitations

The infested sample was collected from wood around holes made by boktor larvae at 1.5 m height and not at the initial stage of the infestation. The infestation occurred in an uncontrolled manner since it was on open land, but the two trees sampled were only two meters apart. The number of samples sequenced in this study was limited to one sample each for two conditions due to the insufficient RNA quality of other samples for further processing.

Availability of data and materials

The data described in this data note can be accessed from the DNA Data Bank of Japan (DDBJ) with accession number DRP007012, and Figshare https://doi.org/10.6084/m9.figshare.14058458.v1. Please see Table

Table 1 Overview of data files/dataset

1 and the list of references [24, 25] for details and links to the data.

Abbreviations

CTAB:

Cetyltrimethylammonium bromide

RNA:

Ribonucleic acid

RNA-seq:

RNA sequencing

nr:

Non-redundant protein

nt:

Nucleotide sequences

TrEMBL:

Translated European Molecular Biology Laboratory

KEGG:

Kyoto Encyclopedia of Genes and Genomes

References

  1. 1.

    Siregar UJ, Rachmi A, Massijaya MY, Ishibashi N, Ando K. Economic analysis of sengon (Paraserianthes falcataria) community forest plantation, a fast-growing species in East Java, Indonesia. For Pol Econ. 2007;9(7):822–9.

    Article  Google Scholar 

  2. 2.

    Krisnawati H, Varis E, Kallio MH, Kanninen M. Paraseriathes falcataria (L.) Nielsen. Ecology, silviculture, and productivity. Bogor (ID): CIFOR; 2011.

  3. 3.

    Irianto RS, Matsumoto K. Adult biology of the albizia borer, Xystrocera festiva Thomson (Coleoptera: Cerambycidae), based on laboratory breeding, with particular reference to its oviposition schedule. J Trop For Sci. 1998;10(3):367–78.

    Google Scholar 

  4. 4.

    Kasno, Husaeni EA. 1998. An integrated control of sengon stem borer in Java. Paper to IUFRO Workshop on Pest Management in Tropical Forest Plantations. Canthaburi, Thailand 28–29 May 1998.

  5. 5.

    Siregar UJ, Situmorang IM, Pasaribu FA, Lestari A, Istikorini Y, Haneda NF. Trypsin inhibitor activities as defense mechanism of sengon (Falcataria moluccana) against pest attacks. IOP Conf Ser Mater Sci Eng. 2020;935:012034.

    CAS  Article  Google Scholar 

  6. 6.

    Siregar UJ, Rahmawati D, Damayanti A. Fingerprinting sengon (Falcataria moluccana) accessions resistant to boktor pest and gall-rust disease using microsatellite markers. Biodiversitas. 2019;20(9):2698–706.

    Article  Google Scholar 

  7. 7.

    Shabrina H, Siregar UJ, Matra DD, Siregar IZ. The dataset of de novo transcriptome assembly of Falcataria moluccana cambium from gall-rust (Uromycladium falcatarium) infected and non-infected tree. Data Brief. 2019;26:104489.

    Article  Google Scholar 

  8. 8.

    Indriani F, Siregar UJ, Matra DD, Siregar IZ. De novo transcriptome datasets of Shorea balangeran leaves and basal stem in waterlogged and dry soil. Data Brief. 2020;28:104998.

    Article  Google Scholar 

  9. 9.

    Siregar IZ, Dwiyanti FG, Siregar UJ, Matra DD. De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media. BMC Res Notes. 2020;13:405.

    CAS  Article  Google Scholar 

  10. 10.

    Beijing Genomics Institute. RNA extraction standard operating procedure for plant samples. Hong Kong: Beijing Genomics Institute (BGI); 2016.

    Google Scholar 

  11. 11.

    Illumina: Ribo-Zero rRNA Removal Kit (Plant). 2018. https://www.illumina.com/content/illumina-marketing/emea/en_GB/products/by-type/molecular-biology-reagents/ribo-zero-rrna-removal-plant.html. Accessed 27 Oct 2018.

  12. 12.

    Andrews S. FastQC: A quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 23 Jan 2019.

  13. 13.

    Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Palma FD, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52. https://doi.org/10.1038/nbt.1883.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Matra DD, Kozaki T, Ishii K, Poerwanto R, Inoue E. Comparative transcriptome analysis of translucent flesh disorder in mangosteen (Garcinia mangostana L.) fruits in response to different water regimes. PLoS ONE. 2019;14(7):e021997. https://doi.org/10.1371/journal.pone.0219976.

    CAS  Article  Google Scholar 

  15. 15.

    Huan X, Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999;9(9):868–77.

    Article  Google Scholar 

  16. 16.

    Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–9. https://doi.org/10.1093/bioinformatics/btl158.

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Davidson MN, Oshlack A. Corset: enabling differential gene expression analysis for de novo assembled transcriptomes. Genome Biol. 2014;15(7):410. https://doi.org/10.1186/s13059-014-0410-6.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. https://doi.org/10.1038/nmeth.1923.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-Seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494–512. https://doi.org/10.1038/nprot.2013.084.

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10. https://doi.org/10.1016/S0022-2836(05)80360-2.

    CAS  Article  Google Scholar 

  21. 21.

    Xia Z, Xu H, Zhai J, Li D, Luo H, He C, Huang X. RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Bio. 2011;77:299.

    CAS  Article  Google Scholar 

  22. 22.

    Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization, and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–6. https://doi.org/10.1093/bioinformatics/bti610.

    CAS  Article  PubMed  Google Scholar 

  23. 23.

    Thiel T, Michalek W, Varshney RK. Exploiting EST databases for the development of cDNA-derived microsatellite markers in Barley (Hordeum vulgare L.). Theor Appl Genet. 2003;2003(106):411–22.

    Article  Google Scholar 

  24. 24.

    DNA Data Bank of Japan. 2020. https://trace.ddbj.nig.ac.jp/DRASearch/study?acc=DRP007012 Accessed 1 Mar 2021.

  25. 25.

    Siregar UJ, Nugroho A, Shabrina H, Indriani F, Damayanti A, Matra DD. Data and summary transcriptome analysis of Xystrocera festiva infested and non-infested Falcataria moluccana tree. 2021. Figshare. https://doi.org/10.6084/m9.figshare.14058458.v1.

Download references

Acknowledgements

The Authors would like to thank Mr. Kuatman from the Indonesian Institute of Sciences-Botanical Gardens for his assistance in collecting samples from the field.

Funding

This research was funded by SEAMEO-BIOTROP DIPA Fund Number 039.5/PSRP/SC/SPK-PNLT/II/2019 and partially supported by USAID-SHERA through the CDSR Project, led by UGM and IPB University as affiliate members.

Author information

Affiliations

Authors

Contributions

UJS designed the experiment and overall study. AD and FI designed the sampling methods, collecting samples, and pre-processed raw RNA-seq data. DDM and HS performed the RNA-Seq data assembly, analysis, and interpretation. UJS, FI and DDM prepared the first draft of the manuscript, while HS and AN made major contributions to the article. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Ulfah J. Siregar.

Ethics declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Siregar, U.J., Nugroho, A., Shabrina, H. et al. De novo transcriptome assembly data for sengon (Falcataria moluccana) trees displaying resistance and susceptibility to boktor stem borers (Xystrocera festiva Pascoe). BMC Res Notes 14, 261 (2021). https://doi.org/10.1186/s13104-021-05675-9

Download citation

Keywords

  • Falcataria moluccana
  • Resistance
  • Transcriptome
  • Xystroscera festiva