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

Siregar U.J., Nugroho A., Shabrina H., Indriani F., Damayanti A., Matra D.D.

Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Indonesia, Bogor, Indonesia; SEAMEO BIOTROP, Bogor, Indonesia; Tropical Silviculture Program, Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia; Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University (Bogor Agricultural University), Bogor, Indonesia


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. © 2021, The Author(s).

Falcataria moluccana; Resistance; Transcriptome; Xystroscera festiva


Journal

BMC Research Notes

Publisher: BioMed Central Ltd

Volume 14, Issue 1, Art No 261, Page – , Page Count


Journal Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85109609735&doi=10.1186%2fs13104-021-05675-9&partnerID=40&md5=5a391741c5eb9a8a24030b7632fec3b8

doi: 10.1186/s13104-021-05675-9

Issn: 17560500

Type: All Open Access, Gold, Green


References

Siregar, U.J., Rachmi, A., Massijaya, M.Y., Ishibashi, N., Ando, K., Economic analysis of sengon (Paraserianthes falcataria) community forest plantation, a fast-growing species in East Java, Indonesia (2007) For Pol Econ, 9 (7), pp. 822-829; Ecology, silviculture, and productivity (2011) Bogor (ID): CIFOR; Irianto, R.S., Matsumoto, K., Adult biology of the albizia borer, Xystrocera festiva Thomson (Coleoptera: Cerambycidae), based on laboratory breeding, with particular reference to its oviposition schedule (1998) J Trop For Sci, 10 (3), pp. 367-378; Kasno, H.E.A., (1998); Siregar, U.J., Situmorang, I.M., Pasaribu, F.A., Lestari, A., Istikorini, Y., Haneda, N.F., Trypsin inhibitor activities as defense mechanism of sengon (Falcataria moluccana) against pest attacks (2020) IOP Conf Ser Mater Sci Eng., 935, p. 012034. , COI: 1:CAS:528:DC%2BB3cXitlaku7jN; Siregar, U.J., Rahmawati, D., Damayanti, A., Fingerprinting sengon (Falcataria moluccana) accessions resistant to boktor pest and gall-rust disease using microsatellite markers (2019) Biodiversitas, 20 (9), pp. 2698-2706; Shabrina, H., Siregar, U.J., Matra, D.D., Siregar, I.Z., The dataset of de novo transcriptome assembly of Falcataria moluccana cambium from gall-rust (Uromycladium falcatarium) infected and non-infected tree (2019) Data Brief, 26, p. 104489; Indriani, F., Siregar, U.J., Matra, D.D., Siregar, I.Z., De novo transcriptome datasets of Shorea balangeran leaves and basal stem in waterlogged and dry soil (2020) Data Brief, 28, p. 104998; Siregar, I.Z., Dwiyanti, F.G., Siregar, U.J., Matra, D.D., De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media (2020) BMC Res Notes, 13, p. 405. , COI: 1:CAS:528:DC%2BB3cXhslajsrfF; (2016) RNA extraction standard operating procedure for plant samples, , Beijing Genomics Institute (BGI), Hong Kong; (2018) Ribo-Zero Rrna Removal Kit (Plant), , 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; Andrews, S.F., (2010) A Quality Control Tool for High Throughput Sequence Data, , http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.Accessed23Jan2019; Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Regev, A., Full-length transcriptome assembly from RNA-Seq data without a reference genome (2011) Nat Biotechnol, 29, pp. 644-652; Matra, D.D., 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 (2019) PLoS ONE, 14 (7); Huan, X., Madan, A., CAP3: a DNA sequence assembly program (1999) Genome Res, 9 (9), pp. 868-877; Li, W., Godzik, A., Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences (2006) Bioinformatics, 22 (13), pp. 1658-1659; Davidson, M.N., Oshlack, A., Corset: enabling differential gene expression analysis for de novo assembled transcriptomes (2014) Genome Biol, 15 (7), p. 410; Langmead, B., Salzberg, S., Fast gapped-read alignment with Bowtie 2 (2012) Nat Methods, 9, pp. 357-359; Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., Couger, M.B., Regev, A., De novo transcript sequence reconstruction from RNA-Seq using the Trinity platform for reference generation and analysis (2013) Nat Protoc, 8 (8), pp. 1494-1512; Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., Basic local alignment search tool (1990) J Mol Biol, 215 (3), pp. 403-410; 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 (2011) Plant Mol Bio, 77, p. 299. , COI: 1:CAS:528:DC%2BC3MXhtFGlsLvP; Conesa, A., Götz, S., García-Gómez, J.M., Terol, J., Talón, M., Robles, M., Blast2GO: a universal tool for annotation, visualization, and analysis in functional genomics research (2005) Bioinformatics, 21 (18), pp. 3674-3676; Thiel, T., Michalek, W., Varshney, R.K., Exploiting EST databases for the development of cDNA-derived microsatellite markers in Barley (Hordeum vulgare L.) (2003) Theor Appl Genet, 2003 (106), pp. 411-422; Siregar, U.J., Nugroho, A., Shabrina, H., Indriani, F., Damayanti, A., Matra, D.D., Data and summary transcriptome analysis of Xystrocera festiva infested and non-infested Falcataria moluccana tree (2021) Figshare

Indexed by Scopus

Leave a Comment