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.

Transcriptome dataset of gall-rust infected Sengon (Falcataria falcata) seedlings using long-read PCR-cDNA sequencing

“… [7] . In addition, the open reading frames (ORFs) within the transcripts were predicted using TransDecoder v.5.5.0 ( https://github.com/TransDecoder/TransDecoder , accessed on 1 November 2022) with the default parameters [ 8 , 9 ]. Cleaned-reads were also mapped back to full-length transcripts using minimap2 v.2.26 [13] .…”

“…With a filtered-UNIPROT database and processed with Blast2go 6.0 software [7] . The TransDecoder program v.5.5.0 with default parameters [ 8 , 9 ] was then used to define open reading frames (ORFs) and generated 2,342 transcripts, of which 34.15% were 5′prime_partial, 8.15% were 3′prime_partial, 8.5% were internal, and 49.14% were complete ( Table 2 ). An overview of the Gene Ontology (GO) classification generated from F. falcata is shown in Fig.…”

Development of Few Significant SNP Markers from Transcriptomic Data for Selection of Sengon (Falcataria falcata (L.) Greuter & R. Rankin) Resistant to Boktor Stem Borer and Gall Rust Disease

“…The assembled transcriptomic data of sengon susceptible and resistant to Boktor stem borer and gall rust disease were obtained from the Data Bank of Japan (DDBJ) (https://www.ddbj.nig.ac.jp) with accession numbers DRA008389 and DRA007983 published by Shabrina et al (2019) and Siregar et al (2021). The read data used were from eight individual trees, where reads of rust-resistant, rust-susceptible, Boktor-resistant, and Boktor-susceptible were the results of sequencing using the BGISEQ-500 platform (Siregar et al 2021). Reads of rust on leaves 1 and 2 and stems 1 and 2 were sequenced using the Illumina HiSeq4000 platform (Shabrina et al 2019).…”

“…However, such GWAS studies are often expensive. This study aimed to bypass such expensive studies by identifying and developing SNP markers using transcriptome data analysis of sengon accessions resistant and susceptible to gall rust disease (Shabrina et al 2019) and sengon accessions resistant and susceptible to Boktor stem borer (Siregar et al 2021). The identified and developed SNP primers were tested on small samples of sengon accessions displaying resistance to the pest and disease.…”

Biotechnology for Tropical Plant Breeding in SEAMEO BIOTROP

“…The coming of the next-generation sequencing era opens the possibility of generating more powerful markers based on genomic or transcriptomic sequences from relatively cheap sequencing processes. Transcriptomic sequences from Sengon having resistance and susceptibility against stem borer pest and gall rust disease have been published recently [8,9]. From the available sequences, it is easy to detect single nucleotide polymorphisms (SNPs) among the sequenced accessions.…”