De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media

Abstract

Objectives: Efforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socioeconomic factors and ecological dynamics attributed to lack of knowledge on the adaptive mechanisms of potential tree species such as Kapur (Dryobalanops aromatica C.F.Gaertn Syn. Dryobalanops sumatrensis J.F. Gmelin A.J.G.H Kostermans). This species is a multipurpose tree that, commonly grows in mineral soils, but also in peat swamp as previously reported, which raised a fundamental question regarding the molecular mechanism of this adaptation. Therefore, a dataset was created aiming to detect candidates of adaptive genes in D. aromatica seedlings, cultivated in two contrasting potting media, namely mineral soil and peat media, based on RNA Sequencing Transcriptome Analysis. Data description: The RNA transcriptome data of D. aromatica's seedlings derived from young leaves of three one-year-old seedlings, raised in each dry mineral soil media and peat media, were generated by using Illumina HiSeq 4000 platform in NovogenAIT, Singapore. The acquired data, as the first transcriptome dataset for D. aromatica, is of a great importance in understanding molecular mechanism and responses of the involved genes of D. aromatica to the contrasting, growing potting media conditions that could also be useful to generate molecular markers.

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

“…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 – 9 ]. Therefore, this dataset was created to obtain differential expression information on candidate genes involved in boktor larvae resistance in sengon trees.…”

DIFFERENTIALLY EXPRESSED GENES(DEGS) Dryobalanops aromaticaYANG DITUMBUHKAN PADA MEDIA GAMBUT DAN TANAH MINERAL

“…Saat ini, informasi mendasar mengenai gen-gen yang berpengaruh terhadap kemampuan adaptasi D. aromatica pada lahan gambut belum tersedia. Analisis transkriptomik throughput tinggi (RNA-Seq) dari D. aromatica sebagai referensi pertama telah dilakukan Siregar, Dwiyanti, Siregar & Matra (2020) Data transkriptomik memungkinkan untuk mengidentifikasi differentially expressed genes (DEGs) dengan membandingkan nilai ekspresi gen antar dua grup sampel dengan perlakuan yang berbeda. Tujuannya adalah untuk menganalisis gen yang menunjukkan level ekspresi yang berbeda di bawah dua kondisi lingkungan berbeda.…”

“…Data transkriptomik berupa hasil de novo assembly dan anotasi D. aromatica yang ditanam di dua jenis media tanam diperoleh dari hasil penelitian Siregar, Dwiyanti, Siregar & Matra (2020). Pengolahan data untuk deteksi DEG dilakukan menggunakan software R v.4.1.0, Bioconductor dengan package edgeR v.3.34.0 untuk memperkirakan tingkat ekspresi semua transkrip (Matra et al, 2019).…”

Effects of two contrasting potting media on the leaf development index, photosynthetic rate, and metabolite profile of camphor (Dryobalanops aromatica) seedlings

“…In natural forests, camphor trees grow in groups on dry sandy or gravel soils [ 8 ]. However, recent evidence suggests that this species also grows naturally in the shallow peat swamp forest in the Singkil Wildlife Reserve (Suaka Margasatwa Singkil), Aceh Province, Sumatera Islands, Indonesia [ 9 ]. These findings provide important baseline information for future replanting plans for this species.…”

“…The question regarding how camphor plants adapt to different habits was initially addressed through RNA sequencing (RNA-Seq) transcriptome analysis of seedlings planted in mineral and peat media [ 9 ]. However, to the best of our knowledge, phenotypic and chemical compound analyses have not yet been carried out.…”