Transcriptome reveals senescing callus tissue of Aquilaria malaccensis, an endangered tropical tree, triggers similar response as wounding with respect to terpenoid biosynthesis

Abstract

Aquilaria malaccensis is an endangered tree species listed in the Appendix II of CITES. It is a main source of highly valuable resinous wood known as agarwood, which is rich in secondary metabolites. De novo assembly of sequences produced by transcriptome sequencing using next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms such as Aquilaria. To investigate the genes and pathways that might control molecular mechanism of A. malaccensis under controlled environment, we sequenced two transcriptome libraries constructed from mRNAs of healthy and senescing callus tissues using Illumina sequencing. We obtained 200,062,275 and 166,544,202 reads for healthy and senescing callus libraries, respectively. We compiled 231,594 transcripts and identified 107,593 transcripts by similarity analysis against the National Center for Biotechnology Information (NCBI) public database. A total of 96,743 transcripts were functionally annotated using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. We assigned 46,076 of the transcripts to a total of 144 KEGG pathways. We focused on genes identified as contributing to fragrant compound synthesis and defense response pathways, which are important pathways leading to agarwood compound formation. This study provides abundant transcriptomic data and valuable sequence resources for future genomic studies on A. malaccensis. This is the first report of callus transcriptome from A. malaccensis.

Time-based LC-MS/MS analysis provides insights into early responses to mechanical wounding, a major trigger to agarwood formation in Aquilaria malaccensis Lam

“…Known to be a component in the Aquilaria plant defense system, agarwood acts to close the wound and protect the tree from further pathogen or fungal invasion. 14,28 In this study, protein changes in A. malaccensis upon wounding treatment and the underlying process, complement and validate the existing knowledge on agarwood formation. Additionally, we applied PCA to serve as an exploratory data analysis method in identifying proteins that are highly relevant to the treatment and also to substantiate that they were not randomly picked.…”

“…Although proteome studies have been carried out in model plants such as Arabidopsis and rice, 11,12 they still could not properly characterize proteins from woody plants with long life cycles and with special features that offer them a greater key to survival. This phenomenon applies to the mechanism of stressinduced biosynthesis in agarwood, which is actively being investigated using Aquilaria transcriptomes, [13][14][15] but has been limited in proteomic approaches. A dra genome from A. agallocha (synonym A. malaccensis) originating from Myanmar has been reported, 16 and a proposal on the Aquilaria terpenoid biosynthesis pathway and its possible regulators has greatly improved the available genetic information on Aquilaria.…”

Composition variation of agarwood-associated microbial communities from Aquilaria sinensis

“…Sesquiterpenes comprise the main component of agarwood (39). Sesquiterpene synthesis begins with some complex pathways from glycolysis (40, 41). Thus, carbohydrate metabolism with high relative abundance can provide a material for sesquiterpene synthesis in agarwood formation (Fig.…”

Temporal and spatial expression of terpene synthase genes associated with agarwood formation in Aquilaria malaccensis Lam

“…The primers were designed based on the transcriptome sequences of the candidate genes (Siah et al 2016). Polymerase chain reaction (PCR) amplification was performed in the MyCycler Thermal Cycler (Biorad, USA).…”

“…Initially, TPS-encoding genes of partial lengths were amplified using primers derived from sequences of A. malaccensis transcriptome (Siah et al 2016) that matched with high homology to the corresponding candidate genes. PCR products of 932 and 1352 bp for AmSesTPS1 and AmGuaiS1, respectively, were obtained and their identities determined by BLASTX searches against the GenBank database.…”