Comparative transcriptome analysis reveals the differences in wound-induced agarwood formation between Chi-Nan and ordinary germplasm of Aquilaria sinensis

Agarwood is a rare and valuable heartwood derived from <i>Aquilaria sinensis</i> in China. Compared with ordinary germplasm, Chi-Nan, a special germplasm of <i>A. sinensis</i>, has a better agarwood-producing capacity. However, the mechanisms underlying their different qualities remain poorly characterized. Here, a comparative transcriptome analysis of Chi-Nan and ordinary <i>A. sinensis</i> was carried out to investigate the wound responses of both germplasms. A total of 198.19 Gb of clean data were obtained with an average of 6.61 Gb of clean reads for each sample. By comparing with their control groups, more differentially expressed genes (DEGs) were observed in Chi-Nan germplasm. Kyoto Encyclopedia of Genes and Genomes (KEGG) and expression profile analysis suggested that Chi-Nan possesses a stronger ability to respond to wounding. Furthermore, the enrichment of biosynthetic pathways related to sesquiterpenes and 2-(2-phenylethyl) chromones (PECs) were more significant in Chi-Nan than in ordinary germplasm, and related genes showed significantly higher up-regulation in Chi-Nan after wounding. Sixteen candidate genes presumably involved in biosynthesis of agarwood components were identified and found to exhibit higher up-regulation in Chi-Nan than in ordinary germplasm in response to wounding. Overall, these results are helpful in explaining reasons for the higher agarwood-producing properties of Chi-Nan, and contribute to a further understanding of the mechanism of agarwood formation in <i>A. sinensis</i>.