biostudies-literatureSun PChinese Academy of Meteorological SciencesNational Natural Science Foundation of Chinae35874https://www.ebi.ac.uk/biostudies/studies/S-EPMC11388656biostudies-literatureUnknown10(16)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 posseHeliyonComparative transcriptome analysis reveals the differences in wound-induced agarwood formation between Chi-Nan and ordinary germplasm of <i>Aquilaria sinensis</i>.PMC113886562021-I2M-1\u20130328210433282104335Yang YXiao MSun PLv FGao ZWei JHou WXu YfalseComparative transcriptome analysis reveals the differences in wound-induced agarwood formation between Chi-Nan and ordinary germplasm of <i>Aquilaria sinensis</i>.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 posse2024-01-01T00:00:00Z2024 Aug2026-07-15T04:10:00.3Z2025-04-04T11:04:06.275ZS-EPMC113886563926295710.1016/j.heliyon.2024.e35874