Abstract: This study was executed in order to enrich the transcriptome information of flaxseeds and explore the reasons for the difference in the aroma of flaxseed oils from different cultivars at the molecular level. Two specialty flaxseed cultivars (Yiya-3 and Tianya-6) in Xinjiang were selected to perform transcriptome sequencing analysis using the Illumina high-throughput sequencing platform and a variety of bioinformatic methods. The results showed that a total of 61 995 756 high-quality clean reads were obtained. Further, a total of 33 218 unigenes were obtained after de novo assembling of the sequence data. Non-Redundant Protein (NR) database annotations revealed that the flaxseed transcriptome had the highest sequence similarity to Jatropha curcas, and 17 269 unigenes were annotated in the Cluster of Orthologous Group (COG) database, which were divided into 22 branches in three categories, including cellular processes and signals, information storage and processing, and metabolism. There were 1 658 significant differentially expressed genes (DEGs) identified between the two cultivars. Compared to Tianya-6, 825 genes were up-regulated and 833 genes were down-regulated in Yiya-3. The annotation of the DEGs in the Gene Ontology (GO) database showed that they were distributed in three categories: biological processes, cellular components and molecular functions. The 380 DEGs annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were mainly enriched in fatty acid metabolism and other metabolic pathways, and 17 DEGs could be annotated in the fatty acid metabolism pathway, with eight being annotated in the unsaturated fatty acid metabolism pathway. This study provides a theoretical basis and technical support for the analysis of the difference in the aroma of flaxseed oils from different cultivars in Xinjiang.

Key words: flaxseed; transcriptome; differentially expressed genes; functional annotation