Abstract: Fagopyrum gene resources are relatively limited. Taking roots of F. esculentum and F. Cymosum as experimental material, this study conducted transcriptome sequence by Illumina HiSeqTM 2000. After de novo assembly, a total of 64 618 unigenes were obtained, among which 37 546 unigenes were annotated. A total of 4 709 differentially expressed genes (DEGs) was obtained through screening the DEGs between F. esculentum root and F. cymosum root. Among them, 2 460 were upregulated, whereas 2 249 were downregulated. GO annotation of these DEGs were focused on 10 cellular components, 12 molecular function, and 22 biological processes. After upgraded the metabolic pathways, the DEGs involved in 40 and 18 metabolic pathways were significantly enriched in upregulated genes and downregulated genes, respectively. These significantly enriched metabolic pathways were involved in the biological regulatory of F. esculentum root and F. cymosum root. At last, we analyzed the key genes that annotated to the pathway of flavonoid biosynthesis, and a total of 21 genes was obtained. This research not only enriched Fagopyrum gene resources, provided data foundation for molecular biology research of Fagopyrum; but also supplied reference for screening expression tendency of related key genes in F. esculentum root and F. cymosum root.

Key words: Fagopyrum, transcriptome, de novo assembly, differentially expressed genes, flavonoid biosynthesis genes

摘要： 荞麦基因资源相对匮乏。以甜荞根和金荞根为材料，利用Illumina HiSeqTM 2000对其进行转录组测序，经过de novo从头组装得到64 618条Unigene，其中37 546条基因得到了有效注释。对甜荞根和金荞根中的差异基因进行筛选，共获得了4 709个差异基因，其中2 460个上调表达，2 249个下调表达。这些差异基因的GO注释集中在10个细胞组分（cellular component）、12个分子功能（molecular function）和22个生物学过程（biological process）中。对差异基因参与的代谢途径进行富集，上调基因中共有40个代谢途径显著富集，下调基因中共有18个代谢途径显著富集，这些显著富集的代谢途径参与甜荞根和金荞根的生物学调控。最后对转录组中注释到黄酮合成途径中的关键基因进行了分析，共有21个基因注释到黄酮合成途径中的关键酶。不仅丰富了荞麦的基因资源，为荞麦分子生物学研究提供数据基础，也为筛选甜荞根和金荞根中相关基因的表达趋势提供参考依据。

关键词: 荞麦, 转录组, 从头组装, 差异基因, 黄酮合成基因