目的 获得茜草Rubia cordifolia转录组学信息及挖掘其蒽醌类化合物生物合成的关键酶基因，为茜草的功能基因克隆与分析提供参考。方法 采用Illunima Hiseq^TM 2000 150PE高通量测序技术对茜草进行转录组测序，使用Trinity软件完成Unigene的de novo拼接，基于BLAST实现Unigene的分类、功能注释、代谢通路分析和蛋白功能注释等。结果 最终获得7.3 Gb数据，通过de novo拼接注释得到Unigene 66 646条，平均长度为1 424 bp，所有Unigene能被NCBI nonredundant protein sequences（NR）、NCBI nucleotide sequences（NT）、kyoto encyclopedia of genes and genomes（KEGG）、A manually annotated and reviewed protein sequence database（Swissprot）、gene ontology（GO）、euKaryotic ortholog groups（KOG）和protein family（Pfam）数据库所注释，注释成功率100%，找到与茜草蒽醌类化合物生物合成相关的基因64条。结论 首次对茜草转录组进行了分析，并获得了茜草蒽醌类化合物生物合成相关的候选基因，为茜草的分子生物学研究提供了丰富的数据资源，也为后期开展茜草蒽醌类化合物次生代谢途径解析奠定了基础。

Objective To obtain the transcriptome sequence database and to identify the genes related to the biosynthesis of anthraquinones in Rubia cordifolia. Methods The transcriptome data of root of Rubia cordifolia was obtained by Illunima Hiseq^TM 2000 150PE sequencing and de novo splicing of Unigene was realized by Trinity. The GO classification, KOG functional, metabolism of KEGG metabolic pathway and protein function annotation analysis were completed based on BLAST. Results 7.3 Gb database was assembled after assembly steps, and 66 646 unigenes were assembled with an average length of 1 424 bp. All Unigenes were annotated in the public databases NR (NCBI nonredundant protein sequence), NT (NCBI nucleotide sequences), KEGG (kyoto encyclopedia of genes and genomes), Swissprot (A manually annotated and reviewed protein sequence database), GO (gene ontology), KOG (euKaryotic ortholog groups) and Pfam (protein family). Based on the assignment of KEGG pathway, 64 Unigenes involved in anthraquinones biosynthesis were found. Conclusion This study was the first comprehensive transcriptome analysis for R. cordifolia, and the candidate genes involved in the biosynthesis of anthraquinones were obtained. The transcriptome data constitutes a much more abundant genetic resource that can be utilized to benefit further molecular biology studies on R. cordifolia.

陕西省教育厅项目（16JK1212，15JK1210）；陕西省教育厅重点项目（11JS038）；陕西省中医管理局项目（ZYMS004）