## 1 Introduction  
_Gentiana rigescens__,_ also named Caine gentian, belongs to Gentiana, a member of the Gentianaceae family. It is a geoherb of great importance to China's Yunnan province. _G. rigescens_ is a perennial, growing amongst hillside grasses, bushes, and trees, at relatively high altitudes. It is usually harvested in late October, with the roots being used as bulk herbs [1] and raw materials for more than 180 different Chinese traditional medicines [2]. Recent research has shown that it possesses potential functions in liver protection and immune promotion [3,4]. The main effective component of _G. rigescens_ is gentiopicroside [3], which is mainly found in the vacuoles of root cells, although it is synthesized in shoots [5,6]. The content of gentiopicroside in roots was far higher than that in shoots at the flower stage [7]. In addition, there are other active components including swertiamarin, sweroside, erythricine, unsolic acid, oleanolic acid, loganic acid, gentianidine, and gentiana aldin [5,8].  
In recent years, the wild resources of _G. rigescens_ have declined sharply, with shortages of gentian, as demand for its use in clinical, pharmaceutical, and veterinary areas increases [1]. It has now been classified as a protected plant in China [1]. Similarly, many other _Gentiana_ species have become endangered species [9]. Studies have suggested that the chromosome number of _Gentiana triflora_, _Gentiana scabra_, _Gentiana manshurica_, and other herbs containing gentiopicroside, is \(2n=26\), while that of _Gentiana lutea_ and _Gentiana punctata_ is \(2n=40\)[10]. The former three share a similar genome size (\(5\times 10^{9}\) bp/1C), approximately 33 times that of _Arabidopsis thaliana_[10,11]. Gentian genome resources are very scarce due to its large genome, genomic heterozygosity brought by distal hybridization, long growth cycle, and the lack of genetic information [10]. The Japanese gentian's genetic linkage map was the first map of the Gentianaceae to be published, although its coverage is still low (about 1/3 genome coverage) and the phenomena of separation distortion (whereby there is unequal segregation of pairs of alleles) emerged in 30% of the molecular markers tested in progeny [10]. Therefore, the development of batches of EST-SSR (Expression Sequence Tag-Simple Sequence Repeat) molecular makers by RNA-Seq would be an improvement. In Japan, _G. scabra_ and _G. triflora_ are important cut and potted flowers, so research has focused on the anthocyanin biosynthesis pathway and its regulation [12, 13, 14]. Other studies have been on seed germination [4,15], elemental analysis [16], and active ingredient content [17,18]. However, there has been little research on the gentiopicroside biosynthesis pathway and its regulation. Recently, a seven-year breeding project of _G. rigescens_, whose goals are high yield, high gentiopicroside content, disease resistance, mechanized production, and wider planting, has been launched in Yunnan province [2].  
To protect wild gentian resources as a source of plant material, a better understanding of the plant's biology and growth is required. Transcriptome research provides a method of fast, high-throughput, comprehensive interpretation of the plant's genome information, including new gene function information, the biosynthesis of the active ingredients and their regulation, and germplasm evaluation and expansion [19].  
The objective of this research was to compare the transcriptomes of the leaf and root of _G. rigescens_, using Illumina Hiseq2000. To determine genes involved in the gentiopicroside biosynthesis pathway and its regulatory mechanism, transcripts from leaves and roots of gentian were isolated, quantified, sequenced, and annotated. The results described here will aid further functional genomic studies in gentian.