Comparative transcriptome of rhizome and leaf in Ligusticum Chuanxiong

The rhizome was the pharmaceutical and breeding organ of Ligusticum chuanxiong , a well-known medicinal herb. In order to understand the molecular mechanism of rhizome formation and development, and the biosynthesis of active metabolites in rhizome of L. chuanxiong , it was necessary to obtain the functional genomic information. In this study, two cDNA libraries, which were constructed from the rhizome and leaf of L. chuanxiong , were sequenced using Illumina platform. More than 26,540,629 high-quality reads were obtained, generating 5.36 gigabase pairs of sequencing data. These reads were assembled into 109,486 unigenes and more than 44,345 unigenes (>40 %) were larger than 500 bp. Among them, 67,373 unique sequences were annotated and 14,494 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. A total of 4102 unigenes were differentially expressed between rhizome and leaf, indicating their different roles in physiological processes. 2677 and 1425 unigenes were up-regulated in rhizome and leaf, respectively. In total, 82 and 124 transcriptional factor genes were up-regulated in rhizome and leaf, respectively. Meanwhile, 22 unigenes, which were involved with the organ formation and development, were discovered in the up-regulated unigenes in rhizome. Analysis of unigenes which were involved in the biosynthesis of ferulic acid indicated that Caffeic acid O-methyltransferase might be the candidate gene of the key enzyme. In conclusion, the extensive transcriptome provided a useful resource for the L. chuanxiong research. Using comparative transcriptome analysis, we detected differently expressing genes and identified a group of potential candidate unigenes by qRT-PCR. These candidate unigenes provide a foundation for future studies on molecular mechanisms underlying formation, development, and secondary metabolism of rhizome.