Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing.
Ephedra plants are taxonomically classified as gymnosperms, and are medicinally important as the botanical origin of crude drugs and as bioresources that contain pharmacologically active chemicals. Here we show a comparative analysis of the transcriptomes of aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing by RNA-Seq. De novo assembly of short cDNA sequence reads generated 23,358, 13,373, and 28,579 contigs longer than 200 bases from aerial stems, roots, or both aerial stems and roots, respectively. The presumed functions encoded by these contig sequences were annotated by BLAST (blastx). Subsequently, these contigs were classified based on gene ontology slims, Enzyme Commission numbers, and the InterPro database. Furthermore, comparative gene expression analysis was performed between aerial stems and roots. These transcriptome analyses revealed differences and similarities between the transcriptomes of aerial stems and roots in E. sinica. Deep transcriptome sequencing of Ephedra should open the door to molecular biological studies based on the entire transcriptome, tissue- or organ-specific transcriptomes, or targeted genes of interest.
Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan.
Taketo
T
Okada
Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan.
Hironobu
H
Takahashi
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
Yutaka
Y
Suzuki
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
Sumio
S
Sugano
Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan.
Masaaki
M
Noji
Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan.
Hiromichi
H
Kenmoku
Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan.
Masao
M
Toyota
Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
Shigehiko
S
Kanaya
Tsukuba Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Ibaraki 305-0843, Japan.
Nobuo
N
Kawahara
Institute of Pharmacognosy, Tokushima Bunri University, Tokushima 770-8514, Japan.
Yoshinori
Y
Asakawa
Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan.
Setsuko
S
Sekita
Comparative transcriptome analysis; EC, Enzyme Commission; Ephedra sinica; Es_R, E. sinica roots; Es_S, E. sinica aerial stems; Es_SR, E. sinica combined aerial stems and roots; GO, gene ontology; High-throughput mRNA sequencing; IPR, InterPro; RNA-Seq