Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing

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• 作者：Taketo Okada^a ; ^{okadat@kph.bunri-u.ac.jp} ; Hironobu Takahashi^b ; Yutaka Suzuki^c ; Sumio Sugano^d ; Masaaki Noji^b ; Hiromichi Kenmoku^b ; Masao Toyota^b ; Shigehiko Kanaya^e ; Nobuo Kawahara^f ; Yoshinori Asakawa^b ; Setsuko Sekita^a
• 关键词：EC ; Enzyme Commission ; Es_R ; E. sinica roots ; Es_S ; E. sinica aerial stems ; Es_SR ; E. sinica combined aerial stems and roots ; GO ; gene ontology ; IPR ; InterPro
• 刊名：Genomics Data
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：10
• 期：Complete
• 页码：4-11
• 全文大小：670 K
• 卷排序：10

文摘

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.