Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing
| Autor: | Setsuko Sekita, Yutaka Suzuki, Masao Toyota, Shigehiko Kanaya, Masaaki Noji, Sumio Sugano, Taketo Okada, Hiromichi Kenmoku, Yoshinori Asakawa, Hironobu Takahashi, Nobuo Kawahara |
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| Rok vydání: | 2016 |
| Předmět: |
IPR
InterPro 0301 basic medicine InterPro lcsh:QH426-470 High-throughput mRNA sequencing EC Enzyme Commission ved/biology.organism_classification_rank.species Comparative transcriptome analysis Sequence assembly Biology Es_R E. sinica roots 01 natural sciences Biochemistry Es_SR E. sinica combined aerial stems and roots Transcriptome 03 medical and health sciences Botany Genetics RNA-Seq Gene Es_S E. sinica aerial stems GO gene ontology Ephedra sinica Contig 010405 organic chemistry ved/biology fungi food and beverages Regular Article Enzyme Commission number 0104 chemical sciences lcsh:Genetics 030104 developmental biology MRNA Sequencing Molecular Medicine Biotechnology |
| Zdroj: | Genomics Data, Vol 10, Iss C, Pp 4-11 (2016) Genomics Data |
| ISSN: | 2213-5960 |
| DOI: | 10.1016/j.gdata.2016.08.003 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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