caa a22 4500 606209492 CHVBK 20210128101028.0 cr unu---uuuuu 210128e20150501xx s 000 0 eng 10.1007/s00425-015-2246-z doi (NATIONALLICENCE)springer-10.1007/s00425-015-2246-z Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza [Elektronische Daten] [Dongqiao Li, Fenjuan Shao, Shanfa Lu] Main conclusion : Identification and characterization of 5,446 mlncRNAs from Salvia miltiorrhiza showed that the majority of identified mlncRNAs were stress responsive, providing a framework for elucidating mlncRNA functions in S. miltiorrhiza. mRNA-like noncoding RNAs (mlncRNAs) are transcribed by RNA polymerase II and are polyadenylated, capped and spliced. They play important roles in plant development and defense responses. However, there is no information available for mlncRNAs in Salvia miltiorrhiza Bunge, the first Chinese medicinal material entering the international market. To perform a transcriptome-wide identification of S. miltiorrhiza mlncRNAs, we assembled over 8 million RNA-seq reads from GenBank database and 5,624 ESTs from PlantGDB into 44422 unigenes. Using a computational identification pipeline, we identified 5446 S. miltiorrhiza mlncRNA candidates from the assembled unigenes. Of the 5446 mlncRNAs, 2 are primary transcripts of conserved miRNAs, and 2030 can be grouped into 470 families with at least two members in a family. Quantitative real-time PCR analysis of mlncRNAs with at least 900nt showed that the majority were differentially expressed in roots, stems, leaves and flowers and responsive to methyl jasmonate (MeJA) treatment in S. miltiorrhiza. Analysis of published RNA-seq data showed that a total of 3,044 mlncRNAs were expressed in hairy roots of S. miltiorrhiza and the expression of 1,904 of the 3,044 mlncRNAs was altered by yeast extract and Ag+ treatment. The results indicate that the majority of mlncRNAs are involved in plant response to stress. This study provides a framework for understanding the roles of mlncRNAs in S. miltiorrhiza. Springer-Verlag Berlin Heidelberg, 2015 Methyl jasmonate nationallicence mRNA-like noncoding RNA nationallicence Salvia nationallicence Traditional Chinese medicine nationallicence Transcriptome-wide analysis nationallicence ncRNA : Noncoding RNA nationallicence qRT-PCR : Quantitative reverse-transcription PCR nationallicence sRNA : Small RNA nationallicence miRNA : MicroRNA nationallicence siRNA : Small-interfering RNA nationallicence lncRNA : Long noncoding RNA nationallicence mlncRNA : mRNA-like noncoding RNA nationallicence pri-miRNA : Primary miRNA nationallicence pre-miRNA : miRNA precursor nationallicence DCL1 : Dicer-like 1 nationallicence MeJA : Methyl jasmonate nationallicence ORF : Open reading frame nationallicence FDA : Food and Drug Administration nationallicence HDS : 4-Hydroxy-3-methylbut-2-en-1-yl diphosphate synthase nationallicence SPS : Solanesyl diphosphate synthase nationallicence Li Dongqiao Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China aut Shao Fenjuan Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China aut Lu Shanfa Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China aut Planta Springer Berlin Heidelberg 241/5(2015-05-01), 1131-1143 0032-0935 241:5<1131 2015 241 425 https://doi.org/10.1007/s00425-015-2246-z text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00425-015-2246-z text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Li Dongqiao Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China aut NATIONALLICENCE 700 1- Shao Fenjuan Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China aut NATIONALLICENCE 700 1- Lu Shanfa Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China aut NATIONALLICENCE 773 0- Planta Springer Berlin Heidelberg 241/5(2015-05-01), 1131-1143 0032-0935 241:5<1131 2015 241 425