Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza

Abstract

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 900 nt 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.

Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza

“…BLAST analysis of the Arabidopsis , rice and S. miltiorrhiza sequences against the S. miltiorrhiza transcriptomic unigenes assembled from ESTs and RNA-seq reads [ 42 ] showed that unigenes could be identified for nine of the 22 cloned S. miltiorrhiza GA metabolism pathway genes. It includes SmKO , SmKAO1 , SmGA3ox2 , SmGA20ox2 – SmGA20ox4 , SmGA2ox3 , SmGA2ox5 and SmGA2ox11 .…”

“…In a previous study, two differently spliced AtKO ( GA3 ) mRNAs had been cloned, sequenced and detected using Northern hybridization [ 45 ]. In order to examine whether genes associated with GA metabolism underwent AS events, we analyzed the assembled S. miltiorrhiza transcriptome [ 42 ] for the 22 cloned GA metabolism pathway genes. Sequence comparison among unigenes, the cloned cDNAs and the genomic DNA showed that SmKO , SmGA20ox3 , SmGA2ox3 and SmGA2ox11 produced splice variants (Fig.…”

“…Roots, stems, leaves and flowers were collected from two-year-old plants and stored immediately in liquid nitrogen until use. Plantlets used for GA treatment were prepared as described previously [ 12 , 42 ]. Plantlets were sub-cultivated on 1/2 MS agar medium [ 59 ] for 6 weeks under a 16/8 h light/dark photoperiod at 25 °C and then transferred to 1/2 MS liquid medium for 2 days.…”

“…RNA-seq reads were mapped to the cloned ORFs of GA metabolism pathway genes using SOAP2 [ 50 ]. The data were analyzed as described previously [ 42 , 61 ]. Genes with the RPKM (RNA-seq reads mapped to an ORF per total million reads from a treatment per kilobases of the ORF length) value greater than 1 were analyzed for differential expression using Fisher’s exact test as described previously [ 61 ].…”

Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering

“…Non-coding RNAs, including small RNAs and long non-coding RNAs, play significant regulatory roles in many aspects of plants (Lu et al, 2005, 2007, 2008; Lu S. et al, 2013; Li D. et al, 2015; Wang et al, 2015). Various microRNAs have been identified to be associated with secondary metabolism (Wu et al, 2012; Lu S. et al, 2013; Fan et al, 2015; Wei et al, 2015).…”