Small RNA and degradome profiling reveals miRNA regulation in the seed germination of ancient eudicot Nelumbo nucifera

Abstract

BackgroundMicroRNAs (miRNAs) play important roles in plant growth and development. MiRNAs and their targets have been widely studied in model plants, but limited knowledge is available concerning this small RNA population and their targets in sacred lotus (Nelumbo nucifera Gaertn.).ResultsIn this study, a total of 145 known miRNAs belonging to 47 families and 78 novel miRNAs were identified during seed germination using high-throughput small RNA sequencing. Furthermore, some miRNA families which have not yet been reported in monocot or eudicot species were detected in N. nucifera, indicating that these miRNAs was divergence from monocots and core eudicots during evolution. Using degradome sequencing, 2580 targets were detected for all the miRNAs. GO (Gene Ontology) and KEGG pathway analyses showed that many target genes enriched in “regulation of transcription” and involved in “carbohydrate”, “amino acid and energy metabolism”. Nine miRNAs and three corresponding targets of them were further validated by quantitative RT-PCR.ConclusionsThe results present here suggested that many miRNAs were involved in the regulation of seed germination of sacred lotus, providing a foundation for future studies of sacred lotus seed longevity. Comparative analysis of miRNAs from different plants also provided insight into the evolutionary gains and losses of miRNAs in plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3032-4) contains supplementary material, which is available to authorized users.

MiRNAs profiling and degradome sequencing between the CMS-line N816S and its maintainer line Ning5m during anther development in pepper (Capsicum annuumL.)

“…The length of unique sRNAs, in both the N816S and Ning5m libraries, the 24 nt category was most abundant (average of 59.15% and 62.90% in N816S and Ning5m libraries, respectively) (Figure 2C-D). This is consistent with the typical lengths of plant sRNAs reported in other studies(Asha et al, 2016;Hu et al, 2016).…”

“…However, few studies on the relationships between miRNA biogenesis and CMS occurrence during anther development in pepper were very limited. MiRNAome and degradation sequencing technology provides an effective way to identify and evaluate the expression profiles of miRNAs and targets associated with CMS occurrence in plant tissues during anther development(Wei et al, 2015;Hu et al, 2016;Bai et al, 2017). To explore the roles of miRNAs during the occurrence of CMS, anthers at the early uninucleate stage were used to examine the expression profiles of the miRNAs in the sterile line N816S and its maintainer line Ning5m using high-throughput sequencing.…”

Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn)

“…To confirm targets of the miRNAs experimentally, a degradome (SRX1598165) of germinating lotus seedlings was analyzed (Hu et al, 2016). The raw reads were first cleaned by removing low-quality nucleotide reads and adapters using NGS QC Toolkit (v2.3.3) (Patel and Jain, 2012).…”

“…Although the population and abundance of miRNAs in lotus have been explored (Zheng et al, 2013; Hu et al, 2016; Pan et al, 2016; Shi et al, 2016), there are no reports on systematic identification and characterization of submergence-related miRNAs in lotus. In this study we determined the submergence response of miRNAs in lotus.…”

Combined RNA-seq, small RNA and degradome sequencing approaches insights into salt-stress responses in Beta vulgaris

“…MicroRNAs (miRNAs) are small, endogenous, noncoding RNAs ranging from 19 to 24 nucleotides that play crucial regulatory roles at the post-transcriptional stage by cleavage or translation repression of their target mRNAs (Bartel 2004). Increasing evidence suggests that miRNA-guided gene regulation is involved in multiple physiological and biochemical processes, such as seedling growth (Hu 2016), floral development (Chen 2004), male and female sterility (Millar 2005 andYan 2015), and responses to environmental stress (Sunkar 2007). Furthermore, a new study has found that plants can export miRNAs to inhibit virulence gene expression in a fungal pathogen (Zhang 2016).Thus, identifying miRNAs and their target mRNAs is essential to elucidating their regulatory mechanisms, and to understand the growth, development, and stress response processes.…”