Integrated Analyses of miRNAome and Transcriptome Reveal The Function of miRNAs in Morphogenesis of Organs and Defense of Endophytes in Pseudostellaria Heterophylla

Abstract Background: miRNAs play a crucial role in plant development and growth by inhibiting the function of targeted gene mRNAs at the post transcription level. However, none miRNAs in Pseudostellaria heterophylla has been reported and their function in morphogenesis of organs and continuous cropping obstacles is still unclear. Results: A total of 163 conserved miRNAs (belonging to 66 families) and 303 level miRNAs were identified and some of them showed specifically up or down regulated expression in different tissues. Further, numbers of unigenes involved in Plant-pathogen interaction and MAPK signaling pathway-plant was targeted by miRNAs from P. heterophylla by using GO and KEGG analysis. Significant negative correlation between expression profiles of 30 miRNAs and their targets gene (37 unigenes) were observed. Further, a large number of genes involving with signal transduction of auxin, zeatin, abscisic acid and jasmonic acid were targeted by identified miRNAs in P. heterophylla. A predicated target gene of a conserved and novel miRNA was validated by 5′RLM-RACE, respectively. A large number of mRNA from four kinds of endophytes was targeted by miRNAs of P. heterophylla, and most genes were targeted by miR414. Conclusion: We report a population of P. heterophylla miRNAs from four different vegetative organs by high throughput sequencing, and analyzed combining with the constructed transcriptome. These results may help to explain the function of miRNA in morphogenesis of organs and defense of endophytes in P. heterophylla, and provide theoretical basis for breeding and genetic improvement of P. heterophylla.