Zhonglong Guo’s Lab

MITEs predispose the miRNA portfolio in angiosperm. Bursts of the Mutator, Tc1/Mariner, and PIF/Harbinger MITE families in angiosperms increase the frequency of appropriately sized MITEs to transpose into introns. These MITEs hitchhike host gene transcription, allowing TIR-seeded regions of the resulting transcripts to fold into hairpin structures recognized by the Dicer-like complex to generate de novo miRNAs. The novel MITE-miRNAs preferentially regulate target genes with biological functions related to responses to environmental stimuli and may thus facilitate plant adaptation to the environment. In certain cases, selection of a miRNA might have a collateral selection of the host gene as a non-coding miRNA precursor through pseudogenization

The recently updated plant miRNA encyclopedia database (PmiREN2.0) provided an opportunity to systemically perform a kingdom-wide survey of species-specific miRNAs. MiRNAs in PmiREN2.0 were identified with a standardized workflow for miRNA identification based on miRDeep-P2 and the newly updated criteria using a plenty of accessible sRNA-seq datasets, which meaned that miRNAs in PmiREN2.0 possessed optimal hairpins and canonical reads distribution profile. In our study, 8,978 miRNA families in 81 species phylogenetically ranging from chlorophytes to angiosperms were used to identify species-specific miRNAs. Using a customized Perl script specifically designed for the seq-based strategy, we identified a total of 5,493 miRNA families.

PmiREN (Plant miRNA ENcyclopedia) is a comprehensive functional plant miRNA database. In version 2.0, it contains 38,186 miRNA loci (MIR) belonging to 7,838 families, 1,668 syntenic blocks and 141,327 predicted miRNA-target pairs in 179 species phylogenetically ranging from chlorophytes to angiosperms. In addition, 2,331 deeply sequenced small RNA libraries were used in quantification of miRNA expression patterns, and 116 PARE-Seq libraries were employed to validate predicted miRNA-target pairs. Compared to version 1.0, PmiREN2.0 not only retains its full functions, but also adds 11 new tools for in-depth data mining and experimental practice, promoting the transition from data collection to fully functional knowledgebase. Furthermore, PmiREN forum was established for sharing resources and new discoveries, research communication and announcement release. We believe the PmiREN2.0 will consistently provide novel insights into miRNA research.