Project description:We charactarize the regulated miRNAs of Prunus persica to preventive treatment of PpPep2 1 µM endogenous peptide. The peptide treatment was applied to leaves and we sequenced the miRNAs after 1 and 24 h using untreated plants as control. miRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. Differential expression analysis of annotated pre_miRNA gene biotypes was performed with R package DESeq2 v1.26.0, considering significant epression values below FDR <0.05. We obtained 117,267,647 raw reads and we identified a total of 33 differential expressed miRNAs (DEM) belonging to 18 miRNA families upon PpPep2 application, accounting for 15% of the P. persica annotated miRNAs. miRNA regulation occurs principally one day after peptide treatment. The predicted mRNA targets and function of orthologous miRNAs are compatible with a regulation of PTI-related processes. Together with the transcriptomic response of P. persica to PpPep2 described at our previous RNA-Seq (Foix et al 2021), this suggests that miRNAs would have an active role in PTI regulation at these stages.
Project description:Rapidly increased studies by third-generation sequencing [Pacific Biosciences (Pacbio) and Oxford Nanopore Technologies (ONT)] have been used in all kinds of research areas. Among them, the plant full-length single-molecule transcriptome studies were most used by Pacbio while ONT was rarely used. Therefore, in this study, we developed ONT RNA-sequencing methods in plants. We performed a detailed evaluation of reads from Pacbio and Nanopore PCR cDNA (ONT Pc) sequencing in plants (Arabidopsis), including the characteristics of raw data and identification of transcripts. We aimed to provide a valuable reference for applications of ONT in plant transcriptome analysis.
Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.
