MOA2010-05_3C_sRNAomics_bioinformatics_miRNA-novel

Version 1

Novel miRNAs and/or novel MIR loci identified in PVYNTN- and mock-inoculated samples of cv. Désirée and NahG-Désirée potato plants. List of novel/known miRNAs with novel MIR loci. For each miRNA, sequence, length, class (C – conserved or N – novel), miRNA family, the genome locations, strand, the predicted hairpin precursor (pre-miRNA) sequences and the location in genome (MIR loci), their lengths, minimal folding energy index (MFEI; calculated as described by Zhang et al. (2006) as well as gene overlap of the miRNA precursors with the gene regions (noncoding (NO) or coding (ID and name of the of the overlapping gene, intron/exon ) are given. Newly identified miRNAs (class novel) which were non homologous to any miRNAs from miRBase were named using "novel" prefix and a sequential identifying number according to their genome location. Some identified miRNAs were unique, while some have identical sequence but were encoded at multiple loci (paralogous MIR genes) – this information is given in column ‘Uniqueness’. For 65 novel miRNAs, the complementary miRNA* sequences were identified. The temporary miRNA names were assigned according to the miRNA annotation criteria (Meyers et al., 2008). The novel miRNA sequences were grouped into the novel miRNA families based on the CD-HIT clustering results. Moreover, novel MIR loci coding for miRNAs homologous to the previously validated non potato miRNAs from miRBase were identified (in bold; class conserved) and named based on an assignment to the conserved miRNA families. The final names for all listed miRNA sequences will be assigned after the manuscript will be accepted for publication and sequences will be deposited to the miRBase.