Gene regulation has been widely regulated by several class of transcriptionally and post-transcriptionally active regulatory elements. Transcriptionally, gene regulation has been widely linked to change in terms of expression whereas post-transcriptionally, non-coding regulatory elements such as microRNAs (miRNAs) have been demonstrated as detrimental regulators of gene regulation. microRNAs (19-24 nt long) short regulatory sequences play a critical role in regulating the gene expression profiles and acts as regulators at several layers through the plant system such as tissue, development and in response to abiotic and biotic stress adaptation. Evolutionary conserved miRNAs such as miR156 plays an important role in plant developmental biology has been shown to be targeting Plant SQUAMOSA-PROMOTER BINDING PROTEIN- LIKE (SPL) genes. Similarly, they have been shown to prefer duplicated genes as a target as compared to singletons (Wang and Adams, 2015). Among that factors that regulate miRNA biogenesis involve the introns, splicing, and/or alternative splicing, which can regulate the pri-miRNAs biogenesis and thus regulates the spliceosomal complex in specific conditions (Szweykowska-Kulinska et al., 2013). Besides these, another class of miRNAs, isomiRs (canonical variants of miRNAs) (Sablok et al., 2015) have been also recently shown to be a part of the miRNAome thus increasing the miRNAs diversity and target selection (Morin et al., 2008). Biogenesis of these canonical microRNA sequence variants can be attributed to either the imprecise cleavage activity by the Rnase III enzyme (Bartel 2004) or due to the post-transcriptional RNA editing events or nucleotidyl transferases (Wyman et al., 2011). Furthermore, based on length and nucleotide variations along the miRNA and non-templated additions (NTAs) such as adenylation and uridylation at the 3′ end with non-random functionality (Wyman et al. 2011), these isomiRs can be classified into 5 ́ isomiR, 3′ isomiR or polymorphic isomiRs (Neilsen et al., 2012; Jeong et al., 2013). isomiRs can differ from the canonical miRNAs either at their 5 ́ end (changing the ‘ seed’ region and suggesting a different target molecule) or their 3 ́-end, or both simultaneously. Global analysis of the isomiRs and canonical miRNAs revealed uridine as the preferential nucleotide at 5′- and 3′ -ends, thus leading to the observation of the preferential ‘U–C’ at the 3′ -end of the isomiRs as compared to the addition of the C at the 3′-end of the plant miRNAs (Zhang et al., 2013). However, isomiRs displayed a frequent truncation of the cytodine from both the ends, presenting a new complex cytodine balance in isomiRs (Xie et al., 2015, Rogans and Rey, 2016), which might reflect the role of uridylation to avoid degradation.

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Till now less efforts have been leveraged to classify the isomiRs in plants thus limiting the potential of using these in addition to canonical miRNAs to unravel the post-transcriptional regulatory events. It is worth to mention that recent reports that combination of isomiRs and canonical miRNAs increase the target binding capability of the canonical miRNAs. In Plant isomiR Atlas, we classify for the first time high throughput identification, expression, target predictions of isomiRs covering 22 angiosperm species representing a total of 667 datasets. We believe that the plant isomiR Atlas will allow for the high throughput portal for isomiRs in plants.