Overview

Soymir is a soybean microRNA database comprising 1,406 mature miRNA sequences, which were identified from 825 small RNA sequencing libraries using miRDeep-P2 software following the latest plant miRNA annotation criteria (Axtell & Meyers, 2018, The Plant Cell). With the exception of 63 previously reported miRNAs that were each detected in a single small RNA sequencing library, all remaining 1,343 mature sequences were supported by at least two independent libraries. The most broadly expressed sequence was found in as many as 795 libraries.

In total, these mature sequences correspond to 2,539 mature–precursor locus pairs. Clustering analysis at a sequence similarity threshold of 0.8 yielded 803 non-redundant miRNA families. Among these, 208 families have been previously documented in miRBase or PmiREN, encompassing 1,125 known miRNA members. Notably, 529 of these known members are isomiRs (a sequence and/or length variant of an archetype miRNA, Wagner et al., 2024,Trends in Genetics). Additionally, 240 novel miRNA members were identified from these known families. The remaining 595 families are newly defined in this study, comprising a total of 1,174 previously unreported miRNA members.

Beyond the core sequence repository, Soymir provides comprehensive functional annotations. The database incorporates expression profiles (normalized as RPM) of the aforementioned 1,406 miRNAs across diverse soybean tissues. Target prediction was conducted for the mature sequences using the CleaveLand4 pipeline based on 68 degradome sequencing datasets. Of these miRNAs, 1,386 mature sequences had predicted targets, yielding a total of 9,534 miRNA–target interaction pairs. Collectively, these data provide a valuable foundation for functional studies of soybean miRNAs.