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. 2022 Dec 9;11:e83691. doi: 10.7554/eLife.83691

Figure 2. Independent evaluation of miRNAs and miRNA-like (mi/milRNA) annotations using sRNA-seq data.

(A) Number of hairpin loci in which the reported mature mi/milRNA sequence is the most-abundant sequence (MAS) (orange), another sequence in the locus is the MAS (pink), the cited sequence is not present in the locus (light gray), or the reported locus has no aligned reads (dark gray). (B) Abundance (aligned reads per million) and strandedness for mi/milRNA loci. Each dot represents a locus, and the colors represent whether the locus passes the 0.5 reads per million cutoff of expression (pass rpm, yellow), has at least 80% of the aligned reads stranded (pass frac, blue), fulfills both criteria (pass both, green), or does not fulfill any of the criteria (none, gray) (C) Proportion of loci passing the three minimal locus profile rules (fn1, fn2, and fn3, described in table below). Arabidopsis thaliana (Artha) and Drosophila melanogaster (Drmel), low (LC) and high-confidence (HC) miRNAs from miRbase tested in a single library are included as a reference. (D) Number of loci without available source sRNA-seq libraries (light gray), loci failing one or more rules indicated in B and C (red), loci passing all rules (yellow), and loci passing all rules in two or more independent libraries (blue-green). For confirmed loci, we show in magenta those passing all the rules for annotating miRNAs in plants described in the ShortStack (Axtell, 2013b) and Axtell-2018 (Axtell and Meyers, 2018) rule sets. (E) Locus count and proportion of loci as in (D), separated by the parent species and including loci for which a valid hairpin could not be identified (dark gray).

Figure 2.

Figure 2—figure supplement 1. Evaluation of reported miRNAs and miRNA-like (mi/milRNA) loci using published rules for plant and animal miRNAs (description of rules is provided in Supplementary file 6).

Figure 2—figure supplement 1.

Libraries from Arabidopsis thaliana (Artha) and Drosophila melanogaster (Drmel) were used to test low- and high-confidence (LC, HC) miRNAs reported in miRbase for each species. Fungi mi/milRNAs are tested using their source libraries (where available) for all valid hairpins.
Figure 2—figure supplement 2. Cumulative density function of raw library depths for source libraries reporting miRNAs and miRNA-like (mi/milRNAs).

Figure 2—figure supplement 2.

We show the proportion of libraries with a given raw read depth. 94.1% of the libraries are 5 million reads or more in depth.
Figure 2—figure supplement 3. Loci count in the context of their confirmation by sRNA-seq.

Figure 2—figure supplement 3.

(A) Proportion and loci count for loci reported from each citation, (B) the annotation tool/approach, and (C) the length of the most-abundant sequence. Colors represent loci which are invalid (dark gray), failed to confirm by sRNA-seq (red), have no available sRNA-seq data (light gray), are confirmed in one library (yellow), or are confirmed in multiple libraries.