Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links

We show the publication identifier used in this work, the organism it pertains to, the publication title, journal, URL, whether the miRNA/milRNA reported were obtained by sRNA-seq analysis (Y:yes; N:no; other context), details of why a study was excluded, whether sRNA-seq data is available (Y: yes, N:no), whether mi/milRNA loci coordinates are provided (Y:yes, N:no), whether biological replication of results has been performed (Y:yes, N:no), whether genetic evidence is provided (Y:yes; N:no), type of targeting evidence provided (prediction, degradome, 5’ RACE, in vitro support for targeting, and detection of target gene modulation through indirect approaches knock-outs of biosynthetic genes and direct approaches which modify the expression of the functional sRNA), and bioinformatic tool used for mi/milRNA identification. This also gives information on the native assembly used for the primary identification of the mi/milRNA loci cited in a publication, including assembly sources, IDs, names, and URLs where applicable.

We show species abbreviations (abbv), full names (species), taxon identifiers (taxid), secondary names (synonyms), kingdom, phylum, class, order, family, genus, whether they are a species reported miRNAs and miRNA-like (mi/milRNAs) analyzed in this work (1: yes; 0: no), relevance to humans, hosts for pathogens/parasites, corresponding genome assemblies used for genomic context and homolog identification (ncbi_assembly), SILVA-db accessions, and whether a genus member was used as a SILVA-db substitute in the case of missing species data.

We show the publication citations used in this work, SRR accession of the libraries, adapter sequence used for trimming, read length of the library, number of reads in the raw library (raw_depth), and the percentage of raw reads in the following categories: trimmed with adapters (have_adap), reads passing cutadapt filters (pass_filter), uniquely mapping reads, multi-mapping reads, percent non-mapping reads, and aligned reads resulting from unique and multi-mapper placement (aligned). Where available, this also gives the alignment rates given by source publications and a manually curated note.

We show identifiers for the miRNAs and miRNA-like (mi/milRNA) locus, citation, and source sRNA-seq library. Locus abundance, hairpin strand abundance, and percent stranding are shown. Other features include the abundance and sequence for the most-abundant sequence determined in this work (MAS), the inferred star for this MAS (MAS*), and the MAS cited in the source publication. Locus and cited MAS designation shown in accordance with Figure 2A. Rule passing is shown as a string, with the rule citation shown with a two-letter prefix (from Supplementary file 6), with the subsequent string pointing to rules passing (1) and failing (0) in numerical order.

We show identifiers for the locus, publication, native and NCBI assemblies used in its analysis, hairpin coordinates used for each assembly, and the most abundant sequence, indicating whether it has been corrected by our sequencing re-analysis. For loci with strong support for a targeting relationship, the type of evidence is shown. Locus details like the hairpin sequence, folding, minimum free energy, and boundary coordinates of the duplex within the hairpin are provided. We report identification details, including the level of coordinate and locus detail provided by the source publication and a locus’s validation status. Confirmation details include the rule set confirmation status, interactions with Rfam (including Rfam descriptions), intersections with genomic features, the status as an intergenic locus, the intergenomic conservation status, and the tier classification of all reported loci. Relevant figures are indicated where available for data columns. Dashes (‘-’) indicate fields that are not evaluated due to an ‘invalid’ hairpin.

Rule identifiers use the prefixes ‘ax’ (Axtell and Meyers, 2018), ‘ku’ (Kuang et al., 2019), ‘mb’ (Kozomara and Griffiths-Jones, 2014), and ‘ss’ (Axtell, 2013b). General rule category and more detailed rule descriptions are presented for each rule.

Here is given the locus and library identifiers, abundance of the locus and all sRNAs aligned to the hairpin strand (l=length, a=abundance). Most-abundant sequence (MAS) and cited MASs are shown for each locus. Lower case nucleotides indicate mismatches with the reference.

Includes annotations for mi/milRNAs in native genomes (where they were first annotated) and best-blast-hits (bbh) in NCBI-sourced assemblies. Annotations also contain two versions, one with all mi/milRNA loci and a second with only top tier loci (tiers 1 and 2, denoted ‘best’).