sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms

Abstract

The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/.

Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine

“…Because of the near-hierarchical evolution of microRNAs, they have a very strong potential not only as taxonomic markers as used in e.g. miRTrace (Kang et al, 2018) or sRNAbench (Aparicio-Puerta et al, 2022), but to also outperform approaches that are based on protein-coding genes such as BUSCO. Those heavily rely on the correct identification of orthologues and paralogues of proteincoding genes, which are much more variable than microRNAs and are therefore often incomplete, and, hence, cannot be used to accurately assess or measure rates of loss.…”

Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions

“…sRNA sequencing data were processed as previously described [ 5 ]. After the trimming of adapter sequences and removing of reads with ambiguous bases (Phred Score quality ≤ 2), the expression profiling of clean sRNA reads was performed by means of the sRNAbench [ 27 , 28 , 29 ] in genome mode. Briefly, the clean reads were first mapped against the latest wheat genome version (iwgsc_refseqv2.1) available in the International Wheat Genome Sequencing Consortium (IWGSC, , accessed on 1 June 2022) without allowing mismatches using bowtie 1 seed option (seed length 19).…”

isomiRdb: microRNA expression at isoform resolution

“…MiRMaster performs adapter trimming via fuzzy string matching and read quality control applying a sliding window approach ( 22 ). Subsequently, collapsed reads were profiled with sRNAbench ( 17 ) in library mode and default parameters using miRBase release 22.1 ( 12 ). Essentially, sRNAbench relies on bowtie ( 24 ) for read alignment (with parameters -f -n 1 -l 19 -a –best –strata ) and multiple-mapping reads are evenly split among receiving sites.…”

“…Many of these databases compile miRNA-seq datasets from a wide spectrum of origins but only a couple provide isomiR expression information (Table 1 ). Furthermore, although publicly available miRNA-seq samples are rapidly increasing ( 17 ), several current resources compile expression data for a limited number of samples. Here, DIANA-miTED ( 18 ) is a remarkable exception hosting over 15 000 datasets.…”

“…Together, these small RNA sequencing data compile 5.9 × 10 11 processed reads, making it a very comprehensive and powerful miRNA expression resource. To present comparable data, we analyzed all data sets from raw fastq files that were uniformly pre-processed with miRMaster followed by downstream processing by sRNAbench ( 17 ). The annotation of miRNAs relies on the latest version of miRbase (release 22.1) ( 12 ).…”