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

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Abstract

RNA interference is an ancient mechanism with many regulatory roles in eukaryotic genomes, with small RNAs acting as their functional element. While there is a wide array of classes of small-RNA-producing loci, those resulting from stem-loop structures (hairpins) have received profuse attention. Such is the case of microRNAs (miRNAs), which have distinct roles in plants and animals. Fungi also produce small RNAs, and several publications have identified miRNAs and miRNA-like (mi/milRNA) hairpin RNAs in diverse fungal species using deep sequencing technologies. Despite this relevant source of information, relatively little is known about mi/milRNA-like features in fungi, mostly due to a lack of established criteria for their annotation. To systematically assess mi/miRNA-like characteristics and annotation confidence, we searched for publications describing mi/milRNA loci and re-assessed the annotations for 41 fungal species. We extracted and normalized the annotation data for 1,727 reported mi/milRNA-like loci and determined their abundance profiles, concluding that less than half of the reported loci passed basic standards used for hairpin RNA discovery. We found that fungal mi/milRNA are generally more similar in size to animal miRNAs and were frequently associated with protein-coding genes. The compiled genomic analyses identified 25 mi/milRNA loci conserved in multiple species. Our pipeline allowed us to build a general hierarchy of locus quality, identifying more than 150 loci with high-quality annotations. We provide a centralized annotation of identified mi/milRNA hairpin RNAs in fungi which will serve as a resource for future research and advance in understanding the characteristics and functions of mi/milRNAs in fungal organisms.

Data availability

Sequencing data used in this work is available in public repositories, with publication details provided in Table S1 and all data accessions provided in Table S3. Results of abundance profiling are found in File S1 and summarized in Table S4.

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Article and author information

Author details

Nathan R Johnson

Facultad de Ciencias, Universidad Mayor, Santiago, Chile

Competing interests
No competing interests declared.
Luis F Larrondo

Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile

Competing interests
Luis F Larrondo, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0002-8832-7109
José M Álvarez

Facultad de Ciencias, Universidad Andrés Bello, Santiago, Chile

For correspondence
jose.alvarez.h@unab.cl

Competing interests
No competing interests declared.
Elena A Vidal

Facultad de Ciencias, Universidad Mayor, Santiago, Chile

For correspondence
elena.vidal@umayor.cl

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-8208-7327

Funding

Fondo Nacional de Desarrollo Científico y Tecnológico (11220727)

Nathan R Johnson

Instituto Milenio de Biologia Integrativa (ICN17_022)

Nathan R Johnson
Luis F Larrondo
Elena A Vidal

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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