Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA‐dominated PHAS loci

Small RNAs regulate key physiological functions in land plants. Small RNAs can be divided into two categories: microRNAs (miRNAs) and short interfering RNAs (siRNAs); siRNAs are further subdivided into transposon/repetitive region‐localized heterochromatic siRNAs and phased siRNAs (phasiRNAs). Phasi...

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Bibliographic Details
Published in:Plant direct 2018-12, Vol.2 (12), p.e00101-n/a
Main Authors: Polydore, Seth, Lunardon, Alice, Axtell, Michael J.
Format: Article
Language:English
Subjects:
Algorithms
Biosynthesis
Genomes
heterochromatic siRNA
MicroRNAs
MIR2275
miRNA
Original Research
phased siRNA
Proteins
RNA polymerase
siRNA
small RNA
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Summary:Small RNAs regulate key physiological functions in land plants. Small RNAs can be divided into two categories: microRNAs (miRNAs) and short interfering RNAs (siRNAs); siRNAs are further subdivided into transposon/repetitive region‐localized heterochromatic siRNAs and phased siRNAs (phasiRNAs). PhasiRNAs are produced from the miRNA‐mediated cleavage of a Pol II RNA transcript; the miRNA cleavage site provides a defined starting point from which phasiRNAs are produced in a distinctly phased pattern. 21–22 nucleotide (nt)‐dominated phasiRNA‐producing loci (PHAS) are well represented in all land plants to date. In contrast, 24 nt‐dominated PHAS loci are known to be encoded only in monocots and are generally restricted to male reproductive tissues. Currently, only one miRNA (miR2275) is known to trigger the production of these 24 nt‐dominated PHAS loci. In this study, we use stringent methodologies in order to examine whether or not 24 nt‐dominated PHAS loci also exist in Arabidopsis thaliana. We find that highly expressed heterochromatic siRNAs were consistently misidentified as 24 nt‐dominated PHAS loci using multiple PHAS‐detecting algorithms. We also find that MIR2275 is not found in A. thaliana, and it seems to have been lost in the last common ancestor of Brassicales. Altogether, our research highlights the potential issues with widely used PHAS‐detecting algorithms which may lead to false positives when trying to annotate new PHAS, especially 24 nt‐dominated loci.
ISSN:2475-4455
2475-4455
DOI:10.1002/pld3.101