RT Journal Article
SR Electronic
T1 Several phased siRNA annotation methods can produce frequent false-positives for 24 nucleotide RNA-dominated loci in plants
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 409417
DO 10.1101/409417
A1 Seth Polydore
A1 Alice Lunardon
A1 Michael J. Axtell
YR 2018
UL http://biorxiv.org/content/early/2018/09/06/409417.abstract
AB 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 sub-divided into the imprecisely processed heterochromatic siRNAs and more precisely processed phased siRNAs (phasiRNAs). 21-22 nucleotide (nt)-dominated phasiRNA-producing loci (PHAS) are well represented in all land plants to date, but male reproductive tissue-associated 24 nt-dominated PHAS loci are known only in monocots.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 24 nt heterochromatic siRNA loci can consistently be mis-identified as PHAS loci in different libraries and using different 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 siRNA phasing-detecting algorithms which may lead to false positives when trying to annotate new PHAS loci, especially 24 nt-dominated loci.