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Plant Cell. 2014 Dec;26(12):4584-601. doi: 10.1105/tpc.114.131847. Epub 2014 Dec 2.

An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes.

Author information

1
Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
2
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
3
Division of Plant Science, University of Missouri, Columbia, Missouri 65211.
4
Unidad de Morfologia y Función, FES Iztacala, Universidad Nacional Autónoma de México, Los Reyes Iztacala, Tlalnepantla 54090,Mexico.
5
National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211.
6
Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 meyers@dbi.udel.edu.

Abstract

Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNA-dependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; from PHAS loci), of which 483 overlapped annotated protein-coding genes. Via the integration of miRNAs with parallel analysis of RNA end (PARE) data, 20 miRNA triggers of 127 PHAS loci were detected. The primary class of PHAS loci (208 or 41% of the total) corresponded to NB-LRR genes; some of these small RNAs preferentially accumulate in nodules. Among the PHAS loci, novel representatives of TAS3 and noncanonical phasing patterns were also observed. A noncoding PHAS locus, triggered by miR4392, accumulated preferentially in anthers; the phasiRNAs are predicted to target transposable elements, with their peak abundance during soybean reproductive development. Thus, phasiRNAs show tremendous diversity in dicots. We identified novel miRNAs and assessed the veracity of soybean miRNAs registered in miRBase, substantially improving the soybean miRNA annotation, facilitating an improvement of miRBase annotations and identifying at high stringency novel miRNAs and their targets.

PMID:
25465409
PMCID:
PMC4311202
DOI:
10.1105/tpc.114.131847
[Indexed for MEDLINE]
Free PMC Article

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