title: An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes.
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.
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
authors.forename: Siwaret
authors.identifier: http://orcid.org/0000-0002-2964-1886
authors.initials: S
authors.lastname: Arikit
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
authors.forename: Rui
authors.identifier: http://orcid.org/0000-0003-2409-1181
authors.initials: R
authors.lastname: Xia
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
authors.forename: Atul
authors.initials: A
authors.lastname: Kakrana
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
authors.forename: Kun
authors.initials: K
authors.lastname: Huang
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711 Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711.
authors.forename: Jixian
authors.initials: J
authors.lastname: Zhai
authors.affiliation: Division of Plant Science, University of Missouri, Columbia, Missouri 65211.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Yan
authors.affiliation: Unidad de Morfologia y Función, FES Iztacala, Universidad Nacional Autónoma de México, Los Reyes Iztacala, Tlalnepantla 54090,Mexico.
authors.forename: Oswaldo
authors.initials: O
authors.lastname: Valdés-López
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211.
authors.forename: Silvas
authors.initials: S
authors.lastname: Prince
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211.
authors.forename: Theresa A
authors.initials: TA
authors.lastname: Musket
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211.
authors.forename: Henry T
authors.identifier: http://orcid.org/0000-0002-7597-1800
authors.initials: HT
authors.lastname: Nguyen
authors.affiliation: Division of Plant Science, University of Missouri, Columbia, Missouri 65211.
authors.forename: Gary
authors.initials: G
authors.lastname: Stacey
authors.affiliation: 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.
authors.forename: Blake C
authors.identifier: http://orcid.org/0000-0003-3436-6097
authors.initials: BC
authors.lastname: Meyers
mesh_terms: D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D058977:Molecular Sequence Annotation; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D013025:Glycine max / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering