An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes. Issue 12 (2nd December 2014)

• Record Type: Journal Article
• Authors: Arikit, Siwaret; Xia, Rui; Kakrana, Atul; Huang, Kun; Zhai, Jixian; Yan, Zhe; Valdés-López, Oswaldo; Prince, Silvas; Musket, Theresa A.; Nguyen, Henry T.; Stacey, Gary; Meyers, Blake C.
• Is Part Of: The Plant Cell. Volume 26:Issue 12(2014)
• Page Start: 4584
• Page End: 4601
• Publication Date: 2014-12-02
• DOI: 10.1105/tpc.114.131847
• Languages: English
• ISSNs: 1040-4651

Abstract

Abstract : An extensive analysis of small RNAs in soybean identified many miRNAs and phased, secondary siRNA (phasiRNA) loci; some of these miRNAs were the triggers of the phasiRNA loci. 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.