title: Analyses of a Glycine max degradome library identify microRNA targets and microRNAs that trigger secondary siRNA biogenesis.
abstract: Plant microRNAs (miRNAs) regulate gene expression mainly by guiding cleavage of target mRNAs. In this study, a degradome library constructed from different soybean (Glycine max (L.) Merr.) tissues was deep-sequenced. 428 potential targets of small interfering RNAs and 25 novel miRNA families were identified. A total of 211 potential miRNA targets, including 174 conserved miRNA targets and 37 soybean-specific miRNA targets, were identified. Among them, 121 targets were first discovered in soybean. The signature distribution of soybean primary miRNAs (pri-miRNAs) showed that most pri-miRNAs had the characteristic pattern of Dicer processing. The biogenesis of TAS3 small interfering RNAs (siRNAs) was conserved in soybean, and nine Auxin Response Factors were identified as TAS3 siRNA targets. Twenty-three miRNA targets produced secondary small interfering RNAs (siRNAs) in soybean. These targets were guided by five miRNAs: gma-miR393, gma-miR1508, gma-miR1510, gma-miR1514, and novel-11. Multiple targets of these secondary siRNAs were detected. These 23 miRNA targets may be the putative novel TAS genes in soybean. Global identification of miRNA targets and potential novel TAS genes will contribute to research on the functions of miRNAs in soybean.
authors.affiliation: The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Hu
authors.forename: Qiyan
authors.initials: Q
authors.lastname: Jiang
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Ni
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.forename: Shuo
authors.initials: S
authors.lastname: Xu
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020871:RNA Stability / Q000235:genetics*; D018749:RNA, Plant / Q000096:biosynthesis* / Q000235:genetics; D034741:RNA, Small Interfering / Q000096:biosynthesis* / Q000235:genetics; D013025:Glycine max / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering