title: Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean.
abstract: A wide range of RNA species interacting with microRNAs (miRNAs) form a complex gene regulation network and play vital roles in diverse biological processes. In this study, we performed a genome-wide identification of endogenous target mimics (eTMs) for miRNAs and phased-siRNA-producing loci (PHAS) in soybean with a focus on those involved in lipid metabolism. The results showed that a large number of eTMs and PHAS genes could be found in soybean. Additionally, we found that lipid metabolism related genes were potentially regulated by 28 miRNAs, and nine of them were potentially further regulated by a number of eTMs with expression evidence. Thirty-three miRNAs were found to trigger production of phasiRNAs from 49 PHAS genes, which were able to target lipid metabolism related genes. Degradome data supported miRNA- and/or phasiRNA-mediated cleavage of genes involved in lipid metabolism. Most eTMs for miRNAs involved in lipid metabolism and phasiRNAs targeting lipid metabolism related genes showed a tissue-specific expression pattern. Our bioinformatical evidences suggested that lipid metabolism in soybean is potentially regulated by a complex non-coding network, including miRNAs, eTMs, and phasiRNAs, and the results extended our knowledge on functions of non-coding RNAs.
authors.affiliation: Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University Hangzhou, China.
authors.forename: Chu-Yu
authors.initials: CY
authors.lastname: Ye
authors.affiliation: Guhe Information Hangzhou, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Xu
authors.affiliation: Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University Hangzhou, China.
authors.forename: Enhui
authors.initials: E
authors.lastname: Shen
authors.affiliation: Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University Hangzhou, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University Hangzhou, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University Hangzhou, China.
authors.forename: Yifei
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University Hangzhou, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Qiu
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship Canberra, ACT, Australia.
authors.forename: Qian-Hao
authors.initials: QH
authors.lastname: Zhu
authors.affiliation: Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University Hangzhou, China.
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
keywords: endogenous target mimics; lipid metabolism; miRNA; phasiRNA; soybean