PendoTMBase: A Database for Plant Endogenous Target Mimics
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ORIGINAL RESEARCH ARTICLE
PendoTMBase: A Database for Plant Endogenous Target Mimics Jiacong Deng1,2 · Qingyun Li4 · Likun Huang3 · Weiqi Tang1 · Kehui Zheng5 · Jiqiang Yan5 · Weiren Wu1,3 Received: 25 February 2020 / Revised: 4 September 2020 / Accepted: 14 September 2020 © International Association of Scientists in the Interdisciplinary Areas 2020
Abstract With fast-evolving next-generation sequencing technology, a great amount of plant genome and transcriptome data are becoming available. Due to the availability of mature microRNA (miRNA) sequence information from the miRBase (release 21) database, it is possible to predict endogenous target mimics (eTMs) in plant by searching seed-matched target sites. We identified a total of 2669 non-redundant eTM records in 43 plant species to create a specialized web-based database platform. The platform is named PendoTMBase, which can provide details of the eTMs. Predicted pairing structure between eTMs and their target miRNA, expression levels of eTMs pairs and associated GO annotations are also stored in the database. With evaluations performed in silico, we have found that the eTMs are representative and fit for genetic studies and high value-added plants breeding. The platform also provides a function of predicting novel eTMs based on the miRNA sequences submitted by users. Keywords Plant · Target mimics · microRNA · Database
1 Introduction Competing endogenous RNAs (ceRNAs) function as traps for microRNA (miRNA) binding. They regulate the abundance of other RNA transcripts by competing for shared miRNAs, thus forming a ceRNA network [1]. ceRNAs include mRNAs and non-coding RNAs, of which the latter
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12539-020-00396-2) contains supplementary material, which is available to authorized users. * Weiren Wu [email protected] 1
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
College of Ocean Science and Biochemistry Engineering, Fuqing Branch of Fujian Normal University, Fuqing 350300, China
3
Fujian Provincial Key Laboratory of Crop Breeding by Design, , Fujian Agriculture and Forestry University, Fuzhou 350002, China
4
Agricultural Big‑Data Research Center and College of Plant Protection, Shandong Agriculture University, Tai’an 271018, China
5
College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
include long non-coding RNAs (lncRNAs), circular small RNAs (circRNAs) and pseudogenes [2–5]. As a kind of lncRNAs, plant endogenous target mimics (eTMs) can attenuate the regulatory effects of miRNAs, providing an important way of gene expression regulation [6–8]. The eTM-mediated gene regulation networks have become a new research hotspot. Identification of eTMs can be achieved by experiments and software prediction [9–11]. For example, Franco-Zorrilla et al. found an IPS1 gene that does not encode a protein in Arabidopsis. Although IPS1 contains a moti
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