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Open Access Highly Accessed Research article

Identification of RNA silencing components in soybean and sorghum

Xiang Liu12, Tao Lu1, Yongchao Dou1, Bin Yu1* and Chi Zhang1*

Author Affiliations

1 School of Biological Sciences & Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE 68588, USA

2 Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China

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BMC Bioinformatics 2014, 15:4  doi:10.1186/1471-2105-15-4

Published: 4 January 2014

Abstract

Background

RNA silencing is a process triggered by 21–24 small RNAs to repress gene expression. Many organisms including plants use RNA silencing to regulate development and physiology, and to maintain genome stability. Plants possess two classes of small RNAs: microRNAs (miRNAs) and small interfering RNAs (siRNAs). The frameworks of miRNA and siRNA pathways have been established in the model plant, Arabidopsis thaliana (Arabidopsis).

Results

Here we report the identification of putative genes that are required for the generation and function of miRNAs and siRNAs in soybean and sorghum, based on knowledge obtained from Arabidopsis. The gene families, including DCL, HEN1, SE, HYL1, HST, RDR, NRPD1, NRPD2/NRPE2, NRPE1, and AGO, were analyzed for gene structures, phylogenetic relationships, and protein motifs. The gene expression was validated using RNA-seq, expressed sequence tags (EST), and reverse transcription PCR (RT-PCR).

Conclusions

The identification of these components could provide not only insight into RNA silencing mechanism in soybean and sorghum but also basis for further investigation. All data are available at http://sysbio.unl.edu/ webcite.