Open Access Highly Accessed Research article

Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.)

Chuan-Zhi Zhao12, Han Xia12, Taylor Price Frazier3, Ying-Yin Yao45, Yu-Ping Bi12, Ai-Qin Li12, Meng-Jun Li12, Chang-Sheng Li12, Bao-Hong Zhang2 and Xing-Jun Wang12*

Author Affiliations

1 High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture; Jinan 250100, PR China

2 Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China

3 Department of Biology, East Carolina University, Greenville, NC 27858, USA

4 Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, PR China

5 Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, PR China

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BMC Plant Biology 2010, 10:3  doi:10.1186/1471-2229-10-3

Published: 5 January 2010

Abstract

Background

MicroRNAs (miRNAs) are a new class of small, endogenous RNAs that play a regulatory role in the cell by negatively affecting gene expression at the post-transcriptional level. miRNAs have been shown to control numerous genes involved in various biological and metabolic processes. There have been extensive studies on discovering miRNAs and analyzing their functions in model species, such as Arabidopsis and rice. Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy.

Results

In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. Next generation high through-put Solexa sequencing showed that peanuts have a complex small RNA population and the length of small RNAs varied, 24-nt being the predominant length for a majority of the small RNAs. Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. All 14 novel peanut miRNAs are considered to be species-specific because no homologs have been found in other plant species except ahy-miRn1, which has a homolog in soybean. qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts.

Conclusions

This study led to the discovery of 14 novel and 22 conserved miRNA families from peanut. These results show that regulatory miRNAs exist in agronomically important peanuts and may play an important role in peanut growth, development, and response to environmental stress.