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

BMC Plant Biology

Research Article

Taylor Price Frazier¹  Chuan-Zhi Zhao²  Ai-Qin Li²  Xing-Jun Wang²  Meng-Jun Li²  Han Xia²  Chang-Sheng Li²  Yu-Ping Bi²  Bao-Hong Zhang³  Ying-Yin Yao⁴ 

[1] Department of Biology, East Carolina University, 27858, Greenville, NC, USA;High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture, 250100, Jinan, PR, China;Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, 250100, Ji'nan, PR, China;Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, 250100, Ji'nan, PR, China;Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100094, Beijing, PR, China;Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100094, Beijing, PR, China;

关键词: miRNA Family;    Mature miRNAs;    miRNA Precursor;    Precursor Sequence;    Solexa Sequencing;   

DOI  :  10.1186/1471-2229-10-3

 received in 2009-07-16, accepted in 2010-01-05,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (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.ResultsIn 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.ConclusionsThis 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.

【 授权许可】

Unknown   
© Zhao et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.