Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.).
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.
Zhao
Chuan-Zhi
CZ
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.
Xia
Han
H
Frazier
Taylor Price
TP
Yao
Ying-Yin
YY
Bi
Yu-Ping
YP
Li
Ai-Qin
AQ
Li
Meng-Jun
MJ
Li
Chang-Sheng
CS
Zhang
Bao-Hong
BH
Wang
Xing-Jun
XJ
D010367:Arachis / Q000235:genetics*; D003001:Cloning, Molecular; D017124:Conserved Sequence; D020224:Expressed Sequence Tags; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA
D035683:MicroRNAs; D018749:RNA, Plant